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Barth; Weinstein, Melvin P.; Baron, Ellen Jo title: Implications of New Technology for Infectious Diseases Practice date: 2006-11-15 journal: Clin Infect Dis DOI: 10.1086/508536 sha: doc_id: 7047 cord_uid: 7ty9mxa9 file: cache/cord-023584-yaxawqhj.json key: cord-023584-yaxawqhj authors: Bucknall, R.A. title: The Continuing Search for Antiviral Drugs date: 2008-04-10 journal: Adv Pharmacol DOI: 10.1016/s1054-3589(08)60460-3 sha: doc_id: 23584 cord_uid: yaxawqhj file: cache/cord-018335-4l7scdqk.json key: cord-018335-4l7scdqk authors: Kiechle, Frederick L.; Arcenas, Rodney C. title: Utilization Management in a Large Community Hospital date: 2016-12-01 journal: Utilization Management in the Clinical Laboratory and Other Ancillary Services DOI: 10.1007/978-3-319-34199-6_14 sha: doc_id: 18335 cord_uid: 4l7scdqk file: cache/cord-024631-yvek5vjz.json key: cord-024631-yvek5vjz authors: Althaus, T.; Thaipadungpanit, J.; Greer, R.C; Swe, M.M.M; Dittrich, S.; Peerawaranun, P.; Smit, P.W; Wangrangsimakul, T.; Blacksell, S.; Winchell, J.M.; Diaz, M.H.; Day, N.P.J; Smithuis, F.; Turner, P.; Lubell, Y. title: Causes of fever in primary care in Southeast Asia and the performance of C-reactive protein in discriminating bacterial from viral pathogens date: 2020-05-11 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.05.016 sha: doc_id: 24631 cord_uid: yvek5vjz file: cache/cord-018271-ybfxtc7x.json key: cord-018271-ybfxtc7x authors: van Doorne, Hans; Roesti, David; Staerk, Alexandra title: Microbiology date: 2015-02-09 journal: Practical Pharmaceutics DOI: 10.1007/978-3-319-15814-3_19 sha: doc_id: 18271 cord_uid: ybfxtc7x file: cache/cord-033420-pjtyv0pv.json key: cord-033420-pjtyv0pv authors: Kalokairinou, Louiza; Zettler, Patricia J; Nagappan, Ashwini; Kyweluk, Moira A; Wexler, Anna title: The promise of direct-to-consumer COVID-19 testing: ethical and regulatory issues date: 2020-09-23 journal: J Law Biosci DOI: 10.1093/jlb/lsaa069 sha: doc_id: 33420 cord_uid: pjtyv0pv file: cache/cord-031567-w2676lrz.json key: cord-031567-w2676lrz authors: Sabit, Maureen; Wong, Cecil; Andaya, Agnes; Ramos, John Donnie title: Pollen allergen skin test and specific IgE reactivity among Filipinos: a community-based study date: 2020-08-12 journal: Allergy Asthma Clin Immunol DOI: 10.1186/s13223-020-00471-9 sha: doc_id: 31567 cord_uid: w2676lrz file: cache/cord-119183-pbliko1k.json key: cord-119183-pbliko1k authors: Cohen, Tomer; Finkelman, Lior; Grimberg, Gal; Shenhar, Gadi; Strichman, Ofer; Strichman, Yonatan; Yeger, Stav title: A combination of 'pooling' with a prediction model can reduce by 73% the number of COVID-19 (Corona-virus) tests date: 2020-05-03 journal: nan DOI: nan sha: doc_id: 119183 cord_uid: pbliko1k file: cache/cord-144448-mqs502xm.json key: cord-144448-mqs502xm authors: Theagarajan, Lakshmi N. title: Group Testing for COVID-19: How to Stop Worrying and Test More date: 2020-04-14 journal: nan DOI: nan sha: doc_id: 144448 cord_uid: mqs502xm file: cache/cord-027445-bpx4qr0i.json key: cord-027445-bpx4qr0i authors: Eisty, Nasir U.; Perez, Danny; Carver, Jeffrey C.; Moulton, J. 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Impact of diagnostic uncertainty in mass testing on the spread of COVID-19 date: 2020-10-21 journal: PLoS One DOI: 10.1371/journal.pone.0240775 sha: doc_id: 262846 cord_uid: 1mhimfsf file: cache/cord-102817-m1l1t0e1.json key: cord-102817-m1l1t0e1 authors: Lucas, T. C.; Pollington, T. M.; Davis, E. L.; Hollingsworth, T. 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Ichou, Houria; Damond, Florence; Bouvet, Elisabeth; Chaix, Marie-Laure; Ferré, Valentine; Delaugerre, Constance; Mahjoub, Nadia; Larrouy, Lucile; Le Hingrat, Quentin; Visseaux, Benoit; Mackiewicz, Vincent; Descamps, Diane; Fidouh-Houhou, Nadhira title: Performance evaluation of two SARS-CoV-2 IgG/IgM rapid tests (Covid-Presto and NG-Test) and one IgG automated immunoassay (Abbott) date: 2020-09-03 journal: J Clin Virol DOI: 10.1016/j.jcv.2020.104618 sha: doc_id: 281495 cord_uid: beb164oy file: cache/cord-320970-ru2iw0py.json key: cord-320970-ru2iw0py authors: Peeling, Rosanna W; Wedderburn, Catherine J; Garcia, Patricia J; Boeras, Debrah; Fongwen, Noah; Nkengasong, John; Sall, Amadou; Tanuri, Amilcar; Heymann, David L title: Serology testing in the COVID-19 pandemic response date: 2020-07-17 journal: Lancet Infect Dis DOI: 10.1016/s1473-3099(20)30517-x sha: doc_id: 320970 cord_uid: ru2iw0py file: cache/cord-283517-7gd0f06m.json key: cord-283517-7gd0f06m authors: Deak, Eszter; Marlowe, Elizabeth M. title: Right-Sizing Technology in the Era of Consumer-Driven Health Care date: 2017-08-01 journal: Clinical Microbiology Newsletter DOI: 10.1016/j.clinmicnews.2017.07.001 sha: doc_id: 283517 cord_uid: 7gd0f06m file: cache/cord-307187-5blsjicu.json key: cord-307187-5blsjicu authors: Missel, Malene; 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(AGAH) date: 2016-02-06 journal: Naunyn Schmiedebergs Arch Pharmacol DOI: 10.1007/s00210-016-1213-y sha: doc_id: 6229 cord_uid: 7yoilsho file: cache/cord-022650-phsr10jp.json key: cord-022650-phsr10jp authors: nan title: Abstracts TPS date: 2018-08-14 journal: Allergy DOI: 10.1111/all.13539 sha: doc_id: 22650 cord_uid: phsr10jp file: cache/cord-023354-f2ciho6o.json key: cord-023354-f2ciho6o authors: nan title: TUESDAY PLENARY SESSION 3 TUESDAY: POSTERS date: 2005-06-08 journal: Vox Sang DOI: 10.1111/j.1423-0410.2005.00654.x sha: doc_id: 23354 cord_uid: f2ciho6o file: cache/cord-023346-8sqbqjm1.json key: cord-023346-8sqbqjm1 authors: nan title: MONDAY: POSTERS date: 2005-06-08 journal: Vox Sang DOI: 10.1111/j.1423-0410.2005.00652.x sha: doc_id: 23346 cord_uid: 8sqbqjm1 file: cache/cord-019347-tj3ye1mx.json key: cord-019347-tj3ye1mx authors: nan title: ABSTRACT BOOK date: 2010-02-19 journal: Ann Allergy Asthma Immunol DOI: 10.1016/s1081-1206(10)61294-x sha: doc_id: 19347 cord_uid: tj3ye1mx file: cache/cord-023095-4dannjjm.json key: cord-023095-4dannjjm authors: nan title: Research Abstract Program of the 2011 ACVIM Forum Denver, Colorado, June 15–18, 2011 date: 2011-05-03 journal: J Vet Intern Med DOI: 10.1111/j.1939-1676.2011.0726.x sha: doc_id: 23095 cord_uid: 4dannjjm file: cache/cord-010092-uftc8inx.json key: cord-010092-uftc8inx authors: nan title: Abstract of 29th Regional Congress of the ISBT date: 2019-06-07 journal: Vox Sang DOI: 10.1111/vox.12792 sha: doc_id: 10092 cord_uid: uftc8inx 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 Reading metadata file and updating bibliogrpahics === updating bibliographic database Building study carrel named keyword-test-cord parallel: Warning: Only enough available processes to run 1 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 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 5 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 30 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: No more processes: Decreasing number of running jobs to 5. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: Only enough available processes to run 42 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: No more processes: Decreasing number of running jobs to 29. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 4. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. /data-disk/reader-compute/reader-cord/bin/cordent2carrel.sh: fork: retry: No child processes parallel: Warning: No more processes: Decreasing number of running jobs to 41. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 4. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 3. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 28. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 40. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes parallel: Warning: No more processes: Decreasing number of running jobs to 39. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 3. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordent2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordpos2carrel.sh: fork: retry: No child processes parallel: Warning: No more processes: Decreasing number of running jobs to 27. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordpos2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordent2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordent2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordent2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable === file2bib.sh === id: cord-001253-3jnkki5z author: Mohammad, Fahim title: Advantages and Limitations of Anticipating Laboratory Test Results from Regression- and Tree-Based Rules Derived from Electronic Health-Record Data date: 2014-04-14 pages: extension: .txt txt: ./txt/cord-001253-3jnkki5z.txt cache: ./cache/cord-001253-3jnkki5z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-001253-3jnkki5z.txt' === file2bib.sh === id: cord-017359-zr0bo9el author: Pfannschmidt, Karlson title: Evaluating Tests in Medical Diagnosis: Combining Machine Learning with Game-Theoretical Concepts date: 2016-05-10 pages: extension: .txt txt: ./txt/cord-017359-zr0bo9el.txt cache: ./cache/cord-017359-zr0bo9el.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-017359-zr0bo9el.txt' === file2bib.sh === id: cord-021511-88xaynf7 author: Werner, Linda L. title: Immunologic and Plasma Protein Disorders date: 2009-05-15 pages: extension: .txt txt: ./txt/cord-021511-88xaynf7.txt cache: ./cache/cord-021511-88xaynf7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-021511-88xaynf7.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: 47556 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-023584-yaxawqhj author: Bucknall, R.A. title: The Continuing Search for Antiviral Drugs date: 2008-04-10 pages: extension: .txt txt: ./txt/cord-023584-yaxawqhj.txt cache: ./cache/cord-023584-yaxawqhj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-023584-yaxawqhj.txt' === file2bib.sh === id: cord-018335-4l7scdqk author: Kiechle, Frederick L. title: Utilization Management in a Large Community Hospital date: 2016-12-01 pages: extension: .txt txt: ./txt/cord-018335-4l7scdqk.txt cache: ./cache/cord-018335-4l7scdqk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-018335-4l7scdqk.txt' === file2bib.sh === id: cord-024631-yvek5vjz author: Althaus, T. title: Causes of fever in primary care in Southeast Asia and the performance of C-reactive protein in discriminating bacterial from viral pathogens date: 2020-05-11 pages: extension: .txt txt: ./txt/cord-024631-yvek5vjz.txt cache: ./cache/cord-024631-yvek5vjz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-024631-yvek5vjz.txt' === file2bib.sh === id: cord-018271-ybfxtc7x author: van Doorne, Hans title: Microbiology date: 2015-02-09 pages: extension: .txt txt: ./txt/cord-018271-ybfxtc7x.txt cache: ./cache/cord-018271-ybfxtc7x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-018271-ybfxtc7x.txt' === file2bib.sh === id: cord-033420-pjtyv0pv author: Kalokairinou, Louiza title: The promise of direct-to-consumer COVID-19 testing: ethical and regulatory issues date: 2020-09-23 pages: extension: .txt txt: ./txt/cord-033420-pjtyv0pv.txt cache: ./cache/cord-033420-pjtyv0pv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-033420-pjtyv0pv.txt' === file2bib.sh === id: cord-031567-w2676lrz author: Sabit, Maureen title: Pollen allergen skin test and specific IgE reactivity among Filipinos: a community-based study date: 2020-08-12 pages: extension: .txt txt: ./txt/cord-031567-w2676lrz.txt cache: ./cache/cord-031567-w2676lrz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-031567-w2676lrz.txt' === file2bib.sh === id: cord-144448-mqs502xm author: Theagarajan, Lakshmi N. title: Group Testing for COVID-19: How to Stop Worrying and Test More date: 2020-04-14 pages: extension: .txt txt: ./txt/cord-144448-mqs502xm.txt cache: ./cache/cord-144448-mqs502xm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-144448-mqs502xm.txt' === file2bib.sh === id: cord-119183-pbliko1k author: Cohen, Tomer title: A combination of 'pooling' with a prediction model can reduce by 73% the number of COVID-19 (Corona-virus) tests date: 2020-05-03 pages: extension: .txt txt: ./txt/cord-119183-pbliko1k.txt cache: ./cache/cord-119183-pbliko1k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-119183-pbliko1k.txt' === file2bib.sh === id: cord-027445-bpx4qr0i author: Eisty, Nasir U. title: Testing Research Software: A Case Study date: 2020-05-25 pages: extension: .txt txt: ./txt/cord-027445-bpx4qr0i.txt cache: ./cache/cord-027445-bpx4qr0i.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-027445-bpx4qr0i.txt' === file2bib.sh === id: cord-021550-evh3b7o2 author: Brokopp, Charles title: Laboratories date: 2007-09-02 pages: extension: .txt txt: ./txt/cord-021550-evh3b7o2.txt cache: ./cache/cord-021550-evh3b7o2.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-021550-evh3b7o2.txt' === file2bib.sh === id: cord-012934-c6pbr64i author: Hao, Weiming title: Vestibular prognosis in idiopathic sudden sensorineural hearing loss with vestibular dysfunction treated with oral or intratympanic glucocorticoids: a protocol for randomized controlled trial date: 2020-07-22 pages: extension: .txt txt: ./txt/cord-012934-c6pbr64i.txt cache: ./cache/cord-012934-c6pbr64i.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-012934-c6pbr64i.txt' === file2bib.sh === id: cord-292209-d1ty9etr author: Horta, Bernardo L title: Prevalence of antibodies against SARS-CoV-2 according to socioeconomic and ethnic status in a nationwide Brazilian survey date: 2020-10-29 pages: extension: .txt txt: ./txt/cord-292209-d1ty9etr.txt cache: ./cache/cord-292209-d1ty9etr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-292209-d1ty9etr.txt' === file2bib.sh === id: cord-280571-ntgt5hy9 author: Ginocchio, Christine C. title: Strengths and Weaknesses of FDA-Approved/Cleared Diagnostic Devices for the Molecular Detection of Respiratory Pathogens date: 2011-05-01 pages: extension: .txt txt: ./txt/cord-280571-ntgt5hy9.txt cache: ./cache/cord-280571-ntgt5hy9.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-280571-ntgt5hy9.txt' === file2bib.sh === id: cord-026215-neqsup40 author: Grzegorzewski, Przemyslaw title: Two-Sample Dispersion Problem for Fuzzy Data date: 2020-05-16 pages: extension: .txt txt: ./txt/cord-026215-neqsup40.txt cache: ./cache/cord-026215-neqsup40.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-026215-neqsup40.txt' === file2bib.sh === id: cord-272995-yvj2pqh1 author: Bergman, Christian title: Recommendations for Welcoming Back Nursing Home Visitors during the COVID-19 Pandemic: Results of a Delphi Panel date: 2020-10-07 pages: extension: .txt txt: ./txt/cord-272995-yvj2pqh1.txt cache: ./cache/cord-272995-yvj2pqh1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-272995-yvj2pqh1.txt' === file2bib.sh === id: cord-102704-wfuzk2dp author: Meza, Diana K. title: Predicting the presence and titer of rabies virus neutralizing antibodies from low-volume serum samples in low-containment facilities date: 2020-04-30 pages: extension: .txt txt: ./txt/cord-102704-wfuzk2dp.txt cache: ./cache/cord-102704-wfuzk2dp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-102704-wfuzk2dp.txt' === file2bib.sh === id: cord-017072-qwe1ne3q author: Poritz, Mark A. title: Multiplex PCR for Detection and Identification of Microbial Pathogens date: 2018-11-10 pages: extension: .txt txt: ./txt/cord-017072-qwe1ne3q.txt cache: ./cache/cord-017072-qwe1ne3q.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-017072-qwe1ne3q.txt' === file2bib.sh === id: cord-262846-1mhimfsf author: Gray, Nicholas title: Is “no test is better than a bad test”? Impact of diagnostic uncertainty in mass testing on the spread of COVID-19 date: 2020-10-21 pages: extension: .txt txt: ./txt/cord-262846-1mhimfsf.txt cache: ./cache/cord-262846-1mhimfsf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-262846-1mhimfsf.txt' === file2bib.sh === id: cord-102817-m1l1t0e1 author: Lucas, T. C. title: Responsible modelling: Unit testing for infectious disease epidemiology date: 2020-08-16 pages: extension: .txt txt: ./txt/cord-102817-m1l1t0e1.txt cache: ./cache/cord-102817-m1l1t0e1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-102817-m1l1t0e1.txt' === file2bib.sh === id: cord-002626-jzwwses4 author: Kaul, Karen L. title: The Case for Laboratory Developed Procedures: Quality and Positive Impact on Patient Care date: 2017-07-16 pages: extension: .txt txt: ./txt/cord-002626-jzwwses4.txt cache: ./cache/cord-002626-jzwwses4.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-002626-jzwwses4.txt' === file2bib.sh === id: cord-296588-q2716lda author: Hanson, Kimberly E title: Infectious Diseases Society of America Guidelines on the Diagnosis of COVID-19 date: 2020-06-16 pages: extension: .txt txt: ./txt/cord-296588-q2716lda.txt cache: ./cache/cord-296588-q2716lda.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-296588-q2716lda.txt' === file2bib.sh === id: cord-025556-oyfx3ij5 author: THUNSTRÖM, LINDA title: Testing for COVID-19: willful ignorance or selfless behavior? date: 2020-05-08 pages: extension: .txt txt: ./txt/cord-025556-oyfx3ij5.txt cache: ./cache/cord-025556-oyfx3ij5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-025556-oyfx3ij5.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: 86497 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-121057-986xoy22 author: Mahdi, Esam title: Simultaneous Diagnostic Testing for Linear-Nonlinear Dependence in Time Series date: 2020-08-18 pages: extension: .txt txt: ./txt/cord-121057-986xoy22.txt cache: ./cache/cord-121057-986xoy22.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-121057-986xoy22.txt' === file2bib.sh === id: cord-278377-jgq3dz3u author: Busson, L. title: Prospective evaluation of diagnostic tools for respiratory viruses in children and adults date: 2019-01-15 pages: extension: .txt txt: ./txt/cord-278377-jgq3dz3u.txt cache: ./cache/cord-278377-jgq3dz3u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-278377-jgq3dz3u.txt' === file2bib.sh === id: cord-270935-t9pym9k0 author: Dumyati, Ghinwa title: Does Universal Testing for COVID-19 Work for Everyone? date: 2020-08-15 pages: extension: .txt txt: ./txt/cord-270935-t9pym9k0.txt cache: ./cache/cord-270935-t9pym9k0.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-270935-t9pym9k0.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-170195-lrg11s5n author: Stoye, Jorg title: A Critical Assessment of Some Recent Work on COVID-19 date: 2020-05-20 pages: extension: .txt txt: ./txt/cord-170195-lrg11s5n.txt cache: ./cache/cord-170195-lrg11s5n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-170195-lrg11s5n.txt' === file2bib.sh === id: cord-298441-77w86l8q author: Lombardi, Andrea title: Characteristics of 1,573 healthcare workers who underwent nasopharyngeal swab for SARS-CoV-2 in Milano, Lombardy, Italy date: 2020-06-20 pages: extension: .txt txt: ./txt/cord-298441-77w86l8q.txt cache: ./cache/cord-298441-77w86l8q.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-298441-77w86l8q.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: 47470 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-286539-3sr4djft author: Mentus, Cassidy title: Analysis and Applications of Adaptive Group Testing Methods for COVID-19 date: 2020-04-07 pages: extension: .txt txt: ./txt/cord-286539-3sr4djft.txt cache: ./cache/cord-286539-3sr4djft.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-286539-3sr4djft.txt' === file2bib.sh === id: cord-271920-1dzkgt6w author: Carpenter, Christopher R. title: Diagnosing COVID‐19 in the Emergency Department: A Scoping Review of Clinical Exam, Labs, Imaging Accuracy and Biases date: 2020-06-16 pages: extension: .txt txt: ./txt/cord-271920-1dzkgt6w.txt cache: ./cache/cord-271920-1dzkgt6w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-271920-1dzkgt6w.txt' === file2bib.sh === id: cord-117424-mp6h9dyl author: Abraham, Louis title: Bloom Origami Assays: Practical Group Testing date: 2020-07-21 pages: extension: .txt txt: ./txt/cord-117424-mp6h9dyl.txt cache: ./cache/cord-117424-mp6h9dyl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-117424-mp6h9dyl.txt' === file2bib.sh === id: cord-263893-zb6h3q4k author: nan title: What to expect from COVID-19 serology in a period of deconfinement? date: 2020-06-01 pages: extension: .txt txt: ./txt/cord-263893-zb6h3q4k.txt cache: ./cache/cord-263893-zb6h3q4k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-263893-zb6h3q4k.txt' === file2bib.sh === id: cord-022653-qa1uph35 author: nan title: Poster Discussion Session PDS date: 2017-08-30 pages: extension: .txt txt: ./txt/cord-022653-qa1uph35.txt cache: ./cache/cord-022653-qa1uph35.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-022653-qa1uph35.txt' === file2bib.sh === id: cord-127025-9ubhd4vf author: Abraham, Louis title: Crackovid: Optimizing Group Testing date: 2020-05-13 pages: extension: .txt txt: ./txt/cord-127025-9ubhd4vf.txt cache: ./cache/cord-127025-9ubhd4vf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-127025-9ubhd4vf.txt' === file2bib.sh === id: cord-022659-chwk2bs4 author: nan title: Abstracts: Poster session date: 2004-10-08 pages: extension: .txt txt: ./txt/cord-022659-chwk2bs4.txt cache: ./cache/cord-022659-chwk2bs4.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-022659-chwk2bs4.txt' === file2bib.sh === id: cord-034948-w59wxu8i author: Kuriyama, Akira title: Performance of the cuff leak test in adults in predicting post-extubation airway complications: a systematic review and meta-analysis date: 2020-11-07 pages: extension: .txt txt: ./txt/cord-034948-w59wxu8i.txt cache: ./cache/cord-034948-w59wxu8i.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-034948-w59wxu8i.txt' === file2bib.sh === id: cord-202376-440zapcw author: Wilder, Bryan title: Tracking disease outbreaks from sparse data with Bayesian inference date: 2020-09-12 pages: extension: .txt txt: ./txt/cord-202376-440zapcw.txt cache: ./cache/cord-202376-440zapcw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-202376-440zapcw.txt' === file2bib.sh === id: cord-030341-uora9qcb author: Ruland, Sebastian title: HybridTiger: Hybrid Model Checking and Domination-based Partitioning for Efficient Multi-Goal Test-Suite Generation (Competition Contribution) date: 2020-03-13 pages: extension: .txt txt: ./txt/cord-030341-uora9qcb.txt cache: ./cache/cord-030341-uora9qcb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-030341-uora9qcb.txt' === file2bib.sh === id: cord-311766-m9yv4qkm author: Demey, Baptiste title: Dynamic profile for the detection of anti-SARS-CoV-2 antibodies using four immunochromatographic assays date: 2020-05-07 pages: extension: .txt txt: ./txt/cord-311766-m9yv4qkm.txt cache: ./cache/cord-311766-m9yv4qkm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-311766-m9yv4qkm.txt' === file2bib.sh === id: cord-298086-pbfi5c8e author: Lyngse, F. P. title: COVID-19 Transmission Within Danish Households: A Nationwide Study from Lockdown to Reopening date: 2020-09-09 pages: extension: .txt txt: ./txt/cord-298086-pbfi5c8e.txt cache: ./cache/cord-298086-pbfi5c8e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-298086-pbfi5c8e.txt' === file2bib.sh === id: cord-150218-javbnjrg author: Gupta, Prateek title: COVI-AgentSim: an Agent-based Model for Evaluating Methods of Digital Contact Tracing date: 2020-10-30 pages: extension: .txt txt: ./txt/cord-150218-javbnjrg.txt cache: ./cache/cord-150218-javbnjrg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-150218-javbnjrg.txt' === file2bib.sh === id: cord-326148-9wpxm5of author: Van Walle, I. title: Meta-analysis of the clinical performance of commercial SARS-CoV-2 nucleic acid, antigen and antibody tests up to 22 August 2020 date: 2020-09-18 pages: extension: .txt txt: ./txt/cord-326148-9wpxm5of.txt cache: ./cache/cord-326148-9wpxm5of.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-326148-9wpxm5of.txt' === file2bib.sh === id: cord-288982-63ddlh20 author: Peeling, Rosanna W. title: Diagnostics in a digital age: an opportunity to strengthen health systems and improve health outcomes date: 2015-11-09 pages: extension: .txt txt: ./txt/cord-288982-63ddlh20.txt cache: ./cache/cord-288982-63ddlh20.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-288982-63ddlh20.txt' === file2bib.sh === id: cord-281241-k1adcls8 author: Döhla, M. title: Rapid point-of-care testing for SARS-CoV-2 in a community screening setting shows low sensitivity date: 2020-04-18 pages: extension: .txt txt: ./txt/cord-281241-k1adcls8.txt cache: ./cache/cord-281241-k1adcls8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-281241-k1adcls8.txt' === file2bib.sh === id: cord-256568-mbkrg98v author: Jantzen, R. title: Epidemiological and socio-economic characteristics of the COVID-19 spring outbreak in Quebec, Canada: A population-based study date: 2020-09-01 pages: extension: .txt txt: ./txt/cord-256568-mbkrg98v.txt cache: ./cache/cord-256568-mbkrg98v.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-256568-mbkrg98v.txt' === file2bib.sh === id: cord-273324-xhpv783y author: Land, Kevin J. title: REASSURED diagnostics to inform disease control strategies, strengthen health systems and improve patient outcomes date: 2018-12-13 pages: extension: .txt txt: ./txt/cord-273324-xhpv783y.txt cache: ./cache/cord-273324-xhpv783y.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-273324-xhpv783y.txt' === file2bib.sh === id: cord-252959-ktet18wl author: Lim, Jong-Min title: Ingestion of Exopolymers from Aureobasidium pullulans Reduces the Duration of Cold and Flu Symptoms: A Randomized, Placebo-Controlled Intervention Study date: 2018-05-30 pages: extension: .txt txt: ./txt/cord-252959-ktet18wl.txt cache: ./cache/cord-252959-ktet18wl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-252959-ktet18wl.txt' === file2bib.sh === id: cord-281495-beb164oy author: Charpentier, Charlotte title: Performance evaluation of two SARS-CoV-2 IgG/IgM rapid tests (Covid-Presto and NG-Test) and one IgG automated immunoassay (Abbott) date: 2020-09-03 pages: extension: .txt txt: ./txt/cord-281495-beb164oy.txt cache: ./cache/cord-281495-beb164oy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-281495-beb164oy.txt' === file2bib.sh === id: cord-320970-ru2iw0py author: Peeling, Rosanna W title: Serology testing in the COVID-19 pandemic response date: 2020-07-17 pages: extension: .txt txt: ./txt/cord-320970-ru2iw0py.txt cache: ./cache/cord-320970-ru2iw0py.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-320970-ru2iw0py.txt' === file2bib.sh === id: cord-307187-5blsjicu author: Missel, Malene title: A stoic and altruistic orientation towards their work: a qualitative study of healthcare professionals’ experiences of awaiting a COVID-19 test result date: 2020-11-11 pages: extension: .txt txt: ./txt/cord-307187-5blsjicu.txt cache: ./cache/cord-307187-5blsjicu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-307187-5blsjicu.txt' === file2bib.sh === id: cord-325455-e464idc0 author: Atchison, Christina title: Usability and acceptability of home-based self-testing for SARS-CoV-2 antibodies for population surveillance date: 2020-08-12 pages: extension: .txt txt: ./txt/cord-325455-e464idc0.txt cache: ./cache/cord-325455-e464idc0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-325455-e464idc0.txt' === file2bib.sh === id: cord-283517-7gd0f06m author: Deak, Eszter title: Right-Sizing Technology in the Era of Consumer-Driven Health Care date: 2017-08-01 pages: extension: .txt txt: ./txt/cord-283517-7gd0f06m.txt cache: ./cache/cord-283517-7gd0f06m.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-283517-7gd0f06m.txt' === file2bib.sh === id: cord-290251-ihq8gdwj author: Hasell, Joe title: A cross-country database of COVID-19 testing date: 2020-10-08 pages: extension: .txt txt: ./txt/cord-290251-ihq8gdwj.txt cache: ./cache/cord-290251-ihq8gdwj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-290251-ihq8gdwj.txt' === file2bib.sh === id: cord-284945-837qlk8y author: Rahmandad, H. title: Estimating the global spread of COVID-19 date: 2020-06-26 pages: extension: .txt txt: ./txt/cord-284945-837qlk8y.txt cache: ./cache/cord-284945-837qlk8y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-284945-837qlk8y.txt' === file2bib.sh === id: cord-307123-h48uwj93 author: Kiechle, Frederick L. title: Establishing benchmarks and metrics for disruptive technologies, inappropriate and obsolete tests in the clinical laboratory date: 2014-01-01 pages: extension: .txt txt: ./txt/cord-307123-h48uwj93.txt cache: ./cache/cord-307123-h48uwj93.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-307123-h48uwj93.txt' === file2bib.sh === id: cord-316047-d9cpe9yl author: Gonzalez, T. title: Influence of COVID-19 confinement on students’ performance in higher education date: 2020-10-09 pages: extension: .txt txt: ./txt/cord-316047-d9cpe9yl.txt cache: ./cache/cord-316047-d9cpe9yl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-316047-d9cpe9yl.txt' === file2bib.sh === id: cord-300930-47a4pu27 author: Beigel, R. title: Rate Estimation and Identification of COVID-19 Infections: Towards Rational Policy Making During Early and Late Stages of Epidemics date: 2020-05-24 pages: extension: .txt txt: ./txt/cord-300930-47a4pu27.txt cache: ./cache/cord-300930-47a4pu27.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-300930-47a4pu27.txt' === file2bib.sh === id: cord-226956-n5qwsvtr author: Arbia, Giuseppe title: A Note on Early Epidemiological Analysis of Coronavirus Disease 2019 Outbreak using Crowdsourced Data date: 2020-03-13 pages: extension: .txt txt: ./txt/cord-226956-n5qwsvtr.txt cache: ./cache/cord-226956-n5qwsvtr.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-226956-n5qwsvtr.txt' === file2bib.sh === id: cord-319436-mlitd45q author: Brinati, D. title: Detection of COVID-19 Infection from Routine Blood Exams with Machine Learning: a Feasibility Study date: 2020-04-25 pages: extension: .txt txt: ./txt/cord-319436-mlitd45q.txt cache: ./cache/cord-319436-mlitd45q.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-319436-mlitd45q.txt' === file2bib.sh === id: cord-324944-ixh3ykrc author: Mitsakakis, Konstantinos title: Diagnostic tools for tackling febrile illness and enhancing patient management date: 2018-12-05 pages: extension: .txt txt: ./txt/cord-324944-ixh3ykrc.txt cache: ./cache/cord-324944-ixh3ykrc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-324944-ixh3ykrc.txt' === file2bib.sh === id: cord-225183-6rusimb5 author: Boukai, Ben title: Bayesian Modeling of COVID-19 Positivity Rate -- the Indiana experience date: 2020-07-09 pages: extension: .txt txt: ./txt/cord-225183-6rusimb5.txt cache: ./cache/cord-225183-6rusimb5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-225183-6rusimb5.txt' === file2bib.sh === id: cord-310714-kqzlwka0 author: Braz, Lucia Maria Almeida title: Visceral Leishmaniasis diagnosis: a rapid test is a must at the hospital bedside date: 2020-06-16 pages: extension: .txt txt: ./txt/cord-310714-kqzlwka0.txt cache: ./cache/cord-310714-kqzlwka0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-310714-kqzlwka0.txt' === file2bib.sh === id: cord-308021-cnf4xljc author: Kohns Vasconcelos, Malte title: SARS-CoV-2 testing and infection control strategies in European paediatric emergency departments during the first wave of the pandemic date: 2020-10-13 pages: extension: .txt txt: ./txt/cord-308021-cnf4xljc.txt cache: ./cache/cord-308021-cnf4xljc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-308021-cnf4xljc.txt' === file2bib.sh === id: cord-300520-vxn7uh41 author: Baunez, C. title: Tracking the Dynamics and Allocating Tests for COVID-19 in Real-Time: an Acceleration Index with an Application to French Age Groups and Departments date: 2020-11-07 pages: extension: .txt txt: ./txt/cord-300520-vxn7uh41.txt cache: ./cache/cord-300520-vxn7uh41.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-300520-vxn7uh41.txt' === file2bib.sh === id: cord-289461-bnusv816 author: Droste, M. C. title: Economic Benefits of COVID-19 Screening Tests date: 2020-10-27 pages: extension: .txt txt: ./txt/cord-289461-bnusv816.txt cache: ./cache/cord-289461-bnusv816.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-289461-bnusv816.txt' === file2bib.sh === id: cord-276577-06boh550 author: Schanzer, Dena L. title: Estimating Sensitivity of Laboratory Testing for Influenza in Canada through Modelling date: 2009-08-18 pages: extension: .txt txt: ./txt/cord-276577-06boh550.txt cache: ./cache/cord-276577-06boh550.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-276577-06boh550.txt' === file2bib.sh === id: cord-295126-lz2jbmcn author: Toresdahl, Brett G. title: Coronavirus Disease 2019 (COVID-19): Considerations for the Competitive Athlete date: 2020-04-06 pages: extension: .txt txt: ./txt/cord-295126-lz2jbmcn.txt cache: ./cache/cord-295126-lz2jbmcn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-295126-lz2jbmcn.txt' === file2bib.sh === id: cord-320864-k9zksbyt author: Remes-Troche, J. M. title: Recommendations for the reopening and activity resumption of the neurogastroenterology units in the face of the COVID-19 pandemic. Position of the Sociedad Latinoamericana de Neurogastroenterología date: 2020-11-01 pages: extension: .txt txt: ./txt/cord-320864-k9zksbyt.txt cache: ./cache/cord-320864-k9zksbyt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-320864-k9zksbyt.txt' === file2bib.sh === id: cord-307500-2jwuzfan author: Gray, Nicholas title: "No test is better than a bad test": Impact of diagnostic uncertainty in mass testing on the spread of Covid-19 date: 2020-04-22 pages: extension: .txt txt: ./txt/cord-307500-2jwuzfan.txt cache: ./cache/cord-307500-2jwuzfan.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-307500-2jwuzfan.txt' === file2bib.sh === id: cord-310195-am3u7z76 author: Waller, J. title: Immunity Passports for SARS-CoV-2: an online experimental study of the impact of antibody test terminology on perceived risk and behaviour date: 2020-05-10 pages: extension: .txt txt: ./txt/cord-310195-am3u7z76.txt cache: ./cache/cord-310195-am3u7z76.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-310195-am3u7z76.txt' === file2bib.sh === id: cord-296306-xcomjvaa author: Rivett, Lucy title: Screening of healthcare workers for SARS-CoV-2 highlights the role of asymptomatic carriage in COVID-19 transmission date: 2020-05-11 pages: extension: .txt txt: ./txt/cord-296306-xcomjvaa.txt cache: ./cache/cord-296306-xcomjvaa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-296306-xcomjvaa.txt' === file2bib.sh === id: cord-312477-2y88gzji author: Mlcochova, P. title: Combined point of care nucleic acid and antibody testing for SARS-CoV-2: a prospective cohort study in suspected moderate to severe COVID-19 disease. date: 2020-06-18 pages: extension: .txt txt: ./txt/cord-312477-2y88gzji.txt cache: ./cache/cord-312477-2y88gzji.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-312477-2y88gzji.txt' === file2bib.sh === id: cord-330721-hmnrnem6 author: Chambliss, Allison B title: Contingency planning in the clinical laboratory: lessons learned amidst COVID-19 date: 2020-04-21 pages: extension: .txt txt: ./txt/cord-330721-hmnrnem6.txt cache: ./cache/cord-330721-hmnrnem6.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-330721-hmnrnem6.txt' === file2bib.sh === id: cord-325956-1kxxg0s9 author: Potluri, Rahul title: Making sense of the Global Coronavirus Data: The role of testing rates in understanding the pandemic and our exit strategy date: 2020-04-11 pages: extension: .txt txt: ./txt/cord-325956-1kxxg0s9.txt cache: ./cache/cord-325956-1kxxg0s9.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-325956-1kxxg0s9.txt' === file2bib.sh === id: cord-323476-rb9n5wc0 author: Poole, Stephen title: How are rapid diagnostic tests for infectious diseases used in clinical practice: a global survey by the International Society of Antimicrobial Chemotherapy (ISAC) date: 2020-09-09 pages: extension: .txt txt: ./txt/cord-323476-rb9n5wc0.txt cache: ./cache/cord-323476-rb9n5wc0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-323476-rb9n5wc0.txt' === file2bib.sh === id: cord-303539-gimz41yb author: Goudouris, Ekaterini S. title: Laboratory diagnosis of COVID-19() date: 2020-08-31 pages: extension: .txt txt: ./txt/cord-303539-gimz41yb.txt cache: ./cache/cord-303539-gimz41yb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-303539-gimz41yb.txt' === file2bib.sh === id: cord-324373-mgdtb98z author: Antonelli, Andrea title: Comparison between the Airgo™ Device and a Metabolic Cart during Rest and Exercise † date: 2020-07-15 pages: extension: .txt txt: ./txt/cord-324373-mgdtb98z.txt cache: ./cache/cord-324373-mgdtb98z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-324373-mgdtb98z.txt' === file2bib.sh === id: cord-292274-upwn9o2m author: Ghaffari, Abdi title: COVID-19 Serological Tests: How Well Do They Actually Perform? date: 2020-07-04 pages: extension: .txt txt: ./txt/cord-292274-upwn9o2m.txt cache: ./cache/cord-292274-upwn9o2m.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-292274-upwn9o2m.txt' === file2bib.sh === id: cord-328294-gii1b7s7 author: Doty, Richard L. title: Olfaction and Its Alteration by Nasal Obstruction, Rhinitis, and Rhinosinusitis date: 2009-01-02 pages: extension: .txt txt: ./txt/cord-328294-gii1b7s7.txt cache: ./cache/cord-328294-gii1b7s7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-328294-gii1b7s7.txt' === file2bib.sh === id: cord-343340-zi0rfidc author: Aragón‐Caqueo, Diego title: Optimization of group size in pool testing strategy for SARS‐CoV‐2: A simple mathematical model date: 2020-05-03 pages: extension: .txt txt: ./txt/cord-343340-zi0rfidc.txt cache: ./cache/cord-343340-zi0rfidc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-343340-zi0rfidc.txt' === file2bib.sh === id: cord-318570-wj7r6953 author: Xiao, Yinzong title: Point-of-Care Tests for Hepatitis B: An Overview date: 2020-10-02 pages: extension: .txt txt: ./txt/cord-318570-wj7r6953.txt cache: ./cache/cord-318570-wj7r6953.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-318570-wj7r6953.txt' === file2bib.sh === id: cord-334274-4jee19hx author: Waelde, K. title: How to remove the testing bias in CoV-2 statistics date: 2020-10-16 pages: extension: .txt txt: ./txt/cord-334274-4jee19hx.txt cache: ./cache/cord-334274-4jee19hx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-334274-4jee19hx.txt' === file2bib.sh === id: cord-331617-1ytcd0ax author: Horvath, Karl title: Antikörpertests bei COVID-19 - Was uns die Ergebnisse sagen date: 2020-05-15 pages: extension: .txt txt: ./txt/cord-331617-1ytcd0ax.txt cache: ./cache/cord-331617-1ytcd0ax.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-331617-1ytcd0ax.txt' === file2bib.sh === id: cord-342181-x14iywtr author: Taipale, J. title: Population-scale testing can suppress the spread of COVID-19 date: 2020-05-01 pages: extension: .txt txt: ./txt/cord-342181-x14iywtr.txt cache: ./cache/cord-342181-x14iywtr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-342181-x14iywtr.txt' === file2bib.sh === id: cord-328320-1f3r80r5 author: Kim, Edward title: Drawing on Israel’s Experience Organizing Volunteers to Operationalize Drive-Through Coronavirus Testing Centers date: 2020-04-16 pages: extension: .txt txt: ./txt/cord-328320-1f3r80r5.txt cache: ./cache/cord-328320-1f3r80r5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-328320-1f3r80r5.txt' === file2bib.sh === id: cord-315077-i1xjcuae author: Branda, John A. title: Utilization management in microbiology date: 2014-01-01 pages: extension: .txt txt: ./txt/cord-315077-i1xjcuae.txt cache: ./cache/cord-315077-i1xjcuae.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-315077-i1xjcuae.txt' === file2bib.sh === id: cord-332481-y0rd70ry author: Ljubic, T. title: The effect of serological screening for SARS-CoV-2 antibodies to participants' attitudes and risk behaviour: a study on a tested population sample of industry workers in Split-Dalmatia County, Croatia date: 2020-06-17 pages: extension: .txt txt: ./txt/cord-332481-y0rd70ry.txt cache: ./cache/cord-332481-y0rd70ry.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-332481-y0rd70ry.txt' === file2bib.sh === id: cord-339122-7vvqtk84 author: Deb, Chaarushena title: Covid-19, Single-Sourced Diagnostic Tests, and Innovation Policy date: 2020-07-07 pages: extension: .txt txt: ./txt/cord-339122-7vvqtk84.txt cache: ./cache/cord-339122-7vvqtk84.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-339122-7vvqtk84.txt' === file2bib.sh === id: cord-354006-j1y42oxu author: Ozdemir, Vural title: Shifting emphasis from pharmacogenomics to theragnostics date: 2006 pages: extension: .txt txt: ./txt/cord-354006-j1y42oxu.txt cache: ./cache/cord-354006-j1y42oxu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-354006-j1y42oxu.txt' === file2bib.sh === id: cord-019490-m1cuuehi author: nan title: Abstracts cont. date: 2015-12-28 pages: extension: .txt txt: ./txt/cord-019490-m1cuuehi.txt cache: ./cache/cord-019490-m1cuuehi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-019490-m1cuuehi.txt' === file2bib.sh === id: cord-354005-q5nj0ku1 author: Richaud, M. title: Specific testing of textiles for transportation date: 2017-09-29 pages: extension: .txt txt: ./txt/cord-354005-q5nj0ku1.txt cache: ./cache/cord-354005-q5nj0ku1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-354005-q5nj0ku1.txt' === file2bib.sh === id: cord-350473-f47i7y5h author: Sen-Crowe, Brendon title: COVID-19 laboratory testing issues and capacities as we transition to surveillance testing and contact tracing date: 2020-05-27 pages: extension: .txt txt: ./txt/cord-350473-f47i7y5h.txt cache: ./cache/cord-350473-f47i7y5h.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-350473-f47i7y5h.txt' === file2bib.sh === id: cord-345454-r1ymzk6n author: Levesque, J. title: A note on COVID-19 seroprevalence studies: a meta-analysis using hierarchical modelling date: 2020-05-06 pages: extension: .txt txt: ./txt/cord-345454-r1ymzk6n.txt cache: ./cache/cord-345454-r1ymzk6n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-345454-r1ymzk6n.txt' === file2bib.sh === id: cord-352111-frk319q1 author: Woodruff, Amelita title: COVID-19 Follow up Testing date: 2020-05-11 pages: extension: .txt txt: ./txt/cord-352111-frk319q1.txt cache: ./cache/cord-352111-frk319q1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-352111-frk319q1.txt' === file2bib.sh === id: cord-337462-9mvk86q6 author: nan title: Humanity tested date: 2020-04-08 pages: extension: .txt txt: ./txt/cord-337462-9mvk86q6.txt cache: ./cache/cord-337462-9mvk86q6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-337462-9mvk86q6.txt' === file2bib.sh === id: cord-349161-4899cq99 author: Whiting, Penny F title: Graphical presentation of diagnostic information date: 2008-04-11 pages: extension: .txt txt: ./txt/cord-349161-4899cq99.txt cache: ./cache/cord-349161-4899cq99.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-349161-4899cq99.txt' === file2bib.sh === id: cord-337458-dc90ecfe author: Markwalter, Christine F. title: Inorganic Complexes and Metal-Based Nanomaterials for Infectious Disease Diagnostics date: 2018-12-04 pages: extension: .txt txt: ./txt/cord-337458-dc90ecfe.txt cache: ./cache/cord-337458-dc90ecfe.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-337458-dc90ecfe.txt' === file2bib.sh === id: cord-023364-ut56gczm author: nan title: EDUCATION DAY MONDAY: PLENARY SESSION 1 MONDAY: PARALLEL SESSIONS date: 2005-06-08 pages: extension: .txt txt: ./txt/cord-023364-ut56gczm.txt cache: ./cache/cord-023364-ut56gczm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 12 resourceName b'cord-023364-ut56gczm.txt' === file2bib.sh === id: cord-006229-7yoilsho author: nan title: Abstracts of the 82(nd) Annual Meeting of the German Society for Experimental and Clinical Pharmacology and Toxicology (DGPT) and the 18(th) Annual Meeting of the Network Clinical Pharmacology Germany (VKliPha) in cooperation with the Arbeitsgemeinschaft für Angewandte Humanpharmakologie e.V. (AGAH) date: 2016-02-06 pages: extension: .txt txt: ./txt/cord-006229-7yoilsho.txt cache: ./cache/cord-006229-7yoilsho.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-006229-7yoilsho.txt' === file2bib.sh === id: cord-022650-phsr10jp author: nan title: Abstracts TPS date: 2018-08-14 pages: extension: .txt txt: ./txt/cord-022650-phsr10jp.txt cache: ./cache/cord-022650-phsr10jp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-022650-phsr10jp.txt' === file2bib.sh === id: cord-023354-f2ciho6o author: nan title: TUESDAY PLENARY SESSION 3 TUESDAY: POSTERS date: 2005-06-08 pages: extension: .txt txt: ./txt/cord-023354-f2ciho6o.txt cache: ./cache/cord-023354-f2ciho6o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-023354-f2ciho6o.txt' === file2bib.sh === id: cord-023346-8sqbqjm1 author: nan title: MONDAY: POSTERS date: 2005-06-08 pages: extension: .txt txt: ./txt/cord-023346-8sqbqjm1.txt cache: ./cache/cord-023346-8sqbqjm1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-023346-8sqbqjm1.txt' === file2bib.sh === id: cord-019347-tj3ye1mx author: nan title: ABSTRACT BOOK date: 2010-02-19 pages: extension: .txt txt: ./txt/cord-019347-tj3ye1mx.txt cache: ./cache/cord-019347-tj3ye1mx.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-019347-tj3ye1mx.txt' === file2bib.sh === id: cord-023095-4dannjjm author: nan title: Research Abstract Program of the 2011 ACVIM Forum Denver, Colorado, June 15–18, 2011 date: 2011-05-03 pages: extension: .txt txt: ./txt/cord-023095-4dannjjm.txt cache: ./cache/cord-023095-4dannjjm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-023095-4dannjjm.txt' === file2bib.sh === id: cord-010092-uftc8inx author: nan title: Abstract of 29th Regional Congress of the ISBT date: 2019-06-07 pages: extension: .txt txt: ./txt/cord-010092-uftc8inx.txt cache: ./cache/cord-010092-uftc8inx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 8 resourceName b'cord-010092-uftc8inx.txt' === 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 18 resourceName b'cord-010119-t1x9gknd.txt' Que is empty; done keyword-test-cord === reduce.pl bib === id = cord-001253-3jnkki5z author = Mohammad, Fahim title = Advantages and Limitations of Anticipating Laboratory Test Results from Regression- and Tree-Based Rules Derived from Electronic Health-Record Data date = 2014-04-14 pages = extension = .txt mime = text/plain words = 3850 sentences = 178 flesch = 55 summary = We used four types of input-age, gender, diagnoses (three-digit ICD-9 codes), and results of laboratory tests on blood samples added to the record in the seven days before a given test was ordered-to build simple, robust models for whether the result of a test would be within the reference interval (''normal'') or outside of it in a given direction (''abnormal''), treating high and low results separately. To determine how well sendout and in-house test results can be anticipated based on basic information available in the medical record, we used two independent methods-generalized linear modeling (GLM) and classification and regression trees (CART)to build simple, robust test-result predictors and then evaluated the performance of these predictors according to the standard clinical metrics of positive predictive value (PPV) and negative predictive value (NPV), as well as sensitivity and specificity via the receiveroperator curve (ROC) area under the curve (AUC). cache = ./cache/cord-001253-3jnkki5z.txt txt = ./txt/cord-001253-3jnkki5z.txt === reduce.pl bib === id = cord-017359-zr0bo9el author = Pfannschmidt, Karlson title = Evaluating Tests in Medical Diagnosis: Combining Machine Learning with Game-Theoretical Concepts date = 2016-05-10 pages = extension = .txt mime = text/plain words = 3335 sentences = 214 flesch = 56 summary = Our approach is motivated and illustrated by a concrete case study in veterinary medicine, namely the diagnosis of a disease in cats called feline infectious peritonitis. An important special case is the use of semi-supervised learning to exploit "unlabeled" data coming from individuals for which tests have been made but the true health condition is unknown. Our approach is motivated by a concrete case study in veterinary medicine, namely the diagnosis of a disease in cats called feline infectious peritonitis (FIP). In addition to the use of (semi-supervised) machine learning methodology in medical diagnosis, we propose a game-theoretical approach for measuring the usefulness of individual tests as well as model-based combinations of such tests. More specifically, what can be estimated in this way is the generalization performance of a model that is trained on a combination A and data in the form of L labeled and U unlabeled examples. Performances of different diagnostic tests for feline infectious peritonitis in challenging clinical cases cache = ./cache/cord-017359-zr0bo9el.txt txt = ./txt/cord-017359-zr0bo9el.txt === reduce.pl bib === id = cord-021511-88xaynf7 author = Werner, Linda L. title = Immunologic and Plasma Protein Disorders date = 2009-05-15 pages = extension = .txt mime = text/plain words = 6195 sentences = 376 flesch = 34 summary = Hypoalbuminemia associated with hepatomegaly; microhepatia; neurologic signs; icterus; decreased blood urea nitrogen (BUN) with or without increased alanine aminotransferase (ALT), serum alkaline phosphatase (SAP), or both; or abnormal hepatic function test results (e.g., serum bile acids) requires a diagnostic workup for hepatic insufficiency (see Chapter 9). Occasionally Indicated • Protein electrophoresis is performed when hyperglobulinemia is not caused by hemoconcentration and either (1) the globulin concentration is high enough to make monoclonal gammopathy a reasonable possibility or (2) humoral immunodeficiencies are suspected. Immunoelectrophoresis is the method of choice to detect urinary and serum Bence Jones protein, a monoclonal protein equivalent to immunoglobulin light chains which occasionally occurs in multiple myeloma and macroglobulinemia. Monoclonal immunoglobulin elevations are also called paraproteins or M proteins and are usually the result of lymphocyte and plasma cell neoplasias (e.g., multiple myeloma, macroglobulinemia, lymphosarcoma; see Table 12 -3). Diagnosis of multiple myeloma in dogs requires finding at least two of the following: lytic skeletal lesions, bone marrow plasmacytosis, Bence Jones proteinuria, or a monoclonal spike on serum protein electrophoresis. cache = ./cache/cord-021511-88xaynf7.txt txt = ./txt/cord-021511-88xaynf7.txt === reduce.pl bib === === reduce.pl bib === id = cord-023584-yaxawqhj author = Bucknall, R.A. title = The Continuing Search for Antiviral Drugs date = 2008-04-10 pages = extension = .txt mime = text/plain words = 8497 sentences = 339 flesch = 48 summary = Of course, if wide-spectrum leads appear, the choice of test virus may be irrelevant, but the antiviral compounds (as distinct from interferon inducers) known at present are characterized by their relatively limited spectrum of activity, e.g., methisazone is active only against poxviruses (Bauer and Sadler, 1960) and possibly adenoviruses (Bauer and Apostolov, 1966) ; l-aminoadamantane is active only against influenza A1 and As and not against other myxo-or paramyxoviruses (Davies et al., 1964) ; guanidine and a-hydroxybenzyl benzimidazole are active only against picornaviruses and not against other small ribonucleic acid (RNA) viruses (Eggers and Tamm, 1961) . In summary, a tissue culture screen should be able to proccss large numbers of tcst compounds, using viruses as relevant as possible to the diseases for which a drug is required, and should employ normal rather than neoplastic cells. cache = ./cache/cord-023584-yaxawqhj.txt txt = ./txt/cord-023584-yaxawqhj.txt === reduce.pl bib === id = cord-018335-4l7scdqk author = Kiechle, Frederick L. title = Utilization Management in a Large Community Hospital date = 2016-12-01 pages = extension = .txt mime = text/plain words = 11062 sentences = 549 flesch = 40 summary = In preparation for the shift from fee-for-service to a valuebased payment system [ 15 ] large community hospitals have been actively engaged in three enterprises which will impact laboratory test utilization: buying physician practices, increasing the use of hospitalists and consolidation of hospitals. Certainly, utilization management of POCT programs will require investigations to determine the relationship between total laboratory turn-around time for results, patient outcome and hospital costs using cost effectiveness analyses [ 36 ] . As technology advances, the traditionally " agrarian society " of the laboratory is becoming more industrialized with the implementation of automation, molecular based testing, and use of mass spectrometry ( MALDI-TOF -Matrix-Assisted Laser Desorption Ionization-Time of Flight). However, all of these technological advances are shortening the time for a laboratory diagnosis and ultimately maximizing the impact to patient care and how physicians at a large community hospital will utilize the more rapid microbiology laboratory services. cache = ./cache/cord-018335-4l7scdqk.txt txt = ./txt/cord-018335-4l7scdqk.txt === reduce.pl bib === id = cord-024631-yvek5vjz author = Althaus, T. title = Causes of fever in primary care in Southeast Asia and the performance of C-reactive protein in discriminating bacterial from viral pathogens date = 2020-05-11 pages = extension = .txt mime = text/plain words = 4327 sentences = 226 flesch = 43 summary = OBJECTIVES: We investigated causes of fever in the primary levels of care in Southeast Asia, and evaluated whether C-reactive protein (CRP) could distinguish bacterial from viral pathogens. In this study, we aim to identify key organisms among acutely febrile children and adults attending primary health care in Southeast Asia, and to evaluate the performance of CRP for discriminating between bacteria and viruses. Specimens were collected from febrile patients recruited into a previously described multi-centre randomised-controlled trial evaluating the impact of C-reactive protein (CRP) testing on antibiotic prescription in primary care [38] . We investigated the spectrum of organisms among febrile children and adults in the community and evaluated the performance of CRP in distinguishing bacteria from viruses including its potential impact on antibiotic prescription compared with current practice. Investigating non-malarial acute febrile illness remains challenging in resource-poor areas [8] , and despite screening for multiple organisms on blood and respiratory specimens, we were only able to identify a probable cause of fever in 227 (29.4%) of patients. cache = ./cache/cord-024631-yvek5vjz.txt txt = ./txt/cord-024631-yvek5vjz.txt === reduce.pl bib === id = cord-018271-ybfxtc7x author = van Doorne, Hans title = Microbiology date = 2015-02-09 pages = extension = .txt mime = text/plain words = 13173 sentences = 794 flesch = 44 summary = Microbial contamination of pharmaceutical preparations may cause health hazard to the patient (e.g. infection, pyrogenic or allergic reaction), altered therapeutic activity of the product, or other decrease in quality (turbidity, loss of consistency, altered pH). Microbiological quality control of pharmaceutical preparations and monitoring of production areas depend on the detection and quantification of micro-organisms. Survival and growth of micro-organisms in pharmaceutical preparations is governed by extrinsic factors (particularly temperature) and intrinsic factors (product composition and physico-chemical characteristics). Suppliers of materials may minimise the risks of contamination of TSE by ensuring [12] : • The source animals and their geographical origin • Nature of animal material used in manufacture and any procedures in place to avoid cross-contamination with higher risk materials • Production process(es) including the quality control and quality assurance system in place to ensure product consistency and traceability Manufacturers of pharmaceutical preparations select their raw materials so they are TSE free (see also Sect. However, since vaccine preparation involves the use of materials of biological origin, such as Chinese Hamster Ovary cells, vaccines are susceptible to contamination by micro-organisms, including viruses [16] [17] [18] . cache = ./cache/cord-018271-ybfxtc7x.txt txt = ./txt/cord-018271-ybfxtc7x.txt === reduce.pl bib === id = cord-033420-pjtyv0pv author = Kalokairinou, Louiza title = The promise of direct-to-consumer COVID-19 testing: ethical and regulatory issues date = 2020-09-23 pages = extension = .txt mime = text/plain words = 6322 sentences = 310 flesch = 48 summary = Although the provision of DTC tests has potential benefits—such as expanding access to testing and reducing the risk of exposure for consumers and medical personnel—it also raises significant ethical and regulatory concerns. The second part discusses five primary issues for DTC COVID-19 tests: test accuracy; potential misinterpretation of results; misleading claims and other misinformation; privacy concerns; and fair allocation of scarce resources. The second part identifies five primary ethical and regulatory issues for DTC COVID-19 tests: uncertainty over the accuracy of test results; potential misinterpretation of test results by users; misleading product promotion and misinformation; privacy concerns; and fair allocation of scarce resources. We conclude with recommendations for regulators, companies, and other relevant stakeholders that can help ensure high-quality, accurate, and equitably distributed COVID-19 tests, and inform the ethical provision of DTC health tests during public health crises. cache = ./cache/cord-033420-pjtyv0pv.txt txt = ./txt/cord-033420-pjtyv0pv.txt === reduce.pl bib === id = cord-031567-w2676lrz author = Sabit, Maureen title = Pollen allergen skin test and specific IgE reactivity among Filipinos: a community-based study date = 2020-08-12 pages = extension = .txt mime = text/plain words = 4280 sentences = 234 flesch = 50 summary = Data characteristics of test subjects (cases and controls) and positive reactions to different pollen allergens using skin prick test and specific IgE ELISA were presented as frequency (percentage) and compared using the Chi square test of homogeneity or Fisher's Exact test or z-test for two sample proportions. Of the 11 species of arboreal plants used for SPT, most of the study subjects tested positive to three pollen sources: Mangifera indica (MAN), Acacia auriculiformis (ACA), and Lantana camara (LAN) as shown in Table 2 . Skin prick tests (SPT), which is an essential procedure to confirm sensitization in IgE-mediated allergic disease in subjects with allergic rhinitis, asthma, and atopic dermatitis, can be performed from infancy to old age [24] . A high percentage of test subjects in this study reported a history of rhinitis and asthma, which, are allergic diseases often associated with sensitization to aeroallergens [46] . cache = ./cache/cord-031567-w2676lrz.txt txt = ./txt/cord-031567-w2676lrz.txt === reduce.pl bib === id = cord-144448-mqs502xm author = Theagarajan, Lakshmi N. title = Group Testing for COVID-19: How to Stop Worrying and Test More date = 2020-04-14 pages = extension = .txt mime = text/plain words = 7392 sentences = 473 flesch = 71 summary = We present multiple group testing algorithms that could reduce the number of tests performed for COVID-19 diagnosis. • Combinatorial group testing (CGT): The combinatorial algorithms require the exact number (or an upper bound) of the infected samples D. • Probabilistic group testing (PGT): The probabilistic algorithms require an upper bound on α and identify all infected samples with certain probability P D . In general, if T is the number of tests for COVID that are to be performed on a swab with viral load V l with r replicates to achieve a sensitivity of 1 − γ * , then the maximum pool size can be derived as The GBS algorithm simply attempts to perform the BSP D times to identify at most D infected samples in a given pool of size N . cache = ./cache/cord-144448-mqs502xm.txt txt = ./txt/cord-144448-mqs502xm.txt === reduce.pl bib === id = cord-119183-pbliko1k author = Cohen, Tomer title = A combination of 'pooling' with a prediction model can reduce by 73% the number of COVID-19 (Corona-virus) tests date = 2020-05-03 pages = extension = .txt mime = text/plain words = 2706 sentences = 163 flesch = 72 summary = In appendices A -C, we survey three different ways to use this data -the first-of-which is a known method due to Dorfman [3] -which we'll call here 'single pooling' (Appendix A): according to this method, if the pool turns out to be positive, all samples in that pool need to be re-tested individually, as shown in the following diagram: The expected number of tests can be calculated, based on the probability of the samples in the pool to be positive, and the size of the pool (see Appendix A for details). Appendix D includes a table comparing the required number of tests per patient with the various methods, as a function of , and also a comparison to a recently introduced method called double-pooling [4] . As before, is the probability for a positive test, is the size of the population, and , in this case, is the number of columns/rows in the matrix. cache = ./cache/cord-119183-pbliko1k.txt txt = ./txt/cord-119183-pbliko1k.txt === reduce.pl bib === id = cord-027445-bpx4qr0i author = Eisty, Nasir U. title = Testing Research Software: A Case Study date = 2020-05-25 pages = extension = .txt mime = text/plain words = 2642 sentences = 143 flesch = 48 summary = Method: Using the ParSplice research software project as a case, we implemented a testing framework based on a statistical testing approach called Multinomial Test. 2.1), the non-determinism stems from (1) the use of stochastic differential equations to model the physics and (2) the order in which communication between the procedures occurs (note however that even though the results from each execution depends upon message ordering, each valid order produces a statistically accurate result, which is the key requirement for the validity of ParSplice simulations). In this paper, we describe a case study of the ParSplice project in which we followed the PSIP methodology to develop a testing framework to address the difficulties of testing non-deterministic parallel research software. The approach we followed to develop the test framework can be a model for other research software projects. cache = ./cache/cord-027445-bpx4qr0i.txt txt = ./txt/cord-027445-bpx4qr0i.txt === reduce.pl bib === id = cord-021550-evh3b7o2 author = Brokopp, Charles title = Laboratories date = 2007-09-02 pages = extension = .txt mime = text/plain words = 9259 sentences = 436 flesch = 34 summary = Federal, state, and local government agencies, such as health departments, operate laboratories or contract with commercial laboratories for testing related to diagnosis, regulatory compliance, investigations, and environmental monitoring. CDC-based scientists have developed and used new technologies to identify outbreaks of disease in cooperation with state and local public health laboratories. The DOE national laboratories develop new technologies for countering biologic and chemical threats, including systems for the detection, modeling, and response to terrorist attacks (see www-ed.fnal.gov/doe/ doc_labs.html). Many state and locally operated laboratories in addition to clinical and public health laboratories produce test results that may be useful for surveillance. The mission of the LRN is "to maintain an integrated national and international network of laboratories that can respond quickly to acts of chemical or biological terrorism, emerging infectious diseases and other public health threats and emergencies." The LRN was first tasked to address state and local public health laboratory preparedness and response for bioterrorism. cache = ./cache/cord-021550-evh3b7o2.txt txt = ./txt/cord-021550-evh3b7o2.txt === reduce.pl bib === id = cord-012934-c6pbr64i author = Hao, Weiming title = Vestibular prognosis in idiopathic sudden sensorineural hearing loss with vestibular dysfunction treated with oral or intratympanic glucocorticoids: a protocol for randomized controlled trial date = 2020-07-22 pages = extension = .txt mime = text/plain words = 5443 sentences = 280 flesch = 43 summary = title: Vestibular prognosis in idiopathic sudden sensorineural hearing loss with vestibular dysfunction treated with oral or intratympanic glucocorticoids: a protocol for randomized controlled trial The primary outcomes will be vestibular function outcomes assessed by sensory organization test, caloric test, video head impulse test, cervical vestibular evoked myogenic potential, and ocular vestibular evoked myogenic potential; the secondary outcomes include self-reported vestibular dysfunction symptoms; dizziness-related handicap, visual analogue scale for vertigo and tinnitus; and pure tone audiometry. To evaluate the recovery of vestibular function, we set the recovery rates of the whole battery of vestibular function tests (SOT/caloric test/vHIT/VEMPs) as the primary outcome, which is the proportion of patients whose abnormal results of vestibular function tests at baseline recover to normal at 4-/8-week follow-up: in this study, we define a 10-dB PTA criterion as clinically significant difference based on a previous RCT [9] . cache = ./cache/cord-012934-c6pbr64i.txt txt = ./txt/cord-012934-c6pbr64i.txt === reduce.pl bib === id = cord-292209-d1ty9etr author = Horta, Bernardo L title = Prevalence of antibodies against SARS-CoV-2 according to socioeconomic and ethnic status in a nationwide Brazilian survey date = 2020-10-29 pages = extension = .txt mime = text/plain words = 4330 sentences = 247 flesch = 53 summary = Subjects answered a questionnaire on household assets, schooling and self-reported skin color/ethnicity using the standard Brazilian classification in five categories: white, black, brown, Asian or indigenous. The present analyses were aimed at assessing socioeconomic and ethnic group inequalities in prevalence of antibodies against SARS-CoV-2 in 133 sentinel cities throughout Brazil, as part of the EPICOVID-19 study (www.epicovid19brasil.org). In summary, the analyses of the three waves of national serological surveys in Brazil showed important inequalities in the prevalence of antibodies against SARS-CoV-2 according to family wealth, education and ethnic groups. Yet, even after adjustment for region, indigenous individuals were about twice as likely as whites to present antibodies against SARS-CoV-2, and in the national analyses including adjustment for region of the country and socioeconomic status, the prevalence ratio remained at around two. cache = ./cache/cord-292209-d1ty9etr.txt txt = ./txt/cord-292209-d1ty9etr.txt === reduce.pl bib === id = cord-280571-ntgt5hy9 author = Ginocchio, Christine C. title = Strengths and Weaknesses of FDA-Approved/Cleared Diagnostic Devices for the Molecular Detection of Respiratory Pathogens date = 2011-05-01 pages = extension = .txt mime = text/plain words = 7521 sentences = 341 flesch = 39 summary = In addition to RADTs, there are U.S. Food and Drug Administration (FDA)-approved/cleared nonmolecular-based viral diagnostic methods with a more rapid time to result, compared with traditional viral tube culture, eg, direct fluorescent antibody (DFA) testing and rapid cell culture. Although these 8 viruses are responsible for a large number of respiratory tract infections, bocavirus, selected coronaviruses (229E, OC43, NL63, and HKU-1), parainfluenza 4, and rhinovirus are also important causes of respiratory disease and are generally only detected using NAATs. Because antiviral therapies are currently limited to the treatment of influenza A, influenza B, cytomegalovirus pneumonia, and varicella zoster virus pneumonia, it is often argued that the specific identification of other viruses is not relevant, because the information would not change patient management. With clinical integration of real-time polymerase chain reaction (PCR) and FDA-approved/cleared simple cartridge-based NAATs, laboratories of all sizes are now able to perform molecular diagnostic tests. cache = ./cache/cord-280571-ntgt5hy9.txt txt = ./txt/cord-280571-ntgt5hy9.txt === reduce.pl bib === id = cord-026215-neqsup40 author = Grzegorzewski, Przemyslaw title = Two-Sample Dispersion Problem for Fuzzy Data date = 2020-05-16 pages = extension = .txt mime = text/plain words = 4713 sentences = 335 flesch = 67 summary = A new permutation two-sample test for dispersion based on fuzzy random variables is proposed. At least some of the problems associated with the lack of a satisfying difference in constructing statistical tools for reasoning based on fuzzy observations could be overcome by using adequate metrics defined in F(R) -for the general overview see [2] . For instance, in most cases we are not able to find the null distribution of a test statistic based on fuzzy data and, consequently, to find either the critical value or to compute the p-value required for rejection or acceptance of the hypothesis under study. All these reasons indicate that the permutation test applied to fuzzy random variables might be also a competitive tool useful in statistical inference for imprecise data. On the other hand, in Fig. 2 we have a histogram made for the test statistic (11) null distribution obtained for two fuzzy samples of the same samle sizes as before but which differ in dispersion. cache = ./cache/cord-026215-neqsup40.txt txt = ./txt/cord-026215-neqsup40.txt === reduce.pl bib === id = cord-272995-yvj2pqh1 author = Bergman, Christian title = Recommendations for Welcoming Back Nursing Home Visitors during the COVID-19 Pandemic: Results of a Delphi Panel date = 2020-10-07 pages = extension = .txt mime = text/plain words = 6339 sentences = 340 flesch = 51 summary = Regarding visitor guidance, the panel made five strong recommendations: 1) maintain strong infection prevention and control precautions, 2) facilitate indoor and outdoor visits, 3) allow limited physical contact with appropriate precautions, 4) assess individual residents' care preferences and level of risk tolerance, and 5) dedicate an essential caregiver and extend the definition of compassionate care visits to include care that promotes psychosocial wellbeing of residents. We edited the final guidance statements for clarity, aiming to capture the consensus of the Delphi aspects of the following topics (see Table 1 ): testing of asymptomatic staff and residents, 111 surveillance testing, visitor guidance, immunity from prior COVID-19 infection and associated 112 risk of infecting others. The panel 144 strongly agreed on some preconditions that would be essential prior to welcoming back visitors, 145 such as universal masking for staff, sufficient disinfecting supplies, PPE, and written plans 146 around isolation, cohorting, screening, testing, and outbreak investigations. cache = ./cache/cord-272995-yvj2pqh1.txt txt = ./txt/cord-272995-yvj2pqh1.txt === reduce.pl bib === id = cord-102704-wfuzk2dp author = Meza, Diana K. title = Predicting the presence and titer of rabies virus neutralizing antibodies from low-volume serum samples in low-containment facilities date = 2020-04-30 pages = extension = .txt mime = text/plain words = 3183 sentences = 192 flesch = 43 summary = Despite small conflicts, titer predictions were correlated across tests repeated on different dates both for dog samples (r = 0.93), and for a second dataset of sera from wild common vampire bats (r = 0.72, N = 41), indicating repeatability. The pmRFFIT enables high-throughput detection of rabies virus neutralizing antibodies in low-biocontainment settings and is suited to studies in wild or captive animals where large serum volumes cannot be obtained. The binomial and log-normal models fit to 193 this data subset included only the fixed effect of the virus-infected N2A cell counts, but the random 194 effects were identical to those explained above (i.e. test date and field). A final distinction is that 316 instead of scoring microscope field or wells as virus positive or negative, the pmRFFIT predicts 317 serological status and RVNA titer from infected cell counts in a single serum dilution using statistical 318 cache = ./cache/cord-102704-wfuzk2dp.txt txt = ./txt/cord-102704-wfuzk2dp.txt === reduce.pl bib === id = cord-017072-qwe1ne3q author = Poritz, Mark A. title = Multiplex PCR for Detection and Identification of Microbial Pathogens date = 2018-11-10 pages = extension = .txt mime = text/plain words = 7205 sentences = 299 flesch = 41 summary = Multiplex respiratory panels have the potential to improve patient management and lower overall healthcare costs by improving use of influenza antivirals, reducing inappropriate use of antibiotics and antivirals, reducing use of healthcare resource (e.g., additional laboratory or imaging procedures), informing appropriate infection control practices, and reducing length of hospital, emergency department, and intensive care unit (ICU) stay. In another study evaluating adult patients with a positive influenza result on a multiplex respiratory panel, Rappo [21] reported a significantly lower odds ratio for hospital admission (p = 0.046), a reduced length of stay (p = 0.040), reductions in antimicrobial duration (p = 0.032), and a reduction in the number of chest radiographs (p = 0.005). As with the individual molecular assays and the MALDI-TOF identification, numerous studies have shown that use of multiplex molecular blood culture panels dramatically reduces the time to organism identification [29] [30] [31] [32] which drives more appropriate pathogen-directed therapy. A retrospective study of the impact of rapid diagnostic testing on time to pathogen identification and antibiotic use for children with positive blood cultures cache = ./cache/cord-017072-qwe1ne3q.txt txt = ./txt/cord-017072-qwe1ne3q.txt === reduce.pl bib === id = cord-262846-1mhimfsf author = Gray, Nicholas title = Is “no test is better than a bad test”? Impact of diagnostic uncertainty in mass testing on the spread of COVID-19 date = 2020-10-21 pages = extension = .txt mime = text/plain words = 6023 sentences = 337 flesch = 55 summary = This strategy would involve detecting those who have successfully overcome the virus, and are likely to have some level of immunity (or at least reduced susceptibility to more serious illness if they are infected again), so are relatively safe to relax their personal lockdown measures. To explore the effect of imperfect testing on the disease dynamics when strategies testing regimes are employed to relax lockdown measures, three new classes were added to the model. implement quarantine in their model but do not incorporate the effects on the dynamics from imperfect testing, nor do they consider how the quality and scale of an available test affect the spread of a disease. Wide-scale screening for antibodies in the general population promises significant scientific value, and targeted antibody testing is likely to have value for reducing risks to NHS and care-sector staff, and other key workers who will need to have close contact with COVID-19 sufferers. cache = ./cache/cord-262846-1mhimfsf.txt txt = ./txt/cord-262846-1mhimfsf.txt === reduce.pl bib === id = cord-102817-m1l1t0e1 author = Lucas, T. C. title = Responsible modelling: Unit testing for infectious disease epidemiology date = 2020-08-16 pages = extension = .txt mime = text/plain words = 6076 sentences = 412 flesch = 66 summary = At the time of writing, infectious disease modellers are playing a central role in the interpretation of available data on the COVID-19 pandemic to inform policy design and evaluation [1] [2] [3] . We do not know of high profile cases of infectious disease models being found to have bugs once published, but as code is not always shared and little post-publication testing of code occurs, this likely represents a failure of detection. It is also notable that there are few texts available which demonstrate the use of unit testing to check infectious disease models. Unit testing is a formally-defined, principled framework that compares comprehensive output scenarios from code to what the programmer expected to happen ( [22] Chapter 7, [23] , [24] ). Instead we devise tests that cover standard usage as well as corner case scenarios: what do we want our function to do if given a negative number e.g. sqrt(-1), or a vector argument containing strings or missing values e.g. sqrt(c(4,"melon",NA))? cache = ./cache/cord-102817-m1l1t0e1.txt txt = ./txt/cord-102817-m1l1t0e1.txt === reduce.pl bib === id = cord-002626-jzwwses4 author = Kaul, Karen L. title = The Case for Laboratory Developed Procedures: Quality and Positive Impact on Patient Care date = 2017-07-16 pages = extension = .txt mime = text/plain words = 14822 sentences = 754 flesch = 40 summary = Clinical laboratories have thus had to develop new assays or modified the existing FDA-approved ones to detect high-risk HPV genotypes in head and neck cancer specimens. The vast majority of reporting laboratories utilized LDPs. 57 KRAS and RAS family gene mutation analysis is also critical in the management of patients with non-small-cell lung cancer (NSCLC) and other tumors, 58 for which FDA approval of kits has not occurred; LDPs or off-label use of kits is required. 74, 75 The FDA approval of anti-EGFR therapies based on clinical trial outcomes data resulted in the need for clinical laboratories to test tumor tissue for the EGFR-sensitizing mutations in order for patients to be eligible for treatment. During those ground-breaking first 15 years of the targeted cancer therapy era, if the laboratory community had been prohibited from providing high-quality, standardized LDP-based testing under existing CLIA guidelines, the negative consequences to patient care in the past and the future would have been substantial. cache = ./cache/cord-002626-jzwwses4.txt txt = ./txt/cord-002626-jzwwses4.txt === reduce.pl bib === id = cord-296588-q2716lda author = Hanson, Kimberly E title = Infectious Diseases Society of America Guidelines on the Diagnosis of COVID-19 date = 2020-06-16 pages = extension = .txt mime = text/plain words = 10179 sentences = 681 flesch = 47 summary = OBJECTIVE: The IDSA's goal was to develop an evidence-based diagnostic guideline to assists clinicians, clinical laboratorians, patients and policymakers in decisions related to the optimal use of SARS-CoV-2 nucleic acid amplification tests. It is important to note as well, that not all specimens were collected from the same patient at the same time, the time of collection from symptom onset was not provided in all studies and various approaches for establishing SARS-CoV-2 positivity were used to define positive results (i.e., clinical evaluation, detection different gene targets versus nucleic acid sequencing). While NP swab collection is widely used and the primary specimen type for commercial direct SARS-CoV-2 test platforms, based on current available evidence, clinical practice, and availability of testing resources, the panel believes there are comparable alternative methods for sampling the nasal passages. cache = ./cache/cord-296588-q2716lda.txt txt = ./txt/cord-296588-q2716lda.txt === reduce.pl bib === id = cord-025556-oyfx3ij5 author = THUNSTRÖM, LINDA title = Testing for COVID-19: willful ignorance or selfless behavior? date = 2020-05-08 pages = extension = .txt mime = text/plain words = 6776 sentences = 296 flesch = 58 summary = Furthermore, willful ignorance often arises when selfish wants conflict with social benefits, which might be particularly likely for potential 'super-spreaders' – people with many social interactions – given people who test positive are urged to self-isolate for two weeks. Furthermore, we expect those at the lowest risk of losing out financially (e.g., risk to labor income or health care costs) or emotionally from self-isolating (i.e., if they are introverts who attach a low value to social interactions) to be the most willing to get tested for COVID-19. We therefore conclude that the positive effect of being an extrovert on willingness to test for COVID-19 is likely due to social health benefits weighing more heavily in their decision than their private costs from potential self-isolation for 14 days, should the test come back positive. cache = ./cache/cord-025556-oyfx3ij5.txt txt = ./txt/cord-025556-oyfx3ij5.txt === reduce.pl bib === === reduce.pl bib === id = cord-121057-986xoy22 author = Mahdi, Esam title = Simultaneous Diagnostic Testing for Linear-Nonlinear Dependence in Time Series date = 2020-08-18 pages = extension = .txt mime = text/plain words = 4230 sentences = 213 flesch = 57 summary = In this respect, Engle (1982) showed that the classical portmanteau tests proposed by Box and Pierce (1970) and Ljung and Box (1978) , based on the autocorrelation function of the residuals, fail to detect the presence of the Autoregressive Conditional Heteroscedasticity, arch , in many financial time series models. In Section 2 we discuss the generalized correlations of residuals and review some test statistics that have been commonly used to detect nonlinearity structure in stationary time series models. In Section 3, we propose new goodness-of-fit (auto-and-cross-correlated) tests that can be used to detect, simultaneously, linear, bilinear, and nonlinear dependency in time series models, and derive their asymptotic distribution as a chi-squared distribution. In this article, we propose four goodness-of-fit tests to detect various types of linear and nonlinear dependency in stationary time series models. cache = ./cache/cord-121057-986xoy22.txt txt = ./txt/cord-121057-986xoy22.txt === reduce.pl bib === id = cord-278377-jgq3dz3u author = Busson, L. title = Prospective evaluation of diagnostic tools for respiratory viruses in children and adults date = 2019-01-15 pages = extension = .txt mime = text/plain words = 4155 sentences = 199 flesch = 48 summary = METHODS: Two hundred ninety-nine respiratory samples were prospectively explored using multiplex molecular techniques (FilmArray Respiratory Panel, Clart Pneumovir), immunological techniques (direct fluorescent assay, lateral flow chromatography) and cell cultures. Meanwhile, important questions concerning these 'new' expensive rapid molecular techniques remain unanswered, such as their cost-effectiveness in terms of patient's management, or the clinical significance of detecting nucleic acids of micro-organisms that could be non-infectious at the time the sample is collected. The objective of this work was to compare the performances of antigen detection and cell cultures techniques routinely used since years for the diagnosis of respiratory viral infections in the setting of a tertiary care hospital to those of newer molecular techniques (Clart Pneumovir, Genomica, Coslada, Spain and FilmArray Respiratory Panel, Biofire, Biomérieux, Marcy L'Etoile, France). False negative results with molecular techniques were significantly more frequent in samples with codetections compared to those with only one pathogen: 12% vs 3% for the FilmArray test (p = 0.034) and 76% vs 11% for the Clart Pneumovir test (p < 0.001). cache = ./cache/cord-278377-jgq3dz3u.txt txt = ./txt/cord-278377-jgq3dz3u.txt === reduce.pl bib === id = cord-270935-t9pym9k0 author = Dumyati, Ghinwa title = Does Universal Testing for COVID-19 Work for Everyone? date = 2020-08-15 pages = extension = .txt mime = text/plain words = 2681 sentences = 179 flesch = 55 summary = Strategies to address COVID-19 infections among nursing home residents vary based on the availability for SARS-CoV-2 tests, the incorporation of tests into broader surveillance efforts, and using results to help mitigate the spread of COVID-19 by identifying asymptomatic and presymptomatic infections. Dr. Jump reports support for this work in part through the Cleveland Geriatric Research 50 While there is general agreement that increased access to testing is important for personal and 23 public health, the selection and use of diagnostic tests to mitigate COVID-19 infections in post-24 acute and long-term care settings is complex and should be tailored to individual sites. Because he met the nursing 36 home's enhanced screening criteria for COVID-19 (Table 1) , 1 he was placed on transmission-37 based precautions and a laboratory test for SARS-CoV-2 was ordered. cache = ./cache/cord-270935-t9pym9k0.txt txt = ./txt/cord-270935-t9pym9k0.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-170195-lrg11s5n author = Stoye, Jorg title = A Critical Assessment of Some Recent Work on COVID-19 date = 2020-05-20 pages = extension = .txt mime = text/plain words = 2764 sentences = 166 flesch = 61 summary = I tentatively re-analyze data from two well-publicized studies on COVID-19, namely the Charit'{e}"viral load in children"and the Bonn"seroprevalence in Heinsberg/Gangelt"study, from information available in the preprints. The authors focus on a hypothesis test as deliverable of their analysis; I would have recommended a nonparametric mean regression with error bands, resulting in some estimated age effect. To the statistically educated reader, the above headlines may suggest that the study tests, and fails to reject, H 0 : "Children have the same viral load as adults." It does not. To take an educated guess, I will now try to recover from the paper a test of H 0 : "Children have the same viral load as adults." To this purpose, I combine the first two and the remaining age bins of Figure 1 to find means of 4.74 and 5.21 with 95% confidence intervals of [4.42, 5.05] and [5.15, 5.27], respectively. cache = ./cache/cord-170195-lrg11s5n.txt txt = ./txt/cord-170195-lrg11s5n.txt === reduce.pl bib === id = cord-298441-77w86l8q author = Lombardi, Andrea title = Characteristics of 1,573 healthcare workers who underwent nasopharyngeal swab for SARS-CoV-2 in Milano, Lombardy, Italy date = 2020-06-20 pages = extension = .txt mime = text/plain words = 1438 sentences = 67 flesch = 52 summary = To answer this question, we reviewed all the 59 nasopharyngeal swab performed in HCWs exposed to confirmed cases of COVID-19 at the 60 Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico located in Milan, the capital 61 of Lombardy, by large the Italian region mostly affected by We assessed 62 frequency of positive tests among symptomatic and asymptomatic HCWs and evaluated the 63 association between occupation, symptoms (type and number), and presence of the infection. Therefore, in middle-and high-resource settings a mass screening for all 163 HCWs exposed to confirmed COVID-19 cases appears the best approach to limit the spread When stratified according to occupation, test-positive frequencies were clearly higher among 177 subsets with direct contact with patients (physicians including residents, nurses and 178 midwives, healthcare assistants and health technicians) than those without (clerical works and 179 technicians). cache = ./cache/cord-298441-77w86l8q.txt txt = ./txt/cord-298441-77w86l8q.txt === reduce.pl bib === === reduce.pl bib === id = cord-286539-3sr4djft author = Mentus, Cassidy title = Analysis and Applications of Adaptive Group Testing Methods for COVID-19 date = 2020-04-07 pages = extension = .txt mime = text/plain words = 5533 sentences = 379 flesch = 65 summary = If a population has a low prevalence of COVID-19 then it is likely for groups of individuals to not have any positive cases. We are therefore able to design a strategy to use less tests to determine whether each individual is positive or negative for the disease by testing mixtures of samples from groups. For each level of prevalence we specify a xed number of individuals to test their combined samples, performing binary search if it is positive. https://doi.org/10.1101/2020.04.05.20050245 doi: medRxiv preprint 9 Performance of group testing methods at dierent prevalences For our performance analysis, we sample populations of sizes N = 100, 1000 at prevelance levels p = .001, .01, .02, .03, .04, .05, .1, .15, .2, and .25. https://doi.org/10.1101/2020.04.05.20050245 doi: medRxiv preprint Figure 11 .1: For GBS32 we sample a population of size 10,000 and record the number of times each case is tested. cache = ./cache/cord-286539-3sr4djft.txt txt = ./txt/cord-286539-3sr4djft.txt === reduce.pl bib === id = cord-271920-1dzkgt6w author = Carpenter, Christopher R. title = Diagnosing COVID‐19 in the Emergency Department: A Scoping Review of Clinical Exam, Labs, Imaging Accuracy and Biases date = 2020-06-16 pages = extension = .txt mime = text/plain words = 7248 sentences = 523 flesch = 48 summary = 3 As waves of COVID-19 patients present to ED's in coming months with symptoms or potential exposures, understanding the diagnostic accuracy and reliability of history, physical exam, routine labs, advanced imaging, and an evolving array of COVID-19 diagnostics will be essential knowledge to inform the timing of testing, optimal specimen and test selection, shared decision-making, and ultimately derivation of clinical instruments to guide disposition, follow-up, and shared The search strategy used a combination of standardized terms and key words, including but not limited to (Covid-19 OR Novel Coronavirus OR SARS-COV-2) AND (diagnosis OR polymerase chain reaction OR serology OR CRISPR-CAS OR sensitivity/specificity) (Appendix). 40,42 It is known, however, that false negatives are frequent, so current recommendations advise incorporating patient's exposure risk, clinical signs and symptoms, routine lab and imaging findings, serology, and (when available) CT results into real-time determination of COVID-19 status. cache = ./cache/cord-271920-1dzkgt6w.txt txt = ./txt/cord-271920-1dzkgt6w.txt === reduce.pl bib === id = cord-117424-mp6h9dyl author = Abraham, Louis title = Bloom Origami Assays: Practical Group Testing date = 2020-07-21 pages = extension = .txt mime = text/plain words = 8661 sentences = 620 flesch = 66 summary = Given n people, test characteristics tpr & tnr and a set of prior probabilities of sample infection (p i ) 1≤i≤n , the best multiset D of m pool designs is the one maximizing the information gain. While Bloom filters have been considered for the low-prevalence COVID-19 testing problem [19, 12] , current methods are based on a simple randomized encoding and decoding process that was designed for internet-scale applications where even linear time was prohibitive and where the keys are not known beforehand. Assuming there are no false negative pool results, one can use the decoder to identify all positive samples and derive optimal dimensions b × g that minimize the number of tests, as shown in the below theorem: The analysis borrows tools from regular Bloom filters and the results shown in [20] . cache = ./cache/cord-117424-mp6h9dyl.txt txt = ./txt/cord-117424-mp6h9dyl.txt === reduce.pl bib === id = cord-263893-zb6h3q4k author = nan title = What to expect from COVID-19 serology in a period of deconfinement? date = 2020-06-01 pages = extension = .txt mime = text/plain words = 710 sentences = 37 flesch = 51 summary = The level of immunity of the French population to Sars-CoV-2 thus seems very low, far from the theoretical threshold of 60% which would allow us to expect a collective level of protection. It should be noted, however, that even if a test with a specificity of 98% is used, the positive predictive value of seropositivity will only be 50% in all regions of the country spared by the epidemic, where seroprevalence is estimated an average of 2% [3] . • that only those tests that will be recommended by the CNRs and validated by the Ministry of Health and Solidarity be used, whether they are unit tests or Elisa tests; • that the sero-epidemiological population surveys be coordinated by the Regional Health Authority (ARS) and that each person recruited be informed personally and confidentially of his or her serological status; cache = ./cache/cord-263893-zb6h3q4k.txt txt = ./txt/cord-263893-zb6h3q4k.txt === reduce.pl bib === id = cord-022653-qa1uph35 author = nan title = Poster Discussion Session PDS date = 2017-08-30 pages = extension = .txt mime = text/plain words = 58292 sentences = 3300 flesch = 53 summary = 0206 | G protein coupled receptor kinase 2 (GRK2) regulates endothelial permeability induced by Bradykinin 0208 | Pharmacokinetics (PK) and pharmacodynamics (PD) of c1 esterase inhibitor of chronic urticaria challenges most commonly identified were the following: time of onset of disease; frequency/duration of and provoking factors for wheals; diurnal variation; occurrence in relation to weekends, holidays, and foreign travel; shape, size, and distribution of wheals; associated angioedema; associated subjective symptoms of lesions; family and personal history regarding urticaria, atopy; previous or current allergies, infections, internal diseases, or other possible causes; psychosomatic and psychiatric diseases; surgical implantations and events during surgery; gastric/ intestinal problems; induction by physical agents or exercise; use of drugs; food allergies; relationship to the menstrual cycle; smoking habits; type of work, hobbies; stress; quality of life and emotional impact; previous therapy and response to therapy, and previous diagnostic procedures/results. cache = ./cache/cord-022653-qa1uph35.txt txt = ./txt/cord-022653-qa1uph35.txt === reduce.pl bib === id = cord-127025-9ubhd4vf author = Abraham, Louis title = Crackovid: Optimizing Group Testing date = 2020-05-13 pages = extension = .txt mime = text/plain words = 4538 sentences = 296 flesch = 64 summary = Our mathematical objective is designed such that the mixture tests it proposes to run in the lab will maximize the amount of information we gain on the ground truth once their lab results are revealed − in expectation, over the randomness of both imperfect tests and prior probabilities of infection per individual. This leads us to the following question: given an initial prior probability distribution p S over the secret, how should we select pool designs to test in the lab? Given numbers n & m, test characteristics tpr & tnr as well as prior probabilities of sample infection p i , the best multiset D of m pool designs is the one maximizing some score, like I(S, T (S, D)) or Confidence(S, T (S, D)). 9 Those prior probabilities can then be readily used by our approach to optimize the pool designs, and the ML system can gradually be improved as we gather more test results. cache = ./cache/cord-127025-9ubhd4vf.txt txt = ./txt/cord-127025-9ubhd4vf.txt === reduce.pl bib === id = cord-022659-chwk2bs4 author = nan title = Abstracts: Poster session date = 2004-10-08 pages = extension = .txt mime = text/plain words = 49153 sentences = 2598 flesch = 49 summary = We investigated the usefulness of informant-based data in Alzheimer's disease (AD) by comparing caregivers' subjective evaluations of 83 probable A D patients' performance on an abbreviated version of the Memory Self-Report Questionnaire to objective evaluations derived from an extensive battery of neuropsychological tests and to clinicians' evaluations. Compared with 89 subjects (mean age 75.2 yr; 34 men, 55 women) with dementia of the Alzheimer type (DAT), there were no significant group differences for comparable Clinical Dementia Rating stages of dementia for measures of language, Activities of Daily Living, or general cognition. The mean age at onset did not differ significantly between handedness groups (F [ l,lOO] = .82), but the mean duration of symptoms ( Alterations in the optical properties of brain can be used to detect pathological changes in patients with Alzheimer's disease (AD). cache = ./cache/cord-022659-chwk2bs4.txt txt = ./txt/cord-022659-chwk2bs4.txt === reduce.pl bib === id = cord-034948-w59wxu8i author = Kuriyama, Akira title = Performance of the cuff leak test in adults in predicting post-extubation airway complications: a systematic review and meta-analysis date = 2020-11-07 pages = extension = .txt mime = text/plain words = 4775 sentences = 268 flesch = 49 summary = We conducted a systematic review and meta-analysis to assess the diagnostic accuracy of the cuff leak test for predicting post-extubation airway complications in intubated adult patients in critical care settings. We included studies that examined the diagnostic accuracy of cuff leak test if post-extubation airway obstruction after extubation or reintubation was explicitly reported as the reference standard. Subgroup analyses suggested that the type of cuff leak test and length of intubation might be the cause of statistical heterogeneity of sensitivity and specificity, respectively, for post-extubation airway obstruction. Consequently, we conducted a systematic review and meta-analysis to assess the diagnostic accuracy of the cuff leak test for predicting post-extubation airway obstruction and subsequent reintubation. We included observational studies (cross-sectional and cohort studies) that examined the diagnostic accuracy of cuff leak test in critical care settings if: (1) the data were extractable into a 2 × 2 table from the reported data, (2) post-extubation airway obstruction after extubation or reintubation was explicitly reported as the reference standard. cache = ./cache/cord-034948-w59wxu8i.txt txt = ./txt/cord-034948-w59wxu8i.txt === reduce.pl bib === id = cord-202376-440zapcw author = Wilder, Bryan title = Tracking disease outbreaks from sparse data with Bayesian inference date = 2020-09-12 pages = extension = .txt mime = text/plain words = 5808 sentences = 347 flesch = 55 summary = The COVID-19 pandemic provides new motivation for a classic problem in epidemiology: estimating the empirical rate of transmission during an outbreak (formally, the time-varying reproduction number) from case counts. Our model places a Gaussian process prior over the unknown reproduction number at each time step and models observations sampled from the distribution of a specific testing program. We now depart from the standard disease model used in previous work and describe a wide-ranging set of examples for how our framework can accommodate models of the process which generates the observed data from the latent (unknown) true infections. However, is complicated by the fact that x is determined by a large number of discrete latent variables, primarily n (the time series of infections) and {t i convert , t i revert } N i=1 , the times when each individual tests positive. cache = ./cache/cord-202376-440zapcw.txt txt = ./txt/cord-202376-440zapcw.txt === reduce.pl bib === id = cord-030341-uora9qcb author = Ruland, Sebastian title = HybridTiger: Hybrid Model Checking and Domination-based Partitioning for Efficient Multi-Goal Test-Suite Generation (Competition Contribution) date = 2020-03-13 pages = extension = .txt mime = text/plain words = 1259 sentences = 73 flesch = 49 summary = title: HybridTiger: Hybrid Model Checking and Domination-based Partitioning for Efficient Multi-Goal Test-Suite Generation (Competition Contribution) In Test-Comp 2019, we applied a random partitioning strategy and used predicate analysis as model checking technique. HybridTiger uses the CoVeriTest [3] algorithm to sequentially combine test-case generation runs utilizing different verification techniques. Each test-case generation run applies the CPA/Tiger-MGP 4 (Tiger Multi-Goal-Partitioning) algorithm, which utilizes the CEGAR algorithm. HybridTiger first extracts test goals from input programs and repeatedly executes reachability analyses provided by CPAchecker until every reachable test goal is covered by at least one test case. HybridTiger receives as inputs a C program and a property specification (i.e., a set of test goals). Second, HybridTiger uses control-flow information to partition test goals which potentially enhances efficiency of test-case generation due to information reuse among similar test goals. Configurable Software Verification: Concretizing the Convergence of Model Checking and Program Analysis cache = ./cache/cord-030341-uora9qcb.txt txt = ./txt/cord-030341-uora9qcb.txt === reduce.pl bib === id = cord-311766-m9yv4qkm author = Demey, Baptiste title = Dynamic profile for the detection of anti-SARS-CoV-2 antibodies using four immunochromatographic assays date = 2020-05-07 pages = extension = .txt mime = text/plain words = 1754 sentences = 92 flesch = 49 summary = Thus, the objective of our study was to evaluate four immunochromatographic assays for the detection of IgM and IgG antibodies to SARS-CoV-2 and to evaluate the kinetics of their detection by these LFA. We evaluated 4 immunochromatographic tests for the detection of IgM and IgG directed against SARS-CoV-2 ( Figure 1 ). Longitudinal immunochromatographic testing in all patients shows heterogeneity in the time to detection of antibodies after symptom reporting (Figure 2 ). With either IgM or IgG detection for a patient on days 5, 10 and 15 since onset of symptom, we calculated a clinical sensitivity between 9 and 24%, 67 and 82% and 100% respectively ( Figure 3B and Table 1 ). In conclusion, we described the kinetics of detection of post-symptom antibodies in 22 patients using immunochromatographic rapid tests and demonstrated the good performance of these tests for the detection of antibodies after SARS-CoV-2 infection. cache = ./cache/cord-311766-m9yv4qkm.txt txt = ./txt/cord-311766-m9yv4qkm.txt === reduce.pl bib === id = cord-298086-pbfi5c8e author = Lyngse, F. P. title = COVID-19 Transmission Within Danish Households: A Nationwide Study from Lockdown to Reopening date = 2020-09-09 pages = extension = .txt mime = text/plain words = 7792 sentences = 547 flesch = 63 summary = Methods We used comprehensive administrative register data from Denmark, comprising the full population and all COVID-19 tests, to estimate household transmission risk and attack rate. To our knowledge, this is the first nationwide study that uses estimates of household attack rates and transmission risks that exploit SARS-CoV-2 test data from an entire population. We defined the attack rate as the proportion of additional household members that tested positive, whereas the transmission risk was the proportion of secondary cases per primary case. To estimate the attack rate, we estimated the proportion of potential secondary household members who received a positive test within 14 days after the test date of the primary case. (In Appendix D, we illustrate changes over all three periods.) Figure 1 panel (a) shows that after receiving a positive test result in the household (t = 0), 36% of potential secondary cases were tested (blue) the day after the positive test result (t = 1) of the primary case was available and 13% of these 36% were positive (red). cache = ./cache/cord-298086-pbfi5c8e.txt txt = ./txt/cord-298086-pbfi5c8e.txt === reduce.pl bib === id = cord-150218-javbnjrg author = Gupta, Prateek title = COVI-AgentSim: an Agent-based Model for Evaluating Methods of Digital Contact Tracing date = 2020-10-30 pages = extension = .txt mime = text/plain words = 13386 sentences = 673 flesch = 54 summary = We use COVI-AgentSim to perform cost-benefit analyses comparing no DCT to: 1) standard binary contact tracing (BCT) that assigns binary recommendations based on binary test results; and 2) a rule-based method for feature-based contact tracing (FCT) that assigns a graded level of recommendation based on diverse individual features. We call these methods feature-based contact tracing (FCT), and hypothesize they could provide an important and effective means of reducing the spread of the disease, perhaps even more effectively than BCT at lower adoption rates. Recognizing this potential, we propose COVI-AgentSim -a software testbed 2 to design, evaluate and benchmark DCT methods using cost-benefit analysis in terms of lives saved, reduction in effective reproductive number (R t ) of the virus, disability-adjusted life years (DALYs) averted, and productive hours lost. A key difference in our simulator is the rich set of individual-level features (including e.g. pre-existing medical conditions), which allow us to benchmark feature-based contact tracing methods, and also allow for stratification over a larger variety of subgroups. cache = ./cache/cord-150218-javbnjrg.txt txt = ./txt/cord-150218-javbnjrg.txt === reduce.pl bib === id = cord-326148-9wpxm5of author = Van Walle, I. title = Meta-analysis of the clinical performance of commercial SARS-CoV-2 nucleic acid, antigen and antibody tests up to 22 August 2020 date = 2020-09-18 pages = extension = .txt mime = text/plain words = 3790 sentences = 218 flesch = 49 summary = title: Meta-analysis of the clinical performance of commercial SARS-CoV-2 nucleic acid, antigen and antibody tests up to 22 August 2020 We reviewed the clinical performance of SARS-CoV-2 nucleic acid, viral antigen and antibody tests based on 94739 test results from 157 published studies and 20205 new test results from 12 EU/EEA Member States. Pooling the results and considering only results with 95% confidence interval width [≤]5%, we found 4 nucleic acid tests, among which 1 point of care test, and 3 antibody tests with a clinical sensitivity [≤]95% for at least one target population (hospitalised, mild or asymptomatic, or unknown). Study heterogeneity was low for 8/14 (57.1%) sensitivity and 68/84 (81.0%) specificity results with confidence interval width [≤]5%, and lower for nucleic acid tests than antibody tests. Studies containing potentially usable data on clinical performance of SARS-CoV-2 nucleic acid, antigen and antibody tests were first extracted from systematic reviews on this topic. cache = ./cache/cord-326148-9wpxm5of.txt txt = ./txt/cord-326148-9wpxm5of.txt === reduce.pl bib === id = cord-288982-63ddlh20 author = Peeling, Rosanna W. title = Diagnostics in a digital age: an opportunity to strengthen health systems and improve health outcomes date = 2015-11-09 pages = extension = .txt mime = text/plain words = 4391 sentences = 216 flesch = 44 summary = Rapid point-of-care (POC) tests for infectious diseases can improve access to diagnosis and patient management, but the quality of these tests vary, quality of testing is often not assured and there are few mechanisms to capture test results for surveillance when the testing is so decentralised. In a digital age, it is possible to link data from diagnostic laboratories and POC test readers and devices to provide data on testing coverage, disease trends and timely information for early warning of infectious disease outbreaks to inform design or optimisation of disease control and elimination programmes. In the last decade, rapid point-of-care (POC) diagnostic tests fulfilling the ASSURED criteria (Affordable, Sensitive, Specific, User-friendly, Rapid and robust, Equipment-free and Deliverable) have become commercially available and are widely used for infectious diseases such as malaria, HIV and syphilis. cache = ./cache/cord-288982-63ddlh20.txt txt = ./txt/cord-288982-63ddlh20.txt === reduce.pl bib === id = cord-281241-k1adcls8 author = Döhla, M. title = Rapid point-of-care testing for SARS-CoV-2 in a community screening setting shows low sensitivity date = 2020-04-18 pages = extension = .txt mime = text/plain words = 1991 sentences = 127 flesch = 59 summary = Objective: With the current SARS-CoV2 outbreak, countless tests need to be performed on potential symptomatic individuals, contacts and travellers. Objective: With the current SARS-CoV2 outbreak, countless tests need to be performed on potential symptomatic individuals, contacts and travellers. We therefore evaluated a rapid antibody IgG/IgMebased testing system in the community setting for its ability, specificity and sensitivity to reliably identify infected individuals. Thirty-nine randomly selected individuals at the centre were tested simultaneously using the SARS-CoV-2 rapid test and the gold standard RT-qPCR method (Altona Diagnostics). The rapid test used for evaluation is a qualitative IgG/IgM detection system to test for a current or past infection of SARS-CoV-2. cache = ./cache/cord-281241-k1adcls8.txt txt = ./txt/cord-281241-k1adcls8.txt === reduce.pl bib === id = cord-256568-mbkrg98v author = Jantzen, R. title = Epidemiological and socio-economic characteristics of the COVID-19 spring outbreak in Quebec, Canada: A population-based study date = 2020-09-01 pages = extension = .txt mime = text/plain words = 7907 sentences = 419 flesch = 54 summary = 7.6% of the participants declared that they have experienced at least one of the four COVID-related symptoms chosen by the Public Health authorities (fever, cough, dyspnea, anosmia) but were not tested. Results from the tree-based model analyzes adjusted on exposure factors show that the combination of dyspnea, dry cough and fever was highly associated with being tested whereas anosmia, fever, and headache were the most discriminant factors for having a positive test among those tested. A multiple logistic regression analyzis showed that place of residence, dweling, risk exposure (medical worker, contact with a COVID-19 positive patient, international travel), having at least one pre-existing condition were independent factors associated with the outcome ( Table 1) . Taking into account socio-demographic, medical and exposure factors (place of residence, dweling, medical worker, contact with a COVID-19 positive patient, international travel, pre-existing condition) as confounding factors and COVID-related symptoms as explanatory variables, we performed a GPLTR analyzis for identifying the combinations of symptoms leading to the most homogeneous sub-groups with respect to being tested. cache = ./cache/cord-256568-mbkrg98v.txt txt = ./txt/cord-256568-mbkrg98v.txt === reduce.pl bib === id = cord-273324-xhpv783y author = Land, Kevin J. title = REASSURED diagnostics to inform disease control strategies, strengthen health systems and improve patient outcomes date = 2018-12-13 pages = extension = .txt mime = text/plain words = 7423 sentences = 298 flesch = 41 summary = For example, as POC technologies for HIV viral load and early infant diagnosis were being developed, there was tremendous emphasis on quality, given the complexity of the test and lessons learned from HIV RDTs. Malaria is estimated to be the cause of at least a million deaths a year worldwide, most of which are in sub-Saharan Africa. Although national TB programmes provide a robust architecture for the implementation of new technologies, challenges associated with the near-POC NAT assay remain as barriers -affordability (molecular assays are device-based and costly, even with subsidy), expertise (more technically demanding than lateral flow RDTs) and sustainability 46 , in addition to power and per-test time. Such tests can only be created by forming strong collaborative partnerships across many disciplinary boundaries, and we look toward a future when data connectivity linking cost-effective ASSURED diagnostics to laboratory systems will form the backbone of health care systems and provide real-time data for evidence-based disease control and prevention strategies, more efficient health systems and improved patient outcomes. cache = ./cache/cord-273324-xhpv783y.txt txt = ./txt/cord-273324-xhpv783y.txt === reduce.pl bib === id = cord-252959-ktet18wl author = Lim, Jong-Min title = Ingestion of Exopolymers from Aureobasidium pullulans Reduces the Duration of Cold and Flu Symptoms: A Randomized, Placebo-Controlled Intervention Study date = 2018-05-30 pages = extension = .txt mime = text/plain words = 6389 sentences = 278 flesch = 45 summary = Subjects for whom the following criteria were applicable were excluded from the experiment: individuals with a body mass index (BMI) under 18 or over 35; individuals who exceeded the normal maximum alanine transaminase and aspartate transaminase levels by 2-fold; females who were pregnant or were breast-feeding; females of childbearing age who did not agree to use contraceptives via medically proven methods (e.g., condoms, lubricant, and femidom) during the test period; individuals with a fasting plasma dextrose concentration over 126 mg/dL; individuals with high blood pressure (systolic blood pressure of 160 mm Hg or diastolic blood pressure of 100 mm Hg); individuals continuously using medicine that could affect the effectiveness assessment (hyperlipidemia medicine, steroid medicines, hormone medicines, immunosuppressants, and antibiotics); individuals who require continuous treatment for psychiatric disorders such as anorexia, depression, and manic depression; individuals with systemic diseases such as immunity-related diseases, serious hepatic and renal insufficiencies, malignant tumors, pulmonary disease, collagenosis, multiple sclerosis, allergic skin conditions, and other autoimmune diseases; individuals with a medical history of drugs and clinically significant allergic reactions; individuals with a history of gastrointestinal disorders that could affect the absorption of the test foods or a history of gastrointestinal surgery (excluding a simple appendectomy or hernia operation); individuals who consumed medicine or herbal medicines within a month of participation in the experiment which could affect immunity; individuals who participated in a different human study or clinical test and took experimental products within 3 months of participation in this experiment (excluding human studies with cosmetics); and individuals whom the researchers otherwise determined might have difficulty completing the experiment. cache = ./cache/cord-252959-ktet18wl.txt txt = ./txt/cord-252959-ktet18wl.txt === reduce.pl bib === id = cord-281495-beb164oy author = Charpentier, Charlotte title = Performance evaluation of two SARS-CoV-2 IgG/IgM rapid tests (Covid-Presto and NG-Test) and one IgG automated immunoassay (Abbott) date = 2020-09-03 pages = extension = .txt mime = text/plain words = 2375 sentences = 122 flesch = 59 summary = title: Performance evaluation of two SARS-CoV-2 IgG/IgM rapid tests (Covid-Presto and NG-Test) and one IgG automated immunoassay (Abbott) The aim of this study was to assess the analytical performances, sensitivity and specificity, of two rapid tests (CovidPresto® test rapid Covid-19 IgG/IgM and NG-Test® IgM-IgG COVID-19) and one automated immunoassay (Abbott SARS-CoV-2 IgG) for detecting antiSARS-CoV-2 antibodies. The aim of this study was to assess the analytical performances (sensitivity and specificity) and agreement of two rapid tests and one automated immunoassay for detecting antibodies against SARS-CoV-2. In the present study, we evaluated two different lateral flow tests (Covid-Presto ® and NG-Test ® ) and compared their performances to that of the automated Abbott immunoassay using the same samples panel. Sensitivity for IgG in samples collected later than 10 days after symptoms onset was excellent with the different tests being equal to 97.1%, 96.2% and 100% for Covid-Presto ® , NG-Test ® , and Abbott, respectively. cache = ./cache/cord-281495-beb164oy.txt txt = ./txt/cord-281495-beb164oy.txt === reduce.pl bib === id = cord-320970-ru2iw0py author = Peeling, Rosanna W title = Serology testing in the COVID-19 pandemic response date = 2020-07-17 pages = extension = .txt mime = text/plain words = 3669 sentences = 186 flesch = 49 summary = On the basis of our knowledge and understanding of viral infectivity and host response, we urge countries without the capacity to do molecular testing at scale to research the use of serology tests to triage symptomatic patients in community settings, to test contacts of confirmed cases, and in situational analysis and surveillance. Point-of-care molecular assays for SARS-CoV-2 detection are now available to enable community-based testing for COVID-19 in LMICs. Unfortunately, the production of these test cartridges takes time and, again, global demand has outstripped supply, leaving LMICs struggling for access. On the basis of our current knowledge and understanding of viral infectivity and host response, we urge countries with restricted capacity for molecular testing to embark on research into the use of serology tests in triaging symptomatic patients in community settings, testing contacts of confirmed cases, and in situational analysis and surveillance. cache = ./cache/cord-320970-ru2iw0py.txt txt = ./txt/cord-320970-ru2iw0py.txt === reduce.pl bib === id = cord-307187-5blsjicu author = Missel, Malene title = A stoic and altruistic orientation towards their work: a qualitative study of healthcare professionals’ experiences of awaiting a COVID-19 test result date = 2020-11-11 pages = extension = .txt mime = text/plain words = 5818 sentences = 286 flesch = 48 summary = title: A stoic and altruistic orientation towards their work: a qualitative study of healthcare professionals' experiences of awaiting a COVID-19 test result The purpose of this study was to explore healthcare professionals' experiences of awaiting a test result for a potential COVID-19 infection. RESULTS: The participating healthcare professionals' experiences of awaiting a COVID-19 test result were found to be associated with a stoic and altruistic orientation towards their work. Therefore, this study aim to shed light on HCPs' experiences of awaiting a test result for a potential COVID-19 infection through individual interviews. The comprehensive understanding illuminated the meaning of the participants' experiences of awaiting a COVID-19 test result as a stoic and altruistic orientation towards their work. cache = ./cache/cord-307187-5blsjicu.txt txt = ./txt/cord-307187-5blsjicu.txt === reduce.pl bib === id = cord-325455-e464idc0 author = Atchison, Christina title = Usability and acceptability of home-based self-testing for SARS-CoV-2 antibodies for population surveillance date = 2020-08-12 pages = extension = .txt mime = text/plain words = 3279 sentences = 204 flesch = 57 summary = BACKGROUND: This study assesses acceptability and usability of home-based self-testing for SARS-CoV-2 antibodies using lateral flow immunoassays (LFIA). On a population level, by conducting seroprevalence surveys through widespread random sampling of the general public, and by adjusting for the sensitivity and specificity characteristics of the LFIA used, it is possible to estimate the levels of past infection with SARS-CoV-2 in the community (3) . Usability research on HIV selftesting has generally found good acceptability, the devices easy to use and high validity in interpretation of self-reported test results (7) (8) (9) . To mitigate against this, and given the scientific Our study is original because focusing on the acceptability and usability of LFIAs for self-testing for SARS-CoV-2 antibody in a home-based setting has not been done at such scale in the general population. Overall, our study has demonstrated that home-based self-testing LFIAs for use in large communitybased seroprevalence surveys of SARS-CoV-2 antibody are both acceptable and feasible. cache = ./cache/cord-325455-e464idc0.txt txt = ./txt/cord-325455-e464idc0.txt === reduce.pl bib === id = cord-283517-7gd0f06m author = Deak, Eszter title = Right-Sizing Technology in the Era of Consumer-Driven Health Care date = 2017-08-01 pages = extension = .txt mime = text/plain words = 6857 sentences = 331 flesch = 45 summary = Today, we have molecular point-ofcare (mPOC) devices that can provide a rapid diagnostic answer within 20 minutes in a clinic, multiplex PCR sample-to-answer devices that can screen for >20 analytes in a single specimen in about an hour, high-volume automation that can enhance throughput and efficiency in the clinical microbiology laboratory with digital imaging, and next-generation sequencing (NGS) that can reveal a treasure trove of information in a single test. Factors may include syndrome-specific diagnostic needs, ease of use, the need for rapid results, improved sensitivity and specificity, operational needs (such as staffing and expertise), laboratory design (such as centralized versus decentralized models), cost, consumer demand, and the potential for improved patient outcomes. Considerations that go into the selection of a test or instrument platform for implementation include perceived turnaround time needs for improved patient care, sample volume requirements, number of tests expected, suitability for the intended laboratory based on available expertise and desired workflow, as well as cost. cache = ./cache/cord-283517-7gd0f06m.txt txt = ./txt/cord-283517-7gd0f06m.txt === reduce.pl bib === id = cord-290251-ihq8gdwj author = Hasell, Joe title = A cross-country database of COVID-19 testing date = 2020-10-08 pages = extension = .txt mime = text/plain words = 3805 sentences = 196 flesch = 52 summary = The database consists of two parts, provided for each included country: (1) a time series for the cumulative and daily number of tests performed, or people tested, plus derived variables (discussed below); (2) metadata including a detailed description of the source and any available information on data quality or comparability issues needed for the interpretation of the time series. Firstly, for a number of countries, figures reported in official sources -including press releases, government websites, dedicated dashboards, and social media accounts of national authorities -are recorded manually as they are released. The time series for cumulative and daily testing for each country-series is then provided in the covid-testing-all-observations.csv file. In covid-testing-all-observations.csv, for those sources only providing daily testing figures, this field is derived as the running total of the raw daily data, and is also provided per thousand people of the country's 2020 population. cache = ./cache/cord-290251-ihq8gdwj.txt txt = ./txt/cord-290251-ihq8gdwj.txt === reduce.pl bib === id = cord-284945-837qlk8y author = Rahmandad, H. title = Estimating the global spread of COVID-19 date = 2020-06-26 pages = extension = .txt mime = text/plain words = 16602 sentences = 1376 flesch = 54 summary = Using data for all 84 countries with reliable testing data (spanning 4.75 billion people) we develop a dynamic epidemiological model integrating data on cases, deaths, excess mortality and other factors to estimate how asymptomatic transmission, disease acuity, hospitalization, and behavioral and policy responses to risk condition prevalence and IFR across nations and over time. Our model captures transmission dynamics for the disease, as well as how, at the country level, transmission rates vary in response to risk perception and weather, testing rates condition infection and death data, and fatality rates depend on demographics and hospitalization. Using testing rate time series and various country-level data points (e.g. population, hospital capacity, comorbidities, age distribution), the model endogenously simulates confirmed new daily cases and deaths over time and matches them against observed data by maximizing the likelihood of observing those data given the model parameters. cache = ./cache/cord-284945-837qlk8y.txt txt = ./txt/cord-284945-837qlk8y.txt === reduce.pl bib === id = cord-307123-h48uwj93 author = Kiechle, Frederick L. title = Establishing benchmarks and metrics for disruptive technologies, inappropriate and obsolete tests in the clinical laboratory date = 2014-01-01 pages = extension = .txt mime = text/plain words = 5416 sentences = 298 flesch = 40 summary = Examples include guidelines for hypothyroidism in adults from the American Association of Clinical Endocrinologists and the American Thyroid Association [30] , definition of myocardial infarction from the American College of Cardiology Foundation and American Heart Association [31] , definition of diabetes mellitus from the American Diabetes Association [32] , pharmacogenetics as well as follow-up testing for metabolic diseases identified by expanded newborn screening using tandem mass spectrometry from the National Academy of Clinical Biochemistry [33, 34] , and use of bone metabolic markers from the Japan Osteoporosis Society [35] . This is an example of testing that was removed from the market based on recommendations from the Centers for Disease Control (CDC) stating that the rapid antigen detection tests for GBS are not sensitive enough to replace the culture based prenatal screening or to use in place of the risk-based approach when culture results are unknown at the time of labor [51] . cache = ./cache/cord-307123-h48uwj93.txt txt = ./txt/cord-307123-h48uwj93.txt === reduce.pl bib === id = cord-316047-d9cpe9yl author = Gonzalez, T. title = Influence of COVID-19 confinement on students’ performance in higher education date = 2020-10-09 pages = extension = .txt mime = text/plain words = 8517 sentences = 451 flesch = 60 summary = This study analyzes the effects of COVID-19 confinement on the autonomous learning performance of students in higher education. We present a study that involves more than 450 students enrolled in 3 subjects from different degrees from the Universidad Autónoma de Madrid (Spain) during three academic years, including data obtained in the 2019/2020 academic year, when the restrictions due to the COVID-19 pandemic have been in force. In the case of "Design of Water Treatment Facilities", a longitudinal study has been performed in academic year 2017/2018 to analyse the effect of rewards in the students' learning strategies, especially those related to time management. The second stage corresponds to the period of COVID-19 confinement (after March 11), where some measurable activities were performed in a different format and statistical differences can be found by comparing experimental and control groups. cache = ./cache/cord-316047-d9cpe9yl.txt txt = ./txt/cord-316047-d9cpe9yl.txt === reduce.pl bib === id = cord-300930-47a4pu27 author = Beigel, R. title = Rate Estimation and Identification of COVID-19 Infections: Towards Rational Policy Making During Early and Late Stages of Epidemics date = 2020-05-24 pages = extension = .txt mime = text/plain words = 4535 sentences = 366 flesch = 64 summary = Mathematically, the problems of identifying infected individuals ( identification ) and estimating the total number of infected individuals in a given population ( infection rate ) are related but in fact can be addressed by subtly different algorithms to reduce the number of tests needed and thereby the total cost of doing testing. However, as we will demonstrate in this brief communication, estimating the number of infected individuals can be solved by novel adaptation of methods developed in theoretical computer science aimed at approximate counting. In addition to rate estimation we provide a review and analysis of several identification algorithms that can be deployed in communities with low infection rates that achieve reasonable improvement over the standard algorithms for group testing that have been previously explored. • Estimate the rate of the infection in the population or approximately count how many people test positive in a population of a given size with as few partially pooled tests as possible. We now describe approximate counting algorithms that use pools of samples to estimate accurate infection rates. cache = ./cache/cord-300930-47a4pu27.txt txt = ./txt/cord-300930-47a4pu27.txt === reduce.pl bib === id = cord-226956-n5qwsvtr author = Arbia, Giuseppe title = A Note on Early Epidemiological Analysis of Coronavirus Disease 2019 Outbreak using Crowdsourced Data date = 2020-03-13 pages = extension = .txt mime = text/plain words = 1763 sentences = 73 flesch = 44 summary = However, the use of crowdsourcing data raises a number of problems from the statistical point of view which run the risk of invalidating the results and of biasing estimation and hypothesis testing. In the paper the crowdsourced data, coming from different sources, are used to estimate several epidemiological parameters of tremendous importance in the process of surveillance and control of the diffusion of the disease such as: The relative risk by age group, the mean age and skewness of infected people, the time of delays between symptoms and seeking care at hospital, the mean incubation period. However, even if data were collected obeying a formal sample design, a further potential source of bias is the fact that the observational units could display a certain degree of spatial/network correlation (Cliff and Ord, 1973; Arbia, 2006) . cache = ./cache/cord-226956-n5qwsvtr.txt txt = ./txt/cord-226956-n5qwsvtr.txt === reduce.pl bib === id = cord-319436-mlitd45q author = Brinati, D. title = Detection of COVID-19 Infection from Routine Blood Exams with Machine Learning: a Feasibility Study date = 2020-04-25 pages = extension = .txt mime = text/plain words = 4603 sentences = 237 flesch = 51 summary = Amplification of viral RNA by (real time) reverse transcription polymerase chain reaction (rRT-PCR) is the current gold standard test for confirmation of infection, although it presents known shortcomings: long turnaround times (3-4 hours to generate results), potential shortage of reagents, false-negative rates as large as 15-20%, the need for certified laboratories, expensive equipment and trained personnel. Material and methods We developed two machine learning classification models using hematochemical values from routine blood exams (namely: white blood cells counts, and the platelets, CRP, AST, ALT, GGT, ALP, LDH plasma levels) drawn from 279 patients who, after being admitted to the San Raffaele Hospital (Milan, Italy) emergency-room with COVID-19 symptoms, were screened with the rRT-PCR test performed on respiratory tract specimens. The best performing model, i.e. the Random Forest classifier, trained on dataset B, achieved the following results on the test/validation set: accuracy = 82% , sensitivity = 92%, PPV = 83%, specificity = 65%, AUC = 84%. cache = ./cache/cord-319436-mlitd45q.txt txt = ./txt/cord-319436-mlitd45q.txt === reduce.pl bib === id = cord-324944-ixh3ykrc author = Mitsakakis, Konstantinos title = Diagnostic tools for tackling febrile illness and enhancing patient management date = 2018-12-05 pages = extension = .txt mime = text/plain words = 20805 sentences = 961 flesch = 45 summary = This review gives an overview of diagnostic technologies featuring a platform based approach: (i) assay (nucleic acid amplification technologies are examined); (ii) cartridge (microfluidic technologies are presented); (iii) instrument (various detection technologies are discussed); and at the end proposes a way that such technologies can be interfaced with electronic clinical decision-making algorithms towards a broad and complete diagnostic ecosystem. In studies that have recorded the clinical presentation of patients (and not only their laboratory results), the causes of fever in outpatients could be classified into four main syndromes: 1) acute respiratory infections (ARI, of any type); 2) diarrhea (gastroenteritis); 3) fever with another clear focus (e.g. meningitis or skin infection); and 4) non-specific fevers [13] (each diagnostic platform described in Section 5 focuses on at least one of the aforementioned cases). cache = ./cache/cord-324944-ixh3ykrc.txt txt = ./txt/cord-324944-ixh3ykrc.txt === reduce.pl bib === id = cord-225183-6rusimb5 author = Boukai, Ben title = Bayesian Modeling of COVID-19 Positivity Rate -- the Indiana experience date = 2020-07-09 pages = extension = .txt mime = text/plain words = 3108 sentences = 235 flesch = 68 summary = In this short technical report we model, within the Bayesian framework, the rate of positive tests reported by the the State of Indiana, accounting also for the substantial variability (and overdispeartion) in the daily count of the tests performed. In this report we model, within the Bayesian framework, the rate of positive tests reported by the the State of Indiana, accounting also for the substantial variability of the daily number test performed. Remark: The choice in (2) for using the Negative Binomial distribution to model the reported daily number of tests k i , could be seen as specific to the Indiana COVID-19 testing data, which might reflect testing capacity limitation and daily variability unique to that state. In a similar manner we obtain the posterior predictive distribution under this Bayesian model and given (X m , N m ), of a 'new' (or 'future') number of tests K * is the Beta-Negative Binomial distribution. cache = ./cache/cord-225183-6rusimb5.txt txt = ./txt/cord-225183-6rusimb5.txt === reduce.pl bib === id = cord-310714-kqzlwka0 author = Braz, Lucia Maria Almeida title = Visceral Leishmaniasis diagnosis: a rapid test is a must at the hospital bedside date = 2020-06-16 pages = extension = .txt mime = text/plain words = 1366 sentences = 76 flesch = 55 summary = At the time of the widespread availability of rapid diagnostic tests for SARS-CoV-2-the causative virus of the COVID-19 pandemic-from drugstores throughout Brazil, there is a distinct lack of use of rapid diagnostic tests for visceral leishmaniasis (VL) at the bedsides of hospitalized patients. As stated by the MS, VL case confirmation is based on clinical suspicion and positive laboratory diagnosis via either parasitological tests (PTs), which are dependent on invasive procedures such as bone marrow aspiration or biopsy, or serological tests such as indirect immunofluorescence (IFI) or immunochromatographic tests (ITs) using rK39 recombinant antigens (5) . The main brands of IT-rK39 that were previously provided by the Brazilian public health system consisted of Kalazar Detectt (InBios International, Seattle, WA, USA), IT LEISH s (BIO-RAD Laboratories Inc., France), and OnSitet Leishmania IgG/IgM Combo test (CTK Biotech, USA), which have now been replaced with the LSH Ab ECO test (Eco Diagnóstica, Nova Lima, MG, Brasil). cache = ./cache/cord-310714-kqzlwka0.txt txt = ./txt/cord-310714-kqzlwka0.txt === reduce.pl bib === id = cord-308021-cnf4xljc author = Kohns Vasconcelos, Malte title = SARS-CoV-2 testing and infection control strategies in European paediatric emergency departments during the first wave of the pandemic date = 2020-10-13 pages = extension = .txt mime = text/plain words = 1981 sentences = 99 flesch = 47 summary = Between February and May 2020, during the first wave of the COVID-19 pandemic, paediatric emergency departments in 12 European countries were prospectively surveyed on their implementation of SARS-CoV-2 disease (COVID-19) testing and infection control strategies. All participating departments (23) implemented standardised case definitions, testing guidelines, early triage and infection control strategies early in the outbreak. Paediatric departments of 23 mostly tertiary care hospitals in 12 European countries (Belgium, Germany, France, Italy, Poland, Portugal, the UK, the Netherlands, Greece, Spain, Lithuania and Switzerland) participated in the surveys (response rate 29%). This changed by April at all three sites, so that afterwards detection of another pathogen that could explain the respiratory symptoms no longer excluded a patient from being a suspect case and from undergoing SARS-CoV-2 testing. In the early stages of the COVID-19 pandemic, paediatric emergency departments implemented standardised case definitions, testing guidelines and infection control measures rapidly. cache = ./cache/cord-308021-cnf4xljc.txt txt = ./txt/cord-308021-cnf4xljc.txt === reduce.pl bib === id = cord-300520-vxn7uh41 author = Baunez, C. title = Tracking the Dynamics and Allocating Tests for COVID-19 in Real-Time: an Acceleration Index with an Application to French Age Groups and Departments date = 2020-11-07 pages = extension = .txt mime = text/plain words = 10376 sentences = 513 flesch = 59 summary = Using French data on cases and tests for the period following the first lock-down from May 13, 2020, onwards our acceleration index shows that the ongoing pandemic resurgence can be dated to begin around July 7. We propose a parsimonious algorithm to allocate tests across age groups and space, based on both our acceleration index and the average positivity rate, and on the extent to which tests reduce the virus propagation. We argue that such reasoning is wrong and that the correct understanding, in terms of measuring the acceleration/deceleration of the pandemic, is gained if a scatter-plot of the number of positive cases against the number of the tests is used in real time, instead of the panels in Figure 1 . cache = ./cache/cord-300520-vxn7uh41.txt txt = ./txt/cord-300520-vxn7uh41.txt === reduce.pl bib === id = cord-289461-bnusv816 author = Droste, M. C. title = Economic Benefits of COVID-19 Screening Tests date = 2020-10-27 pages = extension = .txt mime = text/plain words = 7911 sentences = 444 flesch = 54 summary = The analysis is undertaken using a behavioral SIR model for the United States with 5 age groups, 66 economic sectors, screening and diagnostic testing, and partial adherence to instructions to quarantine or to isolate. Using our epidemiological-economic model, we project 66,000 deaths averted, an increase in GDP of $248 billion, and an increase in federal tax revenues of $68 billion over the counterfactual period of the program, June 1 -December 31, 2020, relative to a baseline with diagnostic but not screening testing. Testing costs are somewhat higher, but because the effective adherence rate is higher under this program than in Panel A, deaths averted rise to 153,000 and the increase in GDP is larger, $544 billion, for weekly testing. Relative to this literature, our main contribution is to provide carefully calibrated and estimated model for assessing the net economic, fiscal, and total (including mortality) benefits of multistep imperfect screening testing in conjunction with diagnostic testing. cache = ./cache/cord-289461-bnusv816.txt txt = ./txt/cord-289461-bnusv816.txt === reduce.pl bib === id = cord-276577-06boh550 author = Schanzer, Dena L. title = Estimating Sensitivity of Laboratory Testing for Influenza in Canada through Modelling date = 2009-08-18 pages = extension = .txt mime = text/plain words = 3960 sentences = 175 flesch = 38 summary = METHODS AND FINDINGS: The weekly number of influenza-negative tests from 1999 to 2006 was modelled as a function of laboratory-confirmed positive tests for influenza, respiratory syncytial virus (RSV), adenovirus and parainfluenza viruses, seasonality, and trend using Poisson regression. The RVDSS collects, collates, and reports weekly data from participating laboratories on the number of tests performed and the number of specimens confirmed positive for influenza, respiratory syncytial virus (RSV), para-influenza virus (PIV), and adenovirus. The overall model fit, and the general consistency of the sensitivity estimates, suggests that these many respiratory viruses were reasonably accounted for by the seasonal baseline and that the strong association between the number of influenza positive and influenza negative tests on a weekly basis is indicative of a significant number of false negative results, rather than the activity of another virus or viruses exactly synchronous with influenza. cache = ./cache/cord-276577-06boh550.txt txt = ./txt/cord-276577-06boh550.txt === reduce.pl bib === id = cord-295126-lz2jbmcn author = Toresdahl, Brett G. title = Coronavirus Disease 2019 (COVID-19): Considerations for the Competitive Athlete date = 2020-04-06 pages = extension = .txt mime = text/plain words = 2405 sentences = 156 flesch = 51 summary = First and foremost, preventing the transmission of COVID-19 is needed to reduce the risk of spread to individuals within a community who are most at risk of severe infection or death, which includes older individuals and the immunocompromised. Sports medicine providers can support athletes and teams during the COVID-19 pandemic by advocating the following preventative measures: With these limitations, testing algorithms offered preference to patients with symptoms (fever, cough, or shortness of breath), an immunocompromised state, or close contact with someone with COVID-19. In-home isolation is recommended for athletes with confirmed or suspected COVID-19 who do not show severe symptoms. If an athlete on a sports team develops symptoms consistent with COVID-19, teammates, coaches, and other staff who had close contact with the athlete (within 6 feet) in the preceding 14 days should begin in-home isolation. Correlation of chest CT and RT-PCR testing in coronavirus disease 2019 (COVID-19) in China: a report of 1014 cases cache = ./cache/cord-295126-lz2jbmcn.txt txt = ./txt/cord-295126-lz2jbmcn.txt === reduce.pl bib === id = cord-320864-k9zksbyt author = Remes-Troche, J. M. title = Recommendations for the reopening and activity resumption of the neurogastroenterology units in the face of the COVID-19 pandemic. Position of the Sociedad Latinoamericana de Neurogastroenterología date = 2020-11-01 pages = extension = .txt mime = text/plain words = 4669 sentences = 256 flesch = 46 summary = When health authorities allow a return to normalcy and in the absence of effective treatment or a preventive vaccine for COVID 19 infection, we recommend a strict protocol to classify patients according to their infectious-contagious status through the appropriate use of tests to detect the virus and its immune response, as well as the use of protective measures to be followed by health personnel to avoid contagion during the performance of a gastrointestinal motility test. Positions have already been established on how to work and/or resume activities at those units (e.g., those issued by the American Neurogastroenterology and Motility Society [ANMS] 4 and the Grupo Español de Motilidad Digestiva [GEMD]) 5 but due to the fact that the epidemiologic behavior, protective equipment avail-ability, serologic diagnostic test performance capacity for corroborating immunity, and socioeconomic context are different throughout Latin America, a group of experts that are members of the Sociedad Latinoamericana de Neurogastroenterología (SLNG) had a virtual meeting to formulate a consensus document with recommendations for the performance of gastrointestinal motility tests. cache = ./cache/cord-320864-k9zksbyt.txt txt = ./txt/cord-320864-k9zksbyt.txt === reduce.pl bib === id = cord-307500-2jwuzfan author = Gray, Nicholas title = "No test is better than a bad test": Impact of diagnostic uncertainty in mass testing on the spread of Covid-19 date = 2020-04-22 pages = extension = .txt mime = text/plain words = 6478 sentences = 361 flesch = 57 summary = Three scenarios for cessation of lock-down measures are explored: (1) immediate end of lock-down measures, (2) continued lock-down with antibody testing based immunity passports, and (3) incremental relaxation of lock-down measures with active viral testing. Sensitivity, specifcity, prevalence and test capacity are modified for both active viral and antibody testing to determine their population level effect on the continuing epidemic. This strategy would involve detecting those who have successfully overcome the virus, and are likely to have some level of immunity (or at least reduced susceptibility to more serious illness if they are infected again), so are relatively safe to relax their personal social distancing measures. To explore the effect of imperfect testing on the disease dynamics when strategies are employed to relax the current social distancing measures the SIR model described in the supplimentary material was modified. In order to explore the possible impact of testing strategies on the relaxation of current social distancing measures several scenarios have been analysed. cache = ./cache/cord-307500-2jwuzfan.txt txt = ./txt/cord-307500-2jwuzfan.txt === reduce.pl bib === id = cord-310195-am3u7z76 author = Waller, J. title = Immunity Passports for SARS-CoV-2: an online experimental study of the impact of antibody test terminology on perceived risk and behaviour date = 2020-05-10 pages = extension = .txt mime = text/plain words = 4813 sentences = 281 flesch = 55 summary = Objective: To assess the impact of describing an antibody-positive test result using the terms Immunity and Passport or Certificate, alone or in combination, on perceived risk of becoming infected with SARS-CoV-2 and intention to continue protective behaviours. Conclusions: Using the term Immunity (vs Antibody) to describe antibody tests for SARS-CoV-2 increases the proportion of people believing that an antibody-positive result means they have no risk of catching coronavirus in the future, a perception that may be associated with less frequent hand washing. This study was designed to test two hypotheses: describing a test indicating the presence of antibodies using the term Immunity (vs Antibody), and describing test results as Passports or Certificates (vs Test), increases the likelihood that those with this test result erroneously perceive they have no risk of becoming infected in the future with coronavirus. . https://doi.org/10.1101/2020.05.06.20093401 doi: medRxiv preprint Primary outcome Proportion of participants perceiving an antibody-positive test result to mean no risk of catching coronavirus in the future, assessed in response to a question with four response options. cache = ./cache/cord-310195-am3u7z76.txt txt = ./txt/cord-310195-am3u7z76.txt === reduce.pl bib === id = cord-296306-xcomjvaa author = Rivett, Lucy title = Screening of healthcare workers for SARS-CoV-2 highlights the role of asymptomatic carriage in COVID-19 transmission date = 2020-05-11 pages = extension = .txt mime = text/plain words = 6500 sentences = 350 flesch = 48 summary = Significant differences exist in the availability of healthcare worker (HCW) SARS-CoV-2 testing between countries, and existing programmes focus on screening symptomatic rather than asymptomatic staff. Table 3 outlines the total number of SARS-CoV-2 tests performed in each screening group (HCW asymptomatic, HCW symptomatic, and HCW symptomatic household contact) categorised according to the ward with the highest anticipated risk of exposure to high; 'amber', medium; 'green', low; . Three subgroups of SARS-CoV-2 positive asymptomatic HCW Each individual in the HCW asymptomatic screening group was contacted by telephone to establish a clinical history, and COVID-19 probability criteria ( Table 1) were retrospectively applied to categorise any symptoms in the month prior to testing ( Figure 2 ). 12/30 (40%) individuals from the HCW asymptomatic screening group reported symptoms > 7 days prior to testing, and the majority experiencing symptoms consistent with a high probability of COVID-19 had appropriately self-isolated during that period. cache = ./cache/cord-296306-xcomjvaa.txt txt = ./txt/cord-296306-xcomjvaa.txt === reduce.pl bib === id = cord-312477-2y88gzji author = Mlcochova, P. title = Combined point of care nucleic acid and antibody testing for SARS-CoV-2: a prospective cohort study in suspected moderate to severe COVID-19 disease. date = 2020-06-18 pages = extension = .txt mime = text/plain words = 4920 sentences = 281 flesch = 52 summary = title: Combined point of care nucleic acid and antibody testing for SARS-CoV-2: a prospective cohort study in suspected moderate to severe COVID-19 disease. Methods We developed (i) an in vitro neutralization assay using a lentivirus expressing a genome encoding luciferase and pseudotyped with spike protein and (ii) an ELISA test to detect IgG antibodies to nucleocapsid (N) and spike (S) proteins from SARS-CoV-2. We then prospectively recruited participants with suspected moderate to severe COVID-19 and tested for SARS-CoV-2 nucleic acid in a combined nasal/throat swab using the standard laboratory RT-PCR and a validated rapid nucleic acid test. We then prospectively recruited participants with suspected moderate to severe COVID-19 and tested for SARS-CoV-2 nucleic acid in a combined nasal/throat swab using the standard laboratory RT-PCR and a validated rapid nucleic acid test. cache = ./cache/cord-312477-2y88gzji.txt txt = ./txt/cord-312477-2y88gzji.txt === reduce.pl bib === id = cord-330721-hmnrnem6 author = Chambliss, Allison B title = Contingency planning in the clinical laboratory: lessons learned amidst COVID-19 date = 2020-04-21 pages = extension = .txt mime = text/plain words = 1248 sentences = 84 flesch = 55 summary = The laboratory should begin contingency planning by assessing baseline operational status, which benches can be offered less frequently (batched as sample stability allows), which can be closed altogether, and the resultant minimum number of staff required to support emergent testing ( Tests that will need to be maintained include complete blood counts, metabolic panels, routine coagulation, troponin, liver function tests, blood gases, and inflammatory markers such as C-reactive protein, lactate dehydrogenase, and procalcitonin (4, 5) . In times of particularly critical shortages of staff and/or reagents, with proper agreement of hospital leadership and use of mass notification mechanisms, non-emergent tests could be temporarily masked from providers in the test ordering system and eliminate the laboratory from receiving them in the first place. Using the Chemistry section as an example, a similar contingency planning tool can be used across core clinical lab specialties to assess benches/testing that can be performed depending upon available staffing. cache = ./cache/cord-330721-hmnrnem6.txt txt = ./txt/cord-330721-hmnrnem6.txt === reduce.pl bib === id = cord-325956-1kxxg0s9 author = Potluri, Rahul title = Making sense of the Global Coronavirus Data: The role of testing rates in understanding the pandemic and our exit strategy date = 2020-04-11 pages = extension = .txt mime = text/plain words = 3967 sentences = 217 flesch = 62 summary = We analysed the number of diagnostic tests performed in proportion to the number of cases and subsequently deaths across different countries and projected pandemic outcomes. Country wise population level pandemic projections were extrapolated utilising three models 1) inherent case per test and death per test rates at the time of obtaining the data (4/4/2020 0900 BST) for each country; 2) rates adjusted according to the countries who conducted at least 100000 tests and 3) rates adjusted according to South Korea. https://doi.org/10.1101/2020.04.06.20054239 doi: medRxiv preprint Discussion COVID-19 statistics are complex and comparing different countries based on number of total cases, deaths and/or case fatality rate does not show the complete picture (Table 1) . In our analyses we showed the deaths and cases in relation to the number of tests performed and presented population level pandemic projections based on these. cache = ./cache/cord-325956-1kxxg0s9.txt txt = ./txt/cord-325956-1kxxg0s9.txt === reduce.pl bib === id = cord-323476-rb9n5wc0 author = Poole, Stephen title = How are rapid diagnostic tests for infectious diseases used in clinical practice: a global survey by the International Society of Antimicrobial Chemotherapy (ISAC) date = 2020-09-09 pages = extension = .txt mime = text/plain words = 1908 sentences = 111 flesch = 47 summary = title: How are rapid diagnostic tests for infectious diseases used in clinical practice: a global survey by the International Society of Antimicrobial Chemotherapy (ISAC) Novel rapid diagnostic tests (RDTs) offer huge potential to optimise clinical care and improve patient outcomes. An electronic survey was devised by the International Society of Antimicrobial Chemotherapy (ISAC) Rapid Diagnostics and Biomarkers working group focussing on the availability, structure and impact of RDTs around the world. The International Society of Antimicrobial Chemotherapy (ISAC)'s Rapid Diagnostics and Biomarkers Working Group conducted this international survey aiming to identify and highlight some key issues related to RDTs and their impacts in clinical practice and provide a number of key points to consider while adopting a RDT. Our survey highlights the availability of these tests in different resource settings, as well as the current models for governance, quality control and reporting. cache = ./cache/cord-323476-rb9n5wc0.txt txt = ./txt/cord-323476-rb9n5wc0.txt === reduce.pl bib === id = cord-303539-gimz41yb author = Goudouris, Ekaterini S. title = Laboratory diagnosis of COVID-19() date = 2020-08-31 pages = extension = .txt mime = text/plain words = 3605 sentences = 220 flesch = 45 summary = DATA SOURCES: Searches in PubMed and Google Scholar for articles made available in 2020, using the terms "diagnosis" OR "diagnostic" OR "diagnostic tests" OR "tests" AND "COVID-19" OR "SARS-CoV-2" in the title. 25 Some studies report patients with mild (or even asymptomatic) COVID-19 present lower levels of SARS-CoV-2-specific antibodies or may even do not develop detectable levels, while patients with more severe conditions have higher levels of these. 38 The data presented suggest that the diagnosis of COVID-19 should be based on clinical manifestations, contact history, imaging tests, laboratory tests, and not only on serological tests and the search for the genetic material of the virus. The gold standard for the diagnosis of SARS-CoV-2 infection is the identification of viral genetic material by RT-PCR, in different samples, with greater sensitivity in bronchoalveolar lavage and nasopharyngeal swab. cache = ./cache/cord-303539-gimz41yb.txt txt = ./txt/cord-303539-gimz41yb.txt === reduce.pl bib === id = cord-324373-mgdtb98z author = Antonelli, Andrea title = Comparison between the Airgo™ Device and a Metabolic Cart during Rest and Exercise † date = 2020-07-15 pages = extension = .txt mime = text/plain words = 7608 sentences = 306 flesch = 45 summary = The goal of the presented work is to compare a metabolic cart, considered a gold standard, with Airgo™ (MYAIR Inc, Boston, MA, USA; MyAirgo Italy Srl, Milan, Italy), a resistance-based wearable device able to derive breathing parameters from body surface motion detection acquired at the level of the lower ribcage. The comparison of the Airgo™ device with the metabolic cart showed that the respiratory rate was the most accurate parameter, in all positions, for both rest and exercise tests in all conditions of physical effort: medians were always positioned on the zero error line with low dispersion around this value. The comparison of the Airgo™ device with the metabolic cart showed that the respiratory rate was the most accurate parameter, in all positions, for both rest and exercise tests in all conditions of physical effort: medians were always positioned on the zero error line with low dispersion around this value. cache = ./cache/cord-324373-mgdtb98z.txt txt = ./txt/cord-324373-mgdtb98z.txt === reduce.pl bib === id = cord-292274-upwn9o2m author = Ghaffari, Abdi title = COVID-19 Serological Tests: How Well Do They Actually Perform? date = 2020-07-04 pages = extension = .txt mime = text/plain words = 4648 sentences = 244 flesch = 44 summary = While IgM and IgG antibodies have been the leading candidates in COVID-19 serological test development, recent studies show that IgA, predominately present in the mucosal tissue, may also play a critical role in the immune response and disease progression [12] . While IgM and IgG antibodies have been the leading candidates in COVID-19 serological test development, recent studies show that IgA, predominately present in the mucosal tissue, may also play a critical role in the immune response and disease progression [12] . Typically, RDT test strips use a drop of blood to detect the presence of patient antibodies (IgG, IgM, or IgA) produced against a specific SARS-CoV-2 antigen ( Figure 2 ). Critics point to gaps in our understanding of immune response to COVID-19 infection, including the ability of serological tests to detect neutralizing antibodies and the capacity of the immune system to provide long-term immunity against SARS-CoV-2. cache = ./cache/cord-292274-upwn9o2m.txt txt = ./txt/cord-292274-upwn9o2m.txt === reduce.pl bib === id = cord-328294-gii1b7s7 author = Doty, Richard L. title = Olfaction and Its Alteration by Nasal Obstruction, Rhinitis, and Rhinosinusitis date = 2009-01-02 pages = extension = .txt mime = text/plain words = 10862 sentences = 531 flesch = 41 summary = The development and proliferation of easy-to-use, self-administered "scratch and sniff" tests of odor identification have significantly increased our understanding of smell function in humans, including the influences of such factors as age, gender, exposure to toxic agents, smoking behavior, and various disease states. 40 In this work, systemic prednisone 50 mg was administered each day for 7 days to 20 anosmic or severely hyposmic patients of several types whose olfactory function was monitored using butanol thresholds and odor identification tests. 43 reported that 28 patients with chronic rhinitis and no associated polyposis or rhinosinusitis had an average olfactory test score (based on a composite of odor identification and detection tests) indicative of moderate hyposmia. The comparatively few studies that have employed modern psychophysical tests to patients with rhinitis or rhinosinusitis have generally found an association between the degree of smell loss and the severity of nasal disease, although, except in cases of marked obstruction, no relationship is apparent between airway patency and olfactory dysfunction. cache = ./cache/cord-328294-gii1b7s7.txt txt = ./txt/cord-328294-gii1b7s7.txt === reduce.pl bib === id = cord-343340-zi0rfidc author = Aragón‐Caqueo, Diego title = Optimization of group size in pool testing strategy for SARS‐CoV‐2: A simple mathematical model date = 2020-05-03 pages = extension = .txt mime = text/plain words = 3319 sentences = 155 flesch = 51 summary = The aim of this study is to propose a simple mathematical model to estimate the optimum number of pooled samples according to the relative prevalence of positive tests in a particular healthcare context, assuming that if a group tests negative, no further testing is done whereas if a group tests positive, all the subjects of the group are retested individually. Therefore, the aim of this study is to provide a mathematical model to estimate the optimum number of pooled samples according to the specific prevalences of positive tests in a particular country context, in order to save as many tests as possible and cover as many people as possible, knowing that if a group tests out positive, all the individuals of the sample would have to be individually tested. This article proposed a simple and landed model to estimate the most optimum group number to implement pool testing strategy for SARS-CoV-2, according to the specific historical positive tests prevalence for a determined healthcare context. cache = ./cache/cord-343340-zi0rfidc.txt txt = ./txt/cord-343340-zi0rfidc.txt === reduce.pl bib === id = cord-318570-wj7r6953 author = Xiao, Yinzong title = Point-of-Care Tests for Hepatitis B: An Overview date = 2020-10-02 pages = extension = .txt mime = text/plain words = 8331 sentences = 350 flesch = 40 summary = If active infection is confirmed, subsequent blood tests are performed to determine the stage of disease and need for treatment, including a hepatitis B virus (HBV) polymerase chain reaction (PCR)-based quantitative DNA level or viral load, a hepatitis B eAg and eAb assay and liver function tests to determine whether an elevated aminotransferase (ALT) indicative of liver inflammation or other signs of impaired liver function are present. POCs usually require small amounts of body fluids (for example, a finger-prick blood sample or oral swab), short turn-around time, and are generally easy to use with minimal required training and therefore can be provided to people in a variety of community and outreach settings by a broad range of trained workers [22] and are scalable to rapidly reach large populations as has been seen with the highly successful Egyptian national hepatitis C screening program [23] . cache = ./cache/cord-318570-wj7r6953.txt txt = ./txt/cord-318570-wj7r6953.txt === reduce.pl bib === id = cord-334274-4jee19hx author = Waelde, K. title = How to remove the testing bias in CoV-2 statistics date = 2020-10-16 pages = extension = .txt mime = text/plain words = 7041 sentences = 518 flesch = 63 summary = Private and public decision making should not be based on time series of CoV-2-infections as the latter do not provide information about the true epidemic dynamics in a country. 3 We show that time series on the number of tests and time series on reported infections do not allow one to obtain information about the true state of an epidemic. It also studies the (lack of) informational content of time series on reported infections and time series on the number of tests, and the properties of the positive rate. Testing increases the positive rate if the number of tests undertaken due to symptoms 17 This paper is about conceptional issues related to the …nding an unbiased estimator for an unobserved time series. If we knew the number of Covid-19 cases, i.e. CoV-2 infections with severe acute respiratory symptoms (SARS), then we would know at least one part of epidemic dynamics (Ĩ symp (t) in our model). cache = ./cache/cord-334274-4jee19hx.txt txt = ./txt/cord-334274-4jee19hx.txt === reduce.pl bib === id = cord-331617-1ytcd0ax author = Horvath, Karl title = Antikörpertests bei COVID-19 - Was uns die Ergebnisse sagen date = 2020-05-15 pages = extension = .txt mime = text/plain words = 2635 sentences = 331 flesch = 55 summary = Da weitgehend alle zur Diagnose eingesetzten Tests nicht vollständig fehlerfrei funktionieren, ist auch bei der Testung auf Vorliegen von SARS-CoV-2 spezifischen AK damit zu rechnen, dass es einen Anteil von Personen gibt, der vom Test falsch klassifiziert wird. Wie groß dieser jeweilig falsch klassifizierte Anteil an allen getesteten Personen ist, d.h. wie sicher ein positives oder negatives Testresultat ist, ist abhängig von der Sensitivität und Spezifität des jeweiligen Tests sowie von der gegebenen Vortestwahrscheinlichkeit. Mit anderen Worten beschreibt die Vortestwahrscheinlichkeit das Risiko, dass bei einer bisher ungetesteten Person eine SARS-CoV-2 Infektion vorliegt bzw. Zu bedenken ist auch, dass sich die Prävalenz einer SARS-CoV-2 Infektion und damit die Vortestwahrscheinlichkeit mit Fortschreiten der Pandemie ändern wird. Auch bei nahezu idealen Testeigenschaften sind bei geringer Vortestwahrscheinlichkeit (wie sie bei der Testung von Personen ohne Symptome und Risikofaktoren für eine SARS-CoV-2 Infektion besteht) positive Testresultate häufig falsch. cache = ./cache/cord-331617-1ytcd0ax.txt txt = ./txt/cord-331617-1ytcd0ax.txt === reduce.pl bib === id = cord-342181-x14iywtr author = Taipale, J. title = Population-scale testing can suppress the spread of COVID-19 date = 2020-05-01 pages = extension = .txt mime = text/plain words = 7522 sentences = 359 flesch = 50 summary = Our model also indicates that unlike sampling-based tests, population-scale testing does not need to be very accurate: false negative rates up to 15% could be tolerated if 80% comply with testing every ten days, and false positives can be almost arbitrarily high when a high fraction of the population is already effectively quarantined. Using the standard (continuous, deterministic) SIR model, the equations in Fig. 2A and Methods show that the optimal population-scale testing strategy will succeed if at least two thirds of all new COVID-19 cases are immediately identified and quarantined. Although a population-scale test does not need to be as accurate as a clinical-grade qRT-PCR test (see above), apart from a potential increase in errors due to sample collection, there is no theoretical reason why a self-test based on isothermal amplification would not achieve the false negative and positive rates that are equivalent to the current state-of-the-art methodology. cache = ./cache/cord-342181-x14iywtr.txt txt = ./txt/cord-342181-x14iywtr.txt === reduce.pl bib === id = cord-328320-1f3r80r5 author = Kim, Edward title = Drawing on Israel’s Experience Organizing Volunteers to Operationalize Drive-Through Coronavirus Testing Centers date = 2020-04-16 pages = extension = .txt mime = text/plain words = 1432 sentences = 76 flesch = 51 summary = title: Drawing on Israel's Experience Organizing Volunteers to Operationalize Drive-Through Coronavirus Testing Centers To increase the country's capacity to test and track suspected coronavirus disease 2019 (COVID-19) cases, Israel launched drive-through testing centers in key cities, including Tel Aviv, Jerusalem, Be'er Sheva, and Haifa. This article examines the challenges that the national emergency medical services and volunteers faced in the process of implementing drive-through testing centers to offer lessons learned and direction to health-care professionals in other countries. 5 Working alongside the Ministry of Health, Magen David Adom (MDA)-Israel's emergency medical, disaster, ambulance, and blood bank service-operationalized drive-through coronavirus testing centers, mirroring the models used by China and South Korea. The testing centers are staffed with medical teams, police officers, security personnel, and volunteer students, and can process 6 lanes of cars in parallel, taking on average 3-5 min per car. To quickly operationalize "drive and test" facilities while allowing for process improvements, MDA used the Plan-Do-Check-Act methodology. cache = ./cache/cord-328320-1f3r80r5.txt txt = ./txt/cord-328320-1f3r80r5.txt === reduce.pl bib === id = cord-315077-i1xjcuae author = Branda, John A. title = Utilization management in microbiology date = 2014-01-01 pages = extension = .txt mime = text/plain words = 4117 sentences = 200 flesch = 35 summary = The results of testing in the microbiology laboratory have significant effects on the cost of clinical care, especially costs related to antimicrobial agents and infection control practices. Consequently many of the successful utilization management interventions described in clinical microbiology have targeted not just the volume of tests performed in the laboratory, but also the downstream costs of care. In a number of cases, the initiative's success arose not only from a reduction in laboratory testing per se, but rather also from its impact in the clinical care arena (for example, a reduction in antibiotic use or hospital length of length-of-stay). Each day, a microbiology fellow and laboratory director review the clinical history, culture results and susceptibility test results for all patients newly started on a carbapenem, to determine appropriate versus inappropriate use of the drugs. cache = ./cache/cord-315077-i1xjcuae.txt txt = ./txt/cord-315077-i1xjcuae.txt === reduce.pl bib === id = cord-332481-y0rd70ry author = Ljubic, T. title = The effect of serological screening for SARS-CoV-2 antibodies to participants' attitudes and risk behaviour: a study on a tested population sample of industry workers in Split-Dalmatia County, Croatia date = 2020-06-17 pages = extension = .txt mime = text/plain words = 3846 sentences = 190 flesch = 47 summary = title: The effect of serological screening for SARS-CoV-2 antibodies to participants' attitudes and risk behaviour: a study on a tested population sample of industry workers in Split-Dalmatia County, Croatia Rapid serological tests for SARS-CoV-2 antibodies have been questioned by scientists and the public because of unexplored effects of negative test results on behaviour and attitudes, that could lower the level of adherence to protective measures. Thus, this study aims at investigating the changes in personal attitudes and behaviour of DIV Group industry workers before and after receiving negative serological test results for SARS-CoV-2 antibodies. The results of this study indicate that the levels of fear of being infected or infecting others with COVID-19, as well as behaviours regarding adherence to protective measure, changed significantly in the timeframe after receiving negative test results. cache = ./cache/cord-332481-y0rd70ry.txt txt = ./txt/cord-332481-y0rd70ry.txt === reduce.pl bib === id = cord-339122-7vvqtk84 author = Deb, Chaarushena title = Covid-19, Single-Sourced Diagnostic Tests, and Innovation Policy date = 2020-07-07 pages = extension = .txt mime = text/plain words = 3117 sentences = 167 flesch = 49 summary = 16 An appropriate model for diagnostic testing development, including innovation incentives, should go beyond simply discouraging test monopolies and promoting confirmatory testing, by also allowing for low R&D costs for test development and yielding fast delivery of high quality tests-preventing the errors highlighted in the Covid-19 testing response from occurring in both emergency and non-emergency situations. And thus any sort of incentive model that relies on granting market exclusivity -such as the traditional patent system, FDA approval exclusivity, or trade secret protection -raises the same sorts of issues, if on a smaller scale, as those grimly demonstrated by the failure of U.S. SARS-CoV-2 testing at the onset of the Covid-19 pandemic, which ultimately resulted in the loss of many lives. But for diagnostic tests which rely on confirmatory testing, innovative improvements, and robust access to supply, single-sourcing creates a host of serious problems. cache = ./cache/cord-339122-7vvqtk84.txt txt = ./txt/cord-339122-7vvqtk84.txt === reduce.pl bib === id = cord-354006-j1y42oxu author = Ozdemir, Vural title = Shifting emphasis from pharmacogenomics to theragnostics date = 2006 pages = extension = .txt mime = text/plain words = 4200 sentences = 142 flesch = 29 summary = As biomarker applications move towards point-of-care to individualize drug therapy, a number of qualitatively different concerns arise relating to gene patents and ethical and therapeutic policy aspects of theragnostic testing 4, 8, 9 . In the present analyses, we 'unpack' and contrast the motivations at play that are driving the pursuit for theragnostic patents and its bioethical corollaries in: (1) fundamental upstream basic research oriented to the discovery of genes for human diseases; and (2) downstream clinical applications at point-of-care as theragnostic tests to stratify patient populations for individualization of pharmacotherapy. While genetic tests hold the promise of a more rational clinical forecast and management of disease risk in the future, they are also raising concerns about the provision of public healthcare services (reduced access) and the impact of market forces on the products of research (commercialization of technologies) and academic freedom. cache = ./cache/cord-354006-j1y42oxu.txt txt = ./txt/cord-354006-j1y42oxu.txt === reduce.pl bib === id = cord-019490-m1cuuehi author = nan title = Abstracts cont. date = 2015-12-28 pages = extension = .txt mime = text/plain words = 93588 sentences = 5683 flesch = 50 summary = Tigecycline Evaluation Surveillance Trial (TEST) -Global in vitro antibacterial activity against selected species of glucose non-fermenting organisms Objective: Despite the introduction of new antimicrobials to treat resistant gram-positive bacteria, Staphylococcus aureus continues to be a therapeutic challenge for the clinician. Two prospective studies from our centre identified common causes of CAP in India to be Mycoplasma pneumoniae [MP] and Legionella pneumophila [LP] by serology in 11% each, and SPN in 10% by culture of respiratory secretions/blood/ Conclusion: Although SPN is the most common isolate, the rising numbers of gram negative organisms (38%) and atypical pathogens associated with increasing mortality stress the need for review of initial antibiotic choice for adults with higher PORT classes. Conclusion: The spectrum of isolates among our patients were shifting towards gram positive bacteria with high resistance to different groups of antimicrobial agents limiting few choices for alternative therapies for infection control. cache = ./cache/cord-019490-m1cuuehi.txt txt = ./txt/cord-019490-m1cuuehi.txt === reduce.pl bib === id = cord-354005-q5nj0ku1 author = Richaud, M. title = Specific testing of textiles for transportation date = 2017-09-29 pages = extension = .txt mime = text/plain words = 11220 sentences = 561 flesch = 48 summary = Then, different aspects of textile testing relevant to the transportation industry are discussed: safety, flammability, hygiene, performance of composite parts, and durability. For instance, the FAA standard on airworthiness of airplanes (FAR/CS 25.853) includes several flammability test methods that apply to textile components: EASA for its part is currently reviewing its legislation on civil aircrafts to take into account the increased air traffic and arrival of new technologies such as drones (Juul, 2016) . A series of test methods for textile-reinforced composites has also been developed by various standardization organizations (Table 14 .9). This includes performance related to safety for airbags, seat belts, tires, and slings; flammability, smoke generation, and toxicity, with test methods and specific requirements for each type of application; hygiene for filters and antimicrobial textiles; destructive and nondestructive tests conducted on textile-reinforced composites at the textile and composite level; and durability. Standard guide for testing fabric-reinforced "Textile" composite materials cache = ./cache/cord-354005-q5nj0ku1.txt txt = ./txt/cord-354005-q5nj0ku1.txt === reduce.pl bib === id = cord-350473-f47i7y5h author = Sen-Crowe, Brendon title = COVID-19 laboratory testing issues and capacities as we transition to surveillance testing and contact tracing date = 2020-05-27 pages = extension = .txt mime = text/plain words = 1099 sentences = 91 flesch = 54 summary = The sensitivity of PCR tests have been estimated at 71%, resulting in ~30% of infected patients having a negative finding. The second type of test is serologic, which detects immunoglobulins (IgG and IgM) specific for SARS-CoV-2 and provides an estimation of population virus exposure 4 . Many FDA-approved serologic tests have high sensitivity and specificity. To address the development of a reliable test, the Department of Health & Human Services (HHS) provided funding for the development of Simplexa COVID-19 Direct Assay and to QIAGEN to accelerate development of their RPS2 test 15 . Additionally, HHS is purchasing the ID NOW COVID-19 rapid point-of-care test (Abbott Diagnostics Scarborough Inc.) for public health labs (Table 1) 16 . Saliva is more sensitive for SARS-CoV-2 detection in COVID-19 patients than nasopharyngeal swabs cache = ./cache/cord-350473-f47i7y5h.txt txt = ./txt/cord-350473-f47i7y5h.txt === reduce.pl bib === id = cord-345454-r1ymzk6n author = Levesque, J. title = A note on COVID-19 seroprevalence studies: a meta-analysis using hierarchical modelling date = 2020-05-06 pages = extension = .txt mime = text/plain words = 3631 sentences = 230 flesch = 61 summary = Many of these studies find an antibody prevalence comparable to the false positive rate of their respective serology tests and the relatively low statistical power associated with each study has invited criticism. To determine the strength of the signal, we perform a meta-analysis on the publicly available seroprevalence data based on Bayesian hierarchical modelling with Markov Chain Monte Carlo and Generalized Linear Mixed Modelling with prediction sampling. The Santa Clara study shows a density function consistent with a high probability of a non-zero antibody prevalence, with a mean and a mode slightly greater than 1%, although we note that the posterior distribution does include zero. Figure 2 : The two dimensional marginal posterior distribution functions for antibody prevalence with the false positive rate at each study location from Bayesian hierarchical model. Figure 7 shows the resulting density functions for the antibody prevalence in each location from the GLMM prediction sampling. cache = ./cache/cord-345454-r1ymzk6n.txt txt = ./txt/cord-345454-r1ymzk6n.txt === reduce.pl bib === id = cord-352111-frk319q1 author = Woodruff, Amelita title = COVID-19 Follow up Testing date = 2020-05-11 pages = extension = .txt mime = text/plain words = 633 sentences = 47 flesch = 64 summary = • 70% of patients met CDC guidelines for release from quarantine & still tested (+); • The average time from onset of symptoms to negative testing was 19 days.  70% of patients met CDC guidelines for release from quarantine & still tested (+)  The average time from onset of symptoms to negative testing was 19 days Dear Editor, There is some uncertainty regarding the incubation period of the SARS-CoV-2 virus. The non-test-based strategy recommends that COVID-19 patients can discontinue self-isolation when they have been afebrile for 72 hours without anti-pyretic medications, have improvement in respiratory symptoms, and have at least 10 days elapse since symptoms started, recently increased from 7 days. The test-based strategy requires resolution of fever without the use of anti-pyretics, improvement of respiratory symptoms, and two consecutive negative COVID-19 nasopharyngeal swabs collected ≥24 hours apart. In our patient population, the average time from the onset of symptoms to negative testing is 19 days. cache = ./cache/cord-352111-frk319q1.txt txt = ./txt/cord-352111-frk319q1.txt === reduce.pl bib === id = cord-337462-9mvk86q6 author = nan title = Humanity tested date = 2020-04-08 pages = extension = .txt mime = text/plain words = 1263 sentences = 59 flesch = 50 summary = The world needs mass at-home serological testing for antibodies elicited by SARS-CoV-2, and rapid and frequent point-of-care testing for the presence of the virus' RNA in selected populations. Singapore, Hong Kong and Taiwan have shown the world that, to contain the propagation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), governments need to quickly implement aggressive testing (by detecting the viral RNA through polymerase chain reaction (PCR)), the isolation of those infected and the tracing and quarantining of their contacts, while educating their citizens about the need for physical distancing and basic public health measures (in particular, frequent hand-washing and staying at home if feeling unwell). Medical-device companies and government and research laboratories around the world have rushed to adapt and scale up nucleic acid tests (mostly employing PCR, but also CRISPR-based detection and loop-mediated isothermal amplification) to detect the virus' RNA, and government agencies are scrambling to assess them via emergency routes (such as the Emergency Use Authorization program 3 by the United States Food and Drug Administration (FDA)). cache = ./cache/cord-337462-9mvk86q6.txt txt = ./txt/cord-337462-9mvk86q6.txt === reduce.pl bib === id = cord-349161-4899cq99 author = Whiting, Penny F title = Graphical presentation of diagnostic information date = 2008-04-11 pages = extension = .txt mime = text/plain words = 5807 sentences = 306 flesch = 41 summary = For diagnostic accuracy studies, measures of test performance (sensitivity, specificity, predictive values, likelihood ratios or diagnostic odds ratio) are plotted on the horizontal axis. ROC plots can be used to present the results of diagnostic systematic reviews, but differ from those used in primary studies as each point typically represents a separate study or data set within a study (individual studies may contribute more than one point). A summary ROC (SROC) curve can be estimated using one of several methods [12] [13] [14] [15] and quantifies test accuracy and the association between sensitivity and specificity based on differences between studies. A number of graphical displays aim to put results of diagnostic test evaluations into clinical context, based either on primary studies or systematic reviews. The inclusion of graphical displays, such as SROC plots or forest plots, in systematic reviews of test accuracy studies allows a visual assessment of heterogeneity between studies by showing the results from each individual study included in the review. cache = ./cache/cord-349161-4899cq99.txt txt = ./txt/cord-349161-4899cq99.txt === reduce.pl bib === id = cord-337458-dc90ecfe author = Markwalter, Christine F. title = Inorganic Complexes and Metal-Based Nanomaterials for Infectious Disease Diagnostics date = 2018-12-04 pages = extension = .txt mime = text/plain words = 40568 sentences = 2391 flesch = 40 summary = In this review, we define the components of a diagnostic to include: (1) the target biomarker, an endogenous indicator of a disease state, which is most often a pathogen or host protein, carbohydrate, or nucleic acid sequence, (2) sample preparation, which allows for biomarker isolation, purification, and/or concentration from complex biological matrices, (3) molecular recognition elements, which specifically capture and detect the target biomarker, (4) signal generation and amplification, and (5) instrumentation for signal read-out. 113, 114 In subsequent studies, the group developed and optimized a hand-held, easy-to-use device 85, 115 (Figure 8A ) in which HRP2-bound, IMAC-functionalized magnetic beads were directly transferred to the sample pad of commercial malaria lateral flow assays. If combined with one of the sample preparation strategies discussed previously (section 3) or integrated with paper or another field-ready substrate, this Ir(III)-based detection strategy could produce a robust and sensitive assay that is applicable in low-resource diagnostic settings. cache = ./cache/cord-337458-dc90ecfe.txt txt = ./txt/cord-337458-dc90ecfe.txt === reduce.pl bib === id = cord-023364-ut56gczm author = nan title = EDUCATION DAY MONDAY: PLENARY SESSION 1 MONDAY: PARALLEL SESSIONS date = 2005-06-08 pages = extension = .txt mime = text/plain words = 130049 sentences = 7334 flesch = 54 summary = • enhancement of automation/computerisation; • process control to provide an 'error-free pathway'; • (national) surveillance and trend analysis of results, preferably based on national working standards; • significantly increased sensitivity, especially from development of antigen/antibody 'combi' assays (e.g. for HIV, and recently, for HCV); • awareness of HBsAg vaccine-escape mutants and design of assays to cope with this; • extension of range of agents and markers tested for (varies in different countries); • increasing range of assays available for testing donors with a relevant history of exposure to malaria or Chagas' disease infection (for retrieval of otherwise wasted blood); • European Union's in vitro diagnostics directive: this has caused some problems and reduced flexibility. cache = ./cache/cord-023364-ut56gczm.txt txt = ./txt/cord-023364-ut56gczm.txt === reduce.pl bib === id = cord-006229-7yoilsho author = nan title = Abstracts of the 82(nd) Annual Meeting of the German Society for Experimental and Clinical Pharmacology and Toxicology (DGPT) and the 18(th) Annual Meeting of the Network Clinical Pharmacology Germany (VKliPha) in cooperation with the Arbeitsgemeinschaft für Angewandte Humanpharmakologie e.V. (AGAH) date = 2016-02-06 pages = extension = .txt mime = text/plain words = 133493 sentences = 6804 flesch = 42 summary = It directly activates Protein Kinase A (PKA) or the Exchange protein directly activated by cAMP (Epac) which is a guanine exchange factor (GEF) for the small monomeric GTPase Rap. As Human umbilical vein endothelial cells (HUVEC) express both cAMP effectors (Epac1 and PKA), we investigated the role of cAMP-signaling using a spheroid based sprouting assay as an in vitro model for angiogenesis. After activation, S1P receptors regulate important processes in the progression of renal diseases, such as mesangial cell migration Methods and Results: Here we demonstrate that dexamethasone treatment lowered S1P 1 mRNA and protein expression levels in rat mesangial cells measured by TaqMan® and Western blot analyses. The aim of this study was to investigate the relevance of IGFBP5 in cardiogenesis and cardiac remodeling and its role as a potential target for ameliorating stress-induced cardiac remodeling Methods and Results: We investigated the expression of Igfbp5 in murine cardiac tissue at different developmental stages by qPCR normalized to Tpt1 (Tumor Protein, Translationally-Controlled 1). cache = ./cache/cord-006229-7yoilsho.txt txt = ./txt/cord-006229-7yoilsho.txt === reduce.pl bib === id = cord-022650-phsr10jp author = nan title = Abstracts TPS date = 2018-08-14 pages = extension = .txt mime = text/plain words = 119675 sentences = 7010 flesch = 55 summary = 0685 | Skin prick test reactivity to aeroallergens in adult allergy clinic in a tertiary hospital: a 12-year retrospective study Results: Five different human sera were screened for specific IgE level against 29 different allergen sources using test methods of three different suppliers. Conclusion: This multicenter prospective study confirmed that stepwise single-dose OFC to egg will help to clarify the severity of egg allergy, and will contribute to improved food allergy manageMethod: The study design was a retrospective cohort study extracting data from the electronic chart of children older than 4 years who visited our out-patient clinic for egg or milk allergy and who underwent an oral food challenge test (OFC) twice within 24 months between November 2013 and December 2017. Results: In the base case analysis, using Italy clinical practice patients with moderate-to severe allergic rhino-conjunctivitis (SS ranging from 6 to 15 points) and a mean age at entry of 21 years, both SCIT and SLIT were associated with increased cost but superior efficacy compared to pharmacotherapy alone. cache = ./cache/cord-022650-phsr10jp.txt txt = ./txt/cord-022650-phsr10jp.txt === reduce.pl bib === id = cord-023354-f2ciho6o author = nan title = TUESDAY PLENARY SESSION 3 TUESDAY: POSTERS date = 2005-06-08 pages = extension = .txt mime = text/plain words = 130046 sentences = 7333 flesch = 54 summary = • enhancement of automation/computerisation; • process control to provide an 'error-free pathway'; • (national) surveillance and trend analysis of results, preferably based on national working standards; • significantly increased sensitivity, especially from development of antigen/antibody 'combi' assays (e.g. for HIV, and recently, for HCV); • awareness of HBsAg vaccine-escape mutants and design of assays to cope with this; • extension of range of agents and markers tested for (varies in different countries); • increasing range of assays available for testing donors with a relevant history of exposure to malaria or Chagas' disease infection (for retrieval of otherwise wasted blood); • European Union's in vitro diagnostics directive: this has caused some problems and reduced flexibility. cache = ./cache/cord-023354-f2ciho6o.txt txt = ./txt/cord-023354-f2ciho6o.txt === reduce.pl bib === id = cord-023346-8sqbqjm1 author = nan title = MONDAY: POSTERS date = 2005-06-08 pages = extension = .txt mime = text/plain words = 130043 sentences = 7330 flesch = 54 summary = • enhancement of automation/computerisation; • process control to provide an 'error-free pathway'; • (national) surveillance and trend analysis of results, preferably based on national working standards; • significantly increased sensitivity, especially from development of antigen/antibody 'combi' assays (e.g. for HIV, and recently, for HCV); • awareness of HBsAg vaccine-escape mutants and design of assays to cope with this; • extension of range of agents and markers tested for (varies in different countries); • increasing range of assays available for testing donors with a relevant history of exposure to malaria or Chagas' disease infection (for retrieval of otherwise wasted blood); • European Union's in vitro diagnostics directive: this has caused some problems and reduced flexibility. cache = ./cache/cord-023346-8sqbqjm1.txt txt = ./txt/cord-023346-8sqbqjm1.txt === reduce.pl bib === id = cord-019347-tj3ye1mx author = nan title = ABSTRACT BOOK date = 2010-02-19 pages = extension = .txt mime = text/plain words = 107926 sentences = 6940 flesch = 53 summary = Method:Case Report:A 15y/o w/f athlete presented with a two month history of recurrent hives and angioedema which she associated with ingestion of Halloween candy .One week before evaluation she had hives with Coconut as well.Her history was othewise unremarkable except for recurrent UTI'S, annual sinusitis, pneumonia in 1998 as well as migraines.She denied sexual activity.Her physical exam was normal.Results:An evaluation for autoimmune disease revealed normal ESR, ANA, DSDNA, mono and hepatitis serology as well as lyme titers however her CH50 was low17u/ml(normal 26-58U/ml)and evaluation of complement revealed c4 14mg/dl(normal 16-47mg//dl)and c2 <1.3mg/dl(normal 1.6-3.5mg/dl)with normal c3, c5-c9.Her father had nor-malc4 but c2 was 1.4mg/dl (normal 1.6-3.5mg/dl)Her sister had c2 of 1.5mg/dl and normal c4 and her mother had normal c2 and c4.Her workup included positive prick skin test to ragweed, ash and grass and she was started on Rhinocort and Clarinex seasonally.She has been followed for one year with resolution of hives and is asymptomatic.Her diagnosis had been confirmed by a pediatric rheumatologist.Conclusion;We present an atypical case of C2 complement deficiency in an currently asymptomatic individual. cache = ./cache/cord-019347-tj3ye1mx.txt txt = ./txt/cord-019347-tj3ye1mx.txt === reduce.pl bib === id = cord-023095-4dannjjm author = nan title = Research Abstract Program of the 2011 ACVIM Forum Denver, Colorado, June 15–18, 2011 date = 2011-05-03 pages = extension = .txt mime = text/plain words = 134226 sentences = 6834 flesch = 51 summary = The purpose of this study was to determine the short-term effects of ivabradine on heart rate (HR), blood pressure, left ventricular (LV) systolic and diastolic function, left atrial (LA) performance, and clinical tolerance in healthy cats after repeated oral doses. The goal of this study was to investigate the relationship between heart rate and ECG time intervals to body mass in apparently healthy horses and ponies and to calculate normal ranges for different weight groups. This study aimed to investigate the prevalence of hypercoagulability in PLN dogs based on thromboelastography (TEG), and to determine whether hypercoagulability in these patients could be predicted by clinical assessments that identify systemic hypertension (systolic blood pressure 4 160 mmHg), hypoalbuminemia (serum albumin o 2.7 mg/dl), antithrombin activity (o 70%), and degree of proteinuria (urine protein:creatinine ratio [UPC] ! cache = ./cache/cord-023095-4dannjjm.txt txt = ./txt/cord-023095-4dannjjm.txt === reduce.pl bib === id = cord-010092-uftc8inx author = nan title = Abstract of 29th Regional Congress of the ISBT date = 2019-06-07 pages = extension = .txt mime = text/plain words = 233304 sentences = 13171 flesch = 54 summary = Prospective testing of blood donations in endemic areas of the U.S. revealed 0.38% of donors were positive for Babesia DNA or antibodies (Moritz, NEJM, 2016) Aims: -To report results of ongoing Babesia clinical trial -To explain significance of Babesia as a TT infection Methods: In cobas â Babesia for use on the cobas â 6800/8800 Systems, is a qualitative polymerase chain reaction nucleic acid amplification test, developed to detect in whole blood (WB) donor samples the 4 Babesia species that cause human disease: B. In sensitivity analyses, there were two discrepant results for HIV testing, three for HCV, and five for anti-HBc. Summary/Conclusions: Elecsys â infectious disease parameters on the cobas e 801 analyser demonstrate high specificity/sensitivity for screening first-time blood donor samples, with similar clinical performance to other commercially available assays. cache = ./cache/cord-010092-uftc8inx.txt txt = ./txt/cord-010092-uftc8inx.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 ===== Reducing email addresses cord-031567-w2676lrz cord-256568-mbkrg98v Creating transaction Updating adr table ===== Reducing keywords cord-001253-3jnkki5z cord-017359-zr0bo9el cord-021511-88xaynf7 cord-023584-yaxawqhj cord-018335-4l7scdqk cord-007047-7ty9mxa9 cord-024631-yvek5vjz cord-018271-ybfxtc7x cord-033420-pjtyv0pv cord-031567-w2676lrz cord-144448-mqs502xm cord-027445-bpx4qr0i cord-012934-c6pbr64i cord-119183-pbliko1k cord-021550-evh3b7o2 cord-292209-d1ty9etr cord-026215-neqsup40 cord-272995-yvj2pqh1 cord-017072-qwe1ne3q cord-102704-wfuzk2dp cord-262846-1mhimfsf cord-002626-jzwwses4 cord-025556-oyfx3ij5 cord-296588-q2716lda cord-121057-986xoy22 cord-179749-qdbmpi7j cord-270935-t9pym9k0 cord-278377-jgq3dz3u cord-266036-qhlo99l7 cord-298441-77w86l8q cord-290978-e7imc11r cord-271920-1dzkgt6w cord-286539-3sr4djft cord-263893-zb6h3q4k cord-117424-mp6h9dyl cord-022653-qa1uph35 cord-280571-ntgt5hy9 cord-022659-chwk2bs4 cord-127025-9ubhd4vf cord-034948-w59wxu8i cord-030341-uora9qcb cord-202376-440zapcw cord-102817-m1l1t0e1 cord-311766-m9yv4qkm cord-150218-javbnjrg cord-170195-lrg11s5n cord-288982-63ddlh20 cord-281241-k1adcls8 cord-256568-mbkrg98v cord-273324-xhpv783y cord-252959-ktet18wl cord-281495-beb164oy cord-307187-5blsjicu cord-320970-ru2iw0py cord-325455-e464idc0 cord-290251-ihq8gdwj cord-283517-7gd0f06m cord-284945-837qlk8y cord-307123-h48uwj93 cord-316047-d9cpe9yl cord-300930-47a4pu27 cord-226956-n5qwsvtr cord-298086-pbfi5c8e cord-319436-mlitd45q cord-225183-6rusimb5 cord-326148-9wpxm5of cord-324944-ixh3ykrc cord-310714-kqzlwka0 cord-308021-cnf4xljc cord-300520-vxn7uh41 cord-289461-bnusv816 cord-276577-06boh550 cord-320864-k9zksbyt cord-296306-xcomjvaa cord-295126-lz2jbmcn cord-310195-am3u7z76 cord-312477-2y88gzji cord-307500-2jwuzfan cord-330721-hmnrnem6 cord-325956-1kxxg0s9 cord-323476-rb9n5wc0 cord-324373-mgdtb98z cord-303539-gimz41yb cord-343340-zi0rfidc cord-328294-gii1b7s7 cord-292274-upwn9o2m cord-331617-1ytcd0ax cord-334274-4jee19hx cord-318570-wj7r6953 cord-342181-x14iywtr cord-328320-1f3r80r5 cord-315077-i1xjcuae cord-339122-7vvqtk84 cord-332481-y0rd70ry cord-354005-q5nj0ku1 cord-354006-j1y42oxu cord-350473-f47i7y5h cord-345454-r1ymzk6n cord-019490-m1cuuehi cord-352111-frk319q1 cord-349161-4899cq99 cord-006229-7yoilsho cord-337462-9mvk86q6 cord-337458-dc90ecfe cord-023364-ut56gczm cord-022650-phsr10jp cord-023346-8sqbqjm1 cord-023354-f2ciho6o cord-019347-tj3ye1mx cord-010092-uftc8inx cord-010119-t1x9gknd cord-023095-4dannjjm Creating transaction Updating wrd table ===== Reducing urls cord-021550-evh3b7o2 cord-025556-oyfx3ij5 cord-278377-jgq3dz3u cord-292209-d1ty9etr cord-012934-c6pbr64i cord-290978-e7imc11r cord-286539-3sr4djft cord-117424-mp6h9dyl cord-263893-zb6h3q4k cord-102817-m1l1t0e1 cord-262846-1mhimfsf cord-296588-q2716lda cord-002626-jzwwses4 cord-127025-9ubhd4vf cord-030341-uora9qcb cord-298086-pbfi5c8e cord-288982-63ddlh20 cord-326148-9wpxm5of cord-256568-mbkrg98v cord-273324-xhpv783y cord-290251-ihq8gdwj cord-283517-7gd0f06m cord-284945-837qlk8y cord-307123-h48uwj93 cord-316047-d9cpe9yl cord-324944-ixh3ykrc cord-300930-47a4pu27 cord-319436-mlitd45q cord-310714-kqzlwka0 cord-308021-cnf4xljc cord-300520-vxn7uh41 cord-289461-bnusv816 cord-307500-2jwuzfan cord-310195-am3u7z76 cord-296306-xcomjvaa cord-312477-2y88gzji cord-330721-hmnrnem6 cord-325956-1kxxg0s9 cord-343340-zi0rfidc cord-334274-4jee19hx cord-342181-x14iywtr cord-332481-y0rd70ry cord-019490-m1cuuehi cord-349161-4899cq99 cord-337462-9mvk86q6 cord-023364-ut56gczm cord-006229-7yoilsho cord-023354-f2ciho6o cord-023346-8sqbqjm1 cord-010092-uftc8inx cord-010119-t1x9gknd Creating transaction Updating url table ===== Reducing named entities cord-017359-zr0bo9el cord-001253-3jnkki5z cord-007047-7ty9mxa9 cord-023584-yaxawqhj cord-018335-4l7scdqk cord-024631-yvek5vjz cord-031567-w2676lrz cord-018271-ybfxtc7x cord-033420-pjtyv0pv cord-144448-mqs502xm cord-119183-pbliko1k cord-021550-evh3b7o2 cord-027445-bpx4qr0i cord-012934-c6pbr64i cord-292209-d1ty9etr cord-280571-ntgt5hy9 cord-026215-neqsup40 cord-272995-yvj2pqh1 cord-102704-wfuzk2dp cord-017072-qwe1ne3q cord-102817-m1l1t0e1 cord-021511-88xaynf7 cord-262846-1mhimfsf cord-025556-oyfx3ij5 cord-121057-986xoy22 cord-002626-jzwwses4 cord-278377-jgq3dz3u cord-270935-t9pym9k0 cord-170195-lrg11s5n cord-266036-qhlo99l7 cord-298441-77w86l8q cord-290978-e7imc11r cord-286539-3sr4djft cord-271920-1dzkgt6w cord-117424-mp6h9dyl cord-263893-zb6h3q4k cord-296588-q2716lda cord-034948-w59wxu8i cord-202376-440zapcw cord-030341-uora9qcb cord-311766-m9yv4qkm cord-298086-pbfi5c8e cord-150218-javbnjrg cord-127025-9ubhd4vf cord-326148-9wpxm5of cord-288982-63ddlh20 cord-179749-qdbmpi7j cord-022659-chwk2bs4 cord-022653-qa1uph35 cord-281241-k1adcls8 cord-252959-ktet18wl cord-256568-mbkrg98v cord-273324-xhpv783y cord-320970-ru2iw0py cord-281495-beb164oy cord-325455-e464idc0 cord-307187-5blsjicu cord-283517-7gd0f06m cord-290251-ihq8gdwj cord-284945-837qlk8y cord-307123-h48uwj93 cord-316047-d9cpe9yl cord-300930-47a4pu27 cord-226956-n5qwsvtr cord-319436-mlitd45q cord-324944-ixh3ykrc cord-225183-6rusimb5 cord-310714-kqzlwka0 cord-308021-cnf4xljc cord-300520-vxn7uh41 cord-289461-bnusv816 cord-276577-06boh550 cord-295126-lz2jbmcn cord-320864-k9zksbyt cord-307500-2jwuzfan cord-310195-am3u7z76 cord-296306-xcomjvaa cord-312477-2y88gzji cord-330721-hmnrnem6 cord-325956-1kxxg0s9 cord-323476-rb9n5wc0 cord-303539-gimz41yb cord-324373-mgdtb98z cord-292274-upwn9o2m cord-328294-gii1b7s7 cord-343340-zi0rfidc cord-318570-wj7r6953 cord-334274-4jee19hx cord-331617-1ytcd0ax cord-342181-x14iywtr cord-328320-1f3r80r5 cord-315077-i1xjcuae cord-332481-y0rd70ry cord-339122-7vvqtk84 cord-354006-j1y42oxu cord-354005-q5nj0ku1 cord-350473-f47i7y5h cord-345454-r1ymzk6n cord-352111-frk319q1 cord-337462-9mvk86q6 cord-349161-4899cq99 cord-337458-dc90ecfe cord-019490-m1cuuehi cord-023364-ut56gczm cord-023354-f2ciho6o cord-023346-8sqbqjm1 cord-019347-tj3ye1mx cord-022650-phsr10jp cord-006229-7yoilsho cord-023095-4dannjjm cord-010092-uftc8inx cord-010119-t1x9gknd Creating transaction Updating ent table ===== Reducing parts of speech cord-001253-3jnkki5z cord-017359-zr0bo9el cord-007047-7ty9mxa9 cord-021511-88xaynf7 cord-024631-yvek5vjz cord-119183-pbliko1k cord-027445-bpx4qr0i cord-033420-pjtyv0pv cord-023584-yaxawqhj cord-031567-w2676lrz cord-292209-d1ty9etr cord-144448-mqs502xm cord-012934-c6pbr64i cord-018335-4l7scdqk cord-026215-neqsup40 cord-102704-wfuzk2dp cord-272995-yvj2pqh1 cord-021550-evh3b7o2 cord-018271-ybfxtc7x cord-280571-ntgt5hy9 cord-017072-qwe1ne3q cord-262846-1mhimfsf cord-102817-m1l1t0e1 cord-025556-oyfx3ij5 cord-121057-986xoy22 cord-278377-jgq3dz3u cord-266036-qhlo99l7 cord-298441-77w86l8q cord-290978-e7imc11r cord-286539-3sr4djft cord-296588-q2716lda cord-263893-zb6h3q4k cord-179749-qdbmpi7j cord-271920-1dzkgt6w cord-127025-9ubhd4vf cord-270935-t9pym9k0 cord-002626-jzwwses4 cord-170195-lrg11s5n cord-117424-mp6h9dyl cord-034948-w59wxu8i cord-202376-440zapcw cord-030341-uora9qcb cord-311766-m9yv4qkm cord-326148-9wpxm5of cord-288982-63ddlh20 cord-298086-pbfi5c8e cord-281241-k1adcls8 cord-281495-beb164oy cord-320970-ru2iw0py cord-325455-e464idc0 cord-252959-ktet18wl cord-273324-xhpv783y cord-256568-mbkrg98v cord-307187-5blsjicu cord-290251-ihq8gdwj cord-226956-n5qwsvtr cord-307123-h48uwj93 cord-150218-javbnjrg cord-283517-7gd0f06m cord-300930-47a4pu27 cord-225183-6rusimb5 cord-319436-mlitd45q cord-308021-cnf4xljc cord-316047-d9cpe9yl cord-310714-kqzlwka0 cord-276577-06boh550 cord-295126-lz2jbmcn cord-320864-k9zksbyt cord-330721-hmnrnem6 cord-310195-am3u7z76 cord-323476-rb9n5wc0 cord-289461-bnusv816 cord-307500-2jwuzfan cord-296306-xcomjvaa cord-312477-2y88gzji cord-300520-vxn7uh41 cord-325956-1kxxg0s9 cord-303539-gimz41yb cord-284945-837qlk8y cord-292274-upwn9o2m cord-324373-mgdtb98z cord-343340-zi0rfidc cord-331617-1ytcd0ax cord-328320-1f3r80r5 cord-318570-wj7r6953 cord-334274-4jee19hx cord-342181-x14iywtr cord-328294-gii1b7s7 cord-315077-i1xjcuae cord-332481-y0rd70ry cord-339122-7vvqtk84 cord-354006-j1y42oxu cord-350473-f47i7y5h cord-345454-r1ymzk6n cord-352111-frk319q1 cord-337462-9mvk86q6 cord-324944-ixh3ykrc cord-349161-4899cq99 cord-354005-q5nj0ku1 cord-022659-chwk2bs4 cord-022653-qa1uph35 cord-337458-dc90ecfe cord-019490-m1cuuehi cord-019347-tj3ye1mx cord-023364-ut56gczm cord-023354-f2ciho6o cord-022650-phsr10jp cord-023346-8sqbqjm1 cord-006229-7yoilsho cord-023095-4dannjjm cord-010092-uftc8inx cord-010119-t1x9gknd Creating transaction Updating pos table Building ./etc/reader.txt cord-022650-phsr10jp cord-010119-t1x9gknd cord-023364-ut56gczm cord-010092-uftc8inx cord-023364-ut56gczm cord-023354-f2ciho6o number of items: 112 sum of words: 2,120,179 average size in words: 19,451 average readability score: 51 nouns: blood; patients; results; test; study; transfusion; tests; testing; donors; group; time; cells; data; samples; methods; cell; patient; treatment; number; disease; cases; plasma; risk; platelet; use; system; years; method; analysis; studies; days; age; donor; antibodies; levels; units; antibody; control; case; day; detection; population; infection; conclusion; sample; symptoms; level; groups; rate; ml verbs: using; show; including; test; performed; increases; based; compared; reports; find; determine; following; detect; identify; evaluated; associated; provide; develop; reduce; require; given; observed; treating; received; making; obtained; collected; assessing; suggests; presenting; considered; aim; related; decreases; improving; taken; confirm; needed; caused; measured; resulting; indicated; demonstrated; induces; investigated; leads; remaining; allows; occurs; analyzed adjectives: positive; clinical; anti; negative; high; different; specific; significant; non; low; higher; first; available; red; new; diagnostic; human; severe; normal; total; allergic; important; many; lower; common; single; whole; similar; mean; medical; respiratory; possible; molecular; several; effective; viral; rapid; large; old; potential; multiple; bacterial; additional; patient; primary; pre; adverse; present; standard; infectious adverbs: also; well; however; significantly; respectively; therefore; even; often; previously; prior; still; highly; currently; clinically; especially; recently; approximately; less; now; statistically; frequently; furthermore; particularly; potentially; commonly; usually; least; later; first; finally; additionally; relatively; mainly; generally; directly; moreover; rather; together; almost; already; alone; successfully; subsequently; yet; fully; typically; much; widely; always; initially pronouns: we; it; our; their; they; its; them; i; he; she; her; his; us; one; you; itself; your; themselves; my; me; him; himself; ourselves; ashcs; s; p210bcr; mg; igg4; yourself; p24ag; fusb; em; siil-33; ocid1001; il-; adrb1; β; y€; y-27632; wether; tssc; srbcs; sont-20; s351; rbcs/100; p<.001; p7sngf; p63rhogef; p206; ours proper nouns: RBC; PCR; mg; C; SARS; COVID-19; CoV-2; Blood; HCV; IgE; HIV; Background; A; T; D; Hb; L; B; AE; Study; ABO; RHD; M; HBV; •; Design; S.; Case; HLA; Transfusion; Studies; Summary; RNA; S; Conclusions; Health; Hospital; Rh; University; IgG; ELISA; IgM; II; RT; NAT; FDA; TM; DNA; PLT; K keywords: test; sars; covid-19; patient; study; pcr; result; method; hiv; cell; group; dna; laboratory; hospital; blood; hbv; treatment; transfusion; system; rna; rhd; rbc; platelet; nat; hla; hcv; fda; donor; diagnostic; dat; anti; abo; testing; sample; poc; ffp; elisa; disease; conclusion; case; antibody; allergic; year; trali; level; day; background; asthma; allergy; virus one topic; one dimension: blood file(s): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3986061/ titles(s): Advantages and Limitations of Anticipating Laboratory Test Results from Regression- and Tree-Based Rules Derived from Electronic Health-Record Data three topics; one dimension: blood; patients; test file(s): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7169716/, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7159469/, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7129916/ titles(s): Abstract Presentations from the AABB Annual Meeting San Diego, CA ctober 7‐10, 2017 | Abstracts TPS | Abstracts cont. five topics; three dimensions: blood transfusion patients; test covid tests; patients asthma study; cells cell effects; test tests testing file(s): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7169716/, https://arxiv.org/pdf/2008.00298v1.pdf, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7159469/, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7100641/, https://doi.org/10.1021/acs.chemrev.8b00136 titles(s): Abstract Presentations from the AABB Annual Meeting San Diego, CA ctober 7‐10, 2017 | What can we learn about SARS-CoV-2 prevalence from testing and hospital data? | Abstracts TPS | Abstracts of the 82(nd) Annual Meeting of the German Society for Experimental and Clinical Pharmacology and Toxicology (DGPT) and the 18(th) Annual Meeting of the Network Clinical Pharmacology Germany (VKliPha) in cooperation with the Arbeitsgemeinschaft für Angewandte Humanpharmakologie e.V. (AGAH) | Inorganic Complexes and Metal-Based Nanomaterials for Infectious Disease Diagnostics Type: cord title: keyword-test-cord date: 2021-05-25 time: 17:03 username: emorgan patron: Eric Morgan email: emorgan@nd.edu input: keywords:test ==== make-pages.sh htm files ==== make-pages.sh complex files ==== make-pages.sh named enities ==== making bibliographics id: cord-117424-mp6h9dyl author: Abraham, Louis title: Bloom Origami Assays: Practical Group Testing date: 2020-07-21 words: 8661.0 sentences: 620.0 pages: flesch: 66.0 cache: ./cache/cord-117424-mp6h9dyl.txt txt: ./txt/cord-117424-mp6h9dyl.txt summary: Given n people, test characteristics tpr & tnr and a set of prior probabilities of sample infection (p i ) 1≤i≤n , the best multiset D of m pool designs is the one maximizing the information gain. While Bloom filters have been considered for the low-prevalence COVID-19 testing problem [19, 12] , current methods are based on a simple randomized encoding and decoding process that was designed for internet-scale applications where even linear time was prohibitive and where the keys are not known beforehand. Assuming there are no false negative pool results, one can use the decoder to identify all positive samples and derive optimal dimensions b × g that minimize the number of tests, as shown in the below theorem: The analysis borrows tools from regular Bloom filters and the results shown in [20] . abstract: We study the problem usually referred to as group testing in the context of COVID-19. Given n samples collected from patients, how should we select and test mixtures of samples to maximize information and minimize the number of tests? Group testing is a well-studied problem with several appealing solutions, but recent biological studies impose practical constraints for COVID-19 that are incompatible with traditional methods. Furthermore, existing methods use unnecessarily restrictive solutions, which were devised for settings with more memory and compute constraints than the problem at hand. This results in poor utility. In the new setting, we obtain strong solutions for small values of n using evolutionary strategies. We then develop a new method combining Bloom filters with belief propagation to scale to larger values of n (more than 100) with good empirical results. We also present a more accurate decoding algorithm that is tailored for specific COVID-19 settings. This work demonstrates the practical gap between dedicated algorithms and well-known generic solutions. Our efforts results in a new and practical multiplex method yielding strong empirical performance without mixing more than a chosen number of patients into the same probe. Finally, we briefly discuss adaptive methods, casting them into the framework of adaptive sub-modularity. url: https://arxiv.org/pdf/2008.02641v1.pdf doi: nan id: cord-127025-9ubhd4vf author: Abraham, Louis title: Crackovid: Optimizing Group Testing date: 2020-05-13 words: 4538.0 sentences: 296.0 pages: flesch: 64.0 cache: ./cache/cord-127025-9ubhd4vf.txt txt: ./txt/cord-127025-9ubhd4vf.txt summary: Our mathematical objective is designed such that the mixture tests it proposes to run in the lab will maximize the amount of information we gain on the ground truth once their lab results are revealed − in expectation, over the randomness of both imperfect tests and prior probabilities of infection per individual. This leads us to the following question: given an initial prior probability distribution p S over the secret, how should we select pool designs to test in the lab? Given numbers n & m, test characteristics tpr & tnr as well as prior probabilities of sample infection p i , the best multiset D of m pool designs is the one maximizing some score, like I(S, T (S, D)) or Confidence(S, T (S, D)). 9 Those prior probabilities can then be readily used by our approach to optimize the pool designs, and the ML system can gradually be improved as we gather more test results. abstract: We study the problem usually referred to as group testing in the context of COVID-19. Given $n$ samples taken from patients, how should we select mixtures of samples to be tested, so as to maximize information and minimize the number of tests? We consider both adaptive and non-adaptive strategies, and take a Bayesian approach with a prior both for infection of patients and test errors. We start by proposing a mathematically principled objective, grounded in information theory. We then optimize non-adaptive optimization strategies using genetic algorithms, and leverage the mathematical framework of adaptive sub-modularity to obtain theoretical guarantees for the greedy-adaptive method. url: https://arxiv.org/pdf/2005.06413v1.pdf doi: nan id: cord-024631-yvek5vjz author: Althaus, T. title: Causes of fever in primary care in Southeast Asia and the performance of C-reactive protein in discriminating bacterial from viral pathogens date: 2020-05-11 words: 4327.0 sentences: 226.0 pages: flesch: 43.0 cache: ./cache/cord-024631-yvek5vjz.txt txt: ./txt/cord-024631-yvek5vjz.txt summary: OBJECTIVES: We investigated causes of fever in the primary levels of care in Southeast Asia, and evaluated whether C-reactive protein (CRP) could distinguish bacterial from viral pathogens. In this study, we aim to identify key organisms among acutely febrile children and adults attending primary health care in Southeast Asia, and to evaluate the performance of CRP for discriminating between bacteria and viruses. Specimens were collected from febrile patients recruited into a previously described multi-centre randomised-controlled trial evaluating the impact of C-reactive protein (CRP) testing on antibiotic prescription in primary care [38] . We investigated the spectrum of organisms among febrile children and adults in the community and evaluated the performance of CRP in distinguishing bacteria from viruses including its potential impact on antibiotic prescription compared with current practice. Investigating non-malarial acute febrile illness remains challenging in resource-poor areas [8] , and despite screening for multiple organisms on blood and respiratory specimens, we were only able to identify a probable cause of fever in 227 (29.4%) of patients. abstract: OBJECTIVES: We investigated causes of fever in the primary levels of care in Southeast Asia, and evaluated whether C-reactive protein (CRP) could distinguish bacterial from viral pathogens. METHODS: Blood and nasopharyngeal swab specimens were taken from children and adults with fever (>37.5˚C) or history of fever (<14 days) in Thailand and Myanmar. RESULTS: Of 773 patients with at least one blood or nasopharyngeal swab specimen collected, 227 (29.4%) had a target organism detected. Influenza virus type A was detected in 85/227 cases (37.5%), followed by dengue virus (30 cases, 13.2%), respiratory syncytial virus (24 cases, 10.6%) and Leptospira spp. (9 cases, 4.0%). Clinical outcome was similar between patients with a bacterial or a viral organism, regardless of antibiotic prescription. CRP was higher among patients with a bacterial organism compared to those with a viral organism (median 18 mg/L, interquartile range [10-49] versus 10 mg/L [≤8-22], p-value 0.003), with an area under the curve of 0.65, 95% confidence interval (0.55-0.75). CONCLUSIONS: Serious bacterial infections requiring antibiotics are exceptions rather than the rule in the first lines of care. CRP-testing could assist in ruling out such cases in settings where diagnostic uncertainty is high and routine antibiotic prescription is common. The original CRP randomised-controlled trial (RCT) was registered with ClinicalTrials.gov, number NCT02758821. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7211754/ doi: 10.1016/j.ijid.2020.05.016 id: cord-324373-mgdtb98z author: Antonelli, Andrea title: Comparison between the Airgo™ Device and a Metabolic Cart during Rest and Exercise † date: 2020-07-15 words: 7608.0 sentences: 306.0 pages: flesch: 45.0 cache: ./cache/cord-324373-mgdtb98z.txt txt: ./txt/cord-324373-mgdtb98z.txt summary: The goal of the presented work is to compare a metabolic cart, considered a gold standard, with Airgo™ (MYAIR Inc, Boston, MA, USA; MyAirgo Italy Srl, Milan, Italy), a resistance-based wearable device able to derive breathing parameters from body surface motion detection acquired at the level of the lower ribcage. The comparison of the Airgo™ device with the metabolic cart showed that the respiratory rate was the most accurate parameter, in all positions, for both rest and exercise tests in all conditions of physical effort: medians were always positioned on the zero error line with low dispersion around this value. The comparison of the Airgo™ device with the metabolic cart showed that the respiratory rate was the most accurate parameter, in all positions, for both rest and exercise tests in all conditions of physical effort: medians were always positioned on the zero error line with low dispersion around this value. abstract: The aim of this study is to compare the accuracy of Airgo™, a non-invasive wearable device that records breath, with respect to a gold standard. In 21 healthy subjects (10 males, 11 females), four parameters were recorded for four min at rest and in different positions simultaneously by Airgo™ and SensorMedics 2900 metabolic cart. Then, a cardio-pulmonary exercise test was performed using the Erg 800S cycle ergometer in order to test Airgo™’s accuracy during physical effort. The results reveal that the relative error median percentage of respiratory rate was of 0% for all positions at rest and for different exercise intensities, with interquartile ranges between 3.5 (standing position) and 22.4 (low-intensity exercise) breaths per minute. During exercise, normalized amplitude and ventilation relative error medians highlighted the presence of an error proportional to the volume to be estimated. For increasing intensity levels of exercise, Airgo™’s estimate tended to underestimate the values of the gold standard instrument. In conclusion, the Airgo™ device provides good accuracy and precision in the estimate of respiratory rate (especially at rest), an acceptable estimate of tidal volume and minute ventilation at rest and an underestimation for increasing volumes. url: https://www.ncbi.nlm.nih.gov/pubmed/32679882/ doi: 10.3390/s20143943 id: cord-343340-zi0rfidc author: Aragón‐Caqueo, Diego title: Optimization of group size in pool testing strategy for SARS‐CoV‐2: A simple mathematical model date: 2020-05-03 words: 3319.0 sentences: 155.0 pages: flesch: 51.0 cache: ./cache/cord-343340-zi0rfidc.txt txt: ./txt/cord-343340-zi0rfidc.txt summary: The aim of this study is to propose a simple mathematical model to estimate the optimum number of pooled samples according to the relative prevalence of positive tests in a particular healthcare context, assuming that if a group tests negative, no further testing is done whereas if a group tests positive, all the subjects of the group are retested individually. Therefore, the aim of this study is to provide a mathematical model to estimate the optimum number of pooled samples according to the specific prevalences of positive tests in a particular country context, in order to save as many tests as possible and cover as many people as possible, knowing that if a group tests out positive, all the individuals of the sample would have to be individually tested. This article proposed a simple and landed model to estimate the most optimum group number to implement pool testing strategy for SARS-CoV-2, according to the specific historical positive tests prevalence for a determined healthcare context. abstract: Coronavirus disease (Covid‐19) has reached unprecedented pandemic levels and is affecting almost every country in the world. Ramping up the testing capacity of a country supposes an essential public health response to this new outbreak. A pool testing strategy where multiple samples are tested in a single reverse transcriptase‐polymerase chain reaction (RT‐PCR) kit could potentially increase a country's testing capacity. The aim of this study is to propose a simple mathematical model to estimate the optimum number of pooled samples according to the relative prevalence of positive tests in a particular healthcare context, assuming that if a group tests negative, no further testing is done whereas if a group tests positive, all the subjects of the group are retested individually. The model predicts group sizes that range from 11 to 3 subjects. For a prevalence of 10% of positive tests, 40.6% of tests can be saved using testing groups of four subjects. For a 20% prevalence, 17.9% of tests can be saved using groups of three subjects. For higher prevalences, the strategy flattens and loses effectiveness. Pool testing individuals for severe acute respiratory syndrome coronavirus 2 is a valuable strategy that could considerably boost a country's testing capacity. However, further studies are needed to address how large these groups can be, without losing sensitivity on the RT‐PCR. The strategy best works in settings with a low prevalence of positive tests. It is best implemented in subgroups with low clinical suspicion. The model can be adapted to specific prevalences, generating a tailored to the context implementation of the pool testing strategy. url: https://doi.org/10.1002/jmv.25929 doi: 10.1002/jmv.25929 id: cord-226956-n5qwsvtr author: Arbia, Giuseppe title: A Note on Early Epidemiological Analysis of Coronavirus Disease 2019 Outbreak using Crowdsourced Data date: 2020-03-13 words: 1763.0 sentences: 73.0 pages: flesch: 44.0 cache: ./cache/cord-226956-n5qwsvtr.txt txt: ./txt/cord-226956-n5qwsvtr.txt summary: However, the use of crowdsourcing data raises a number of problems from the statistical point of view which run the risk of invalidating the results and of biasing estimation and hypothesis testing. In the paper the crowdsourced data, coming from different sources, are used to estimate several epidemiological parameters of tremendous importance in the process of surveillance and control of the diffusion of the disease such as: The relative risk by age group, the mean age and skewness of infected people, the time of delays between symptoms and seeking care at hospital, the mean incubation period. However, even if data were collected obeying a formal sample design, a further potential source of bias is the fact that the observational units could display a certain degree of spatial/network correlation (Cliff and Ord, 1973; Arbia, 2006) . abstract: Crowdsourcing data can prove of paramount importance in monitoring and controlling the spread of infectious diseases. The recent paper by Sun, Chen and Viboud (2020) is important because it contributes to the understanding of the epidemiology and of the spreading of Covid-19 in a period when most of the epidemic characteristics are still unknown. However, the use of crowdsourcing data raises a number of problems from the statistical point of view which run the risk of invalidating the results and of biasing estimation and hypothesis testing. While the work by Sun, Chen and Viboud (2020) has to be commended, given the importance of the topic for worldwide health security, in this paper we deem important to remark the presence of the possible sources of statistical biases and to point out possible solutions to them url: https://arxiv.org/pdf/2003.06207v1.pdf doi: nan id: cord-325455-e464idc0 author: Atchison, Christina title: Usability and acceptability of home-based self-testing for SARS-CoV-2 antibodies for population surveillance date: 2020-08-12 words: 3279.0 sentences: 204.0 pages: flesch: 57.0 cache: ./cache/cord-325455-e464idc0.txt txt: ./txt/cord-325455-e464idc0.txt summary: BACKGROUND: This study assesses acceptability and usability of home-based self-testing for SARS-CoV-2 antibodies using lateral flow immunoassays (LFIA). On a population level, by conducting seroprevalence surveys through widespread random sampling of the general public, and by adjusting for the sensitivity and specificity characteristics of the LFIA used, it is possible to estimate the levels of past infection with SARS-CoV-2 in the community (3) . Usability research on HIV selftesting has generally found good acceptability, the devices easy to use and high validity in interpretation of self-reported test results (7) (8) (9) . To mitigate against this, and given the scientific Our study is original because focusing on the acceptability and usability of LFIAs for self-testing for SARS-CoV-2 antibody in a home-based setting has not been done at such scale in the general population. Overall, our study has demonstrated that home-based self-testing LFIAs for use in large communitybased seroprevalence surveys of SARS-CoV-2 antibody are both acceptable and feasible. abstract: BACKGROUND: This study assesses acceptability and usability of home-based self-testing for SARS-CoV-2 antibodies using lateral flow immunoassays (LFIA). METHODS: We carried out public involvement and pilot testing in 315 volunteers to improve usability. Feedback was obtained through online discussions, questionnaires, observations and interviews of people who tried the test at home. This informed the design of a nationally representative survey of adults in England using two LFIAs (LFIA1 and LFIA2) which were sent to 10,600 and 3,800 participants, respectively, who provided further feedback. RESULTS: Public involvement and pilot testing showed high levels of acceptability, but limitations with the usability of kits. Most people reported completing the test; however, they identified difficulties with practical aspects of the kit, particularly the lancet and pipette, a need for clearer instructions and more guidance on interpretation of results. In the national study, 99.3% (8,693/8,754) of LFIA1 and 98.4% (2,911/2,957) of LFIA2 respondents attempted the test and 97.5% and 97.8% of respondents completed it, respectively. Most found the instructions easy to understand, but some reported difficulties using the pipette (LFIA1: 17.7%) and applying the blood drop to the cassette (LFIA2: 31.3%). Most respondents obtained a valid result (LFIA1: 91.5%; LFIA2: 94.4%). Overall there was substantial concordance between participant and clinician interpreted results (kappa: LFIA1 0.72; LFIA2 0.89). CONCLUSION: Impactful public involvement is feasible in a rapid response setting. Home self-testing with LFIAs can be used with a high degree of acceptability and usability by adults, making them a good option for use in seroprevalence surveys. url: https://doi.org/10.1093/cid/ciaa1178 doi: 10.1093/cid/ciaa1178 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-300520-vxn7uh41 author: Baunez, C. title: Tracking the Dynamics and Allocating Tests for COVID-19 in Real-Time: an Acceleration Index with an Application to French Age Groups and Departments date: 2020-11-07 words: 10376.0 sentences: 513.0 pages: flesch: 59.0 cache: ./cache/cord-300520-vxn7uh41.txt txt: ./txt/cord-300520-vxn7uh41.txt summary: Using French data on cases and tests for the period following the first lock-down from May 13, 2020, onwards our acceleration index shows that the ongoing pandemic resurgence can be dated to begin around July 7. We propose a parsimonious algorithm to allocate tests across age groups and space, based on both our acceleration index and the average positivity rate, and on the extent to which tests reduce the virus propagation. We argue that such reasoning is wrong and that the correct understanding, in terms of measuring the acceleration/deceleration of the pandemic, is gained if a scatter-plot of the number of positive cases against the number of the tests is used in real time, instead of the panels in Figure 1 . abstract: An acceleration index is proposed as a novel indicator to track the dynamics of the COVID-19 in real-time. Using French data on cases and tests for the period following the first lock-down - from May 13, 2020, onwards - our acceleration index shows that the ongoing pandemic resurgence can be dated to begin around July 7. It uncovers that the pandemic acceleration has been stronger than national average for the [59-68] and [69-78] age groups since early September, the latter being associated with the strongest acceleration index, as of October 25. In contrast, acceleration among the [19-28] age group is the lowest and is about half that of the [69-78], as of October 25. In addition, we propose an algorithm to allocate tests among French departments, based on both the acceleration index and the feedback effect of testing. Our acceleration-based allocation differs from the actual distribution over French territories, which is population-based. We argue that both our acceleration index and our allocation algorithm are useful tools to guide public health policies as France enters a second lock-down period with indeterminate duration. url: http://medrxiv.org/cgi/content/short/2020.11.05.20226597v1?rss=1 doi: 10.1101/2020.11.05.20226597 id: cord-300930-47a4pu27 author: Beigel, R. title: Rate Estimation and Identification of COVID-19 Infections: Towards Rational Policy Making During Early and Late Stages of Epidemics date: 2020-05-24 words: 4535.0 sentences: 366.0 pages: flesch: 64.0 cache: ./cache/cord-300930-47a4pu27.txt txt: ./txt/cord-300930-47a4pu27.txt summary: Mathematically, the problems of identifying infected individuals ( identification ) and estimating the total number of infected individuals in a given population ( infection rate ) are related but in fact can be addressed by subtly different algorithms to reduce the number of tests needed and thereby the total cost of doing testing. However, as we will demonstrate in this brief communication, estimating the number of infected individuals can be solved by novel adaptation of methods developed in theoretical computer science aimed at approximate counting. In addition to rate estimation we provide a review and analysis of several identification algorithms that can be deployed in communities with low infection rates that achieve reasonable improvement over the standard algorithms for group testing that have been previously explored. • Estimate the rate of the infection in the population or approximately count how many people test positive in a population of a given size with as few partially pooled tests as possible. We now describe approximate counting algorithms that use pools of samples to estimate accurate infection rates. abstract: Pandemics have a profound impact on our world, causing loss of life, affecting our culture and historically shaping our genetics. The response to a pandemic requires both resilience and imagination. It has been clearly documented that obtaining an accurate estimate and trends of the actual infection rate and mortality risk are very important for policy makers and medical professionals. One cannot estimate mortality rates without an accurate assessment of the number of infected individuals in the population. This need is also aligned with identifying the infected individuals so they can be properly treated, monitored and tracked. However, accurate estimation of the infection rate, locally, geographically and nationally is important independently. These infection rate estimates can guide policy makers at both state, national or world level to achieve a better management of risk to society. The decisions facing policy makers are very different during early stages of an emerging epidemic where the infection rate is low, middle stages where the rate is rapidly climbing, and later stages where the epidemic curve has flattened to a low and relatively sustainable rate. In this paper we provide relatively efficient pooling methods to both estimate infection rates and identify infected individuals for populations with low infection rates. These estimates may provide significant cost reductions for testing in rural communities, third world countries and other situations where the cost of testing is expensive or testing is not widely available. As we prepare for the second wave of the pandemic this line of work may provide new solutions for both the biomedical community and policy makers at all levels. url: https://doi.org/10.1101/2020.05.22.20110585 doi: 10.1101/2020.05.22.20110585 id: cord-272995-yvj2pqh1 author: Bergman, Christian title: Recommendations for Welcoming Back Nursing Home Visitors during the COVID-19 Pandemic: Results of a Delphi Panel date: 2020-10-07 words: 6339.0 sentences: 340.0 pages: flesch: 51.0 cache: ./cache/cord-272995-yvj2pqh1.txt txt: ./txt/cord-272995-yvj2pqh1.txt summary: Regarding visitor guidance, the panel made five strong recommendations: 1) maintain strong infection prevention and control precautions, 2) facilitate indoor and outdoor visits, 3) allow limited physical contact with appropriate precautions, 4) assess individual residents'' care preferences and level of risk tolerance, and 5) dedicate an essential caregiver and extend the definition of compassionate care visits to include care that promotes psychosocial wellbeing of residents. We edited the final guidance statements for clarity, aiming to capture the consensus of the Delphi aspects of the following topics (see Table 1 ): testing of asymptomatic staff and residents, 111 surveillance testing, visitor guidance, immunity from prior COVID-19 infection and associated 112 risk of infecting others. The panel 144 strongly agreed on some preconditions that would be essential prior to welcoming back visitors, 145 such as universal masking for staff, sufficient disinfecting supplies, PPE, and written plans 146 around isolation, cohorting, screening, testing, and outbreak investigations. abstract: Objectives Nursing homes became epicenters of COVID-19 in the spring of 2020. Due to the substantial case fatality rates within congregate settings, federal agencies recommended restrictions to family visits. Six months into the COVID-19 pandemic, these largely remain in place. The objective of this study was to generate consensus guidance statements focusing on essential family caregivers and visitors. Design A modified two-step Delphi process was used to generate consensus statements. Setting and Participants The Delphi panel consisted of 21 US and Canadian post-acute and long-term care experts in clinical medicine, administration, and patient care advocacy. Methods State and federal reopening statements were collected in June 2020 and the panel voted on these using a three-point Likert scale with consensus defined as ≥80% of panel members voting “Agree.” The consensus statements then informed development of the visitor guidance statements. Results The Delphi process yielded 77 consensus statements. Regarding visitor guidance, the panel made five strong recommendations: 1) maintain strong infection prevention and control precautions, 2) facilitate indoor and outdoor visits, 3) allow limited physical contact with appropriate precautions, 4) assess individual residents' care preferences and level of risk tolerance, and 5) dedicate an essential caregiver and extend the definition of compassionate care visits to include care that promotes psychosocial wellbeing of residents. Conclusions and Implications The COVID-19 pandemic has seen substantial regulatory changes without strong consideration of the impact on residents. In the absence of timely and rigorous research, the involvement of clinicians and patient care advocates is important to help create the balance between individual resident preferences and the health of the collective. The results of this evidence-based Delphi process will help guide policy decisions as well as inform future research. url: https://www.sciencedirect.com/science/article/pii/S1525861020308367?v=s5 doi: 10.1016/j.jamda.2020.09.036 id: cord-225183-6rusimb5 author: Boukai, Ben title: Bayesian Modeling of COVID-19 Positivity Rate -- the Indiana experience date: 2020-07-09 words: 3108.0 sentences: 235.0 pages: flesch: 68.0 cache: ./cache/cord-225183-6rusimb5.txt txt: ./txt/cord-225183-6rusimb5.txt summary: In this short technical report we model, within the Bayesian framework, the rate of positive tests reported by the the State of Indiana, accounting also for the substantial variability (and overdispeartion) in the daily count of the tests performed. In this report we model, within the Bayesian framework, the rate of positive tests reported by the the State of Indiana, accounting also for the substantial variability of the daily number test performed. Remark: The choice in (2) for using the Negative Binomial distribution to model the reported daily number of tests k i , could be seen as specific to the Indiana COVID-19 testing data, which might reflect testing capacity limitation and daily variability unique to that state. In a similar manner we obtain the posterior predictive distribution under this Bayesian model and given (X m , N m ), of a ''new'' (or ''future'') number of tests K * is the Beta-Negative Binomial distribution. abstract: In this short technical report we model, within the Bayesian framework, the rate of positive tests reported by the the State of Indiana, accounting also for the substantial variability (and overdispeartion) in the daily count of the tests performed. The approach we take, results with a simple procedure for prediction, a posteriori, of this rate of 'positivity' and allows for an easy and a straightforward adaptation by any agency tracking daily results of COVID-19 tests. The numerical results provided herein were obtained via an updatable R Markdown document. url: https://arxiv.org/pdf/2007.06541v1.pdf doi: nan id: cord-315077-i1xjcuae author: Branda, John A. title: Utilization management in microbiology date: 2014-01-01 words: 4117.0 sentences: 200.0 pages: flesch: 35.0 cache: ./cache/cord-315077-i1xjcuae.txt txt: ./txt/cord-315077-i1xjcuae.txt summary: The results of testing in the microbiology laboratory have significant effects on the cost of clinical care, especially costs related to antimicrobial agents and infection control practices. Consequently many of the successful utilization management interventions described in clinical microbiology have targeted not just the volume of tests performed in the laboratory, but also the downstream costs of care. In a number of cases, the initiative''s success arose not only from a reduction in laboratory testing per se, but rather also from its impact in the clinical care arena (for example, a reduction in antibiotic use or hospital length of length-of-stay). Each day, a microbiology fellow and laboratory director review the clinical history, culture results and susceptibility test results for all patients newly started on a carbapenem, to determine appropriate versus inappropriate use of the drugs. abstract: The available literature concerning utilization management in the clinical microbiology laboratory is relatively limited compared with that for high-volume, automated testing in the central Core Laboratory. However, the same strategies employed elsewhere in the clinical laboratory operation can be applied to utilization management challenges in microbiology, including decision support systems, application of evidence-based medicine, screening algorithms and gatekeeper functions. The results of testing in the microbiology laboratory have significant effects on the cost of clinical care, especially costs related to antimicrobial agents and infection control practices. Consequently many of the successful utilization management interventions described in clinical microbiology have targeted not just the volume of tests performed in the laboratory, but also the downstream costs of care. This article will review utilization management strategies in clinical microbiology, including specific examples from our institution and other healthcare organizations. url: https://www.ncbi.nlm.nih.gov/pubmed/24080434/ doi: 10.1016/j.cca.2013.09.031 id: cord-310714-kqzlwka0 author: Braz, Lucia Maria Almeida title: Visceral Leishmaniasis diagnosis: a rapid test is a must at the hospital bedside date: 2020-06-16 words: 1366.0 sentences: 76.0 pages: flesch: 55.0 cache: ./cache/cord-310714-kqzlwka0.txt txt: ./txt/cord-310714-kqzlwka0.txt summary: At the time of the widespread availability of rapid diagnostic tests for SARS-CoV-2-the causative virus of the COVID-19 pandemic-from drugstores throughout Brazil, there is a distinct lack of use of rapid diagnostic tests for visceral leishmaniasis (VL) at the bedsides of hospitalized patients. As stated by the MS, VL case confirmation is based on clinical suspicion and positive laboratory diagnosis via either parasitological tests (PTs), which are dependent on invasive procedures such as bone marrow aspiration or biopsy, or serological tests such as indirect immunofluorescence (IFI) or immunochromatographic tests (ITs) using rK39 recombinant antigens (5) . The main brands of IT-rK39 that were previously provided by the Brazilian public health system consisted of Kalazar Detectt (InBios International, Seattle, WA, USA), IT LEISH s (BIO-RAD Laboratories Inc., France), and OnSitet Leishmania IgG/IgM Combo test (CTK Biotech, USA), which have now been replaced with the LSH Ab ECO test (Eco Diagnóstica, Nova Lima, MG, Brasil). abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32578827/ doi: 10.6061/clinics/2020/e2036 id: cord-319436-mlitd45q author: Brinati, D. title: Detection of COVID-19 Infection from Routine Blood Exams with Machine Learning: a Feasibility Study date: 2020-04-25 words: 4603.0 sentences: 237.0 pages: flesch: 51.0 cache: ./cache/cord-319436-mlitd45q.txt txt: ./txt/cord-319436-mlitd45q.txt summary: Amplification of viral RNA by (real time) reverse transcription polymerase chain reaction (rRT-PCR) is the current gold standard test for confirmation of infection, although it presents known shortcomings: long turnaround times (3-4 hours to generate results), potential shortage of reagents, false-negative rates as large as 15-20%, the need for certified laboratories, expensive equipment and trained personnel. Material and methods We developed two machine learning classification models using hematochemical values from routine blood exams (namely: white blood cells counts, and the platelets, CRP, AST, ALT, GGT, ALP, LDH plasma levels) drawn from 279 patients who, after being admitted to the San Raffaele Hospital (Milan, Italy) emergency-room with COVID-19 symptoms, were screened with the rRT-PCR test performed on respiratory tract specimens. The best performing model, i.e. the Random Forest classifier, trained on dataset B, achieved the following results on the test/validation set: accuracy = 82% , sensitivity = 92%, PPV = 83%, specificity = 65%, AUC = 84%. abstract: Background - The COVID-19 pandemia due to the SARS-CoV-2 coronavirus, in its first 4 months since its outbreak, has to date reached more than 200 countries worldwide with more than 2 million confirmed cases (probably a much higher number of infected), and almost 200,000 deaths. Amplification of viral RNA by (real time) reverse transcription polymerase chain reaction (rRT-PCR) is the current gold standard test for confirmation of infection, although it presents known shortcomings: long turnaround times (3-4 hours to generate results), potential shortage of reagents, false-negative rates as large as 15-20%, the need for certified laboratories, expensive equipment and trained personnel. Thus there is a need for alternative, faster, less expensive and more accessible tests. Material and methods - We developed two machine learning classification models using hematochemical values from routine blood exams (namely: white blood cells counts, and the platelets, CRP, AST, ALT, GGT, ALP, LDH plasma levels) drawn from 279 patients who, after being admitted to the San Raffaele Hospital (Milan, Italy) emergency-room with COVID-19 symptoms, were screened with the rRT-PCR test performed on respiratory tract specimens. Of these patients, 177 resulted positive, whereas 102 received a negative response. Results - We have developed two machine learning models, to discriminate between patients who are either positive or negative to the SARS-CoV-2: their accuracy ranges between 82% and 86%, and sensitivity between 92% e 95%, so comparably well with respect to the gold standard. We also developed an interpretable Decision Tree model as a simple decision aid for clinician interpreting blood tests (even off-line) for COVID-19 suspect cases. Discussion - This study demonstrated the feasibility and clinical soundness of using blood tests analysis and machine learning as an alternative to rRT-PCR for identifying COVID-19 positive patients. This is especially useful in those countries, like developing ones, suffering from shortages of rRT-PCR reagents and specialized laboratories. We made available a Web-based tool for clinical reference and evaluation. This tool is available at https://covid19-blood-ml.herokuapp.com. url: http://medrxiv.org/cgi/content/short/2020.04.22.20075143v1?rss=1 doi: 10.1101/2020.04.22.20075143 id: cord-021550-evh3b7o2 author: Brokopp, Charles title: Laboratories date: 2007-09-02 words: 9259.0 sentences: 436.0 pages: flesch: 34.0 cache: ./cache/cord-021550-evh3b7o2.txt txt: ./txt/cord-021550-evh3b7o2.txt summary: Federal, state, and local government agencies, such as health departments, operate laboratories or contract with commercial laboratories for testing related to diagnosis, regulatory compliance, investigations, and environmental monitoring. CDC-based scientists have developed and used new technologies to identify outbreaks of disease in cooperation with state and local public health laboratories. The DOE national laboratories develop new technologies for countering biologic and chemical threats, including systems for the detection, modeling, and response to terrorist attacks (see www-ed.fnal.gov/doe/ doc_labs.html). Many state and locally operated laboratories in addition to clinical and public health laboratories produce test results that may be useful for surveillance. The mission of the LRN is "to maintain an integrated national and international network of laboratories that can respond quickly to acts of chemical or biological terrorism, emerging infectious diseases and other public health threats and emergencies." The LRN was first tasked to address state and local public health laboratory preparedness and response for bioterrorism. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7150189/ doi: 10.1016/b978-012369378-5/50010-7 id: cord-023584-yaxawqhj author: Bucknall, R.A. title: The Continuing Search for Antiviral Drugs date: 2008-04-10 words: 8497.0 sentences: 339.0 pages: flesch: 48.0 cache: ./cache/cord-023584-yaxawqhj.txt txt: ./txt/cord-023584-yaxawqhj.txt summary: Of course, if wide-spectrum leads appear, the choice of test virus may be irrelevant, but the antiviral compounds (as distinct from interferon inducers) known at present are characterized by their relatively limited spectrum of activity, e.g., methisazone is active only against poxviruses (Bauer and Sadler, 1960) and possibly adenoviruses (Bauer and Apostolov, 1966) ; l-aminoadamantane is active only against influenza A1 and As and not against other myxo-or paramyxoviruses (Davies et al., 1964) ; guanidine and a-hydroxybenzyl benzimidazole are active only against picornaviruses and not against other small ribonucleic acid (RNA) viruses (Eggers and Tamm, 1961) . In summary, a tissue culture screen should be able to proccss large numbers of tcst compounds, using viruses as relevant as possible to the diseases for which a drug is required, and should employ normal rather than neoplastic cells. abstract: This chapter discusses the continuing search for antiviral drugs. Many virus diseases, both of humans and animals, have been successfully controlled by vaccines. These successes have naturally led to improvements in the spectrum and duration of protection offered by vaccines until, at present it is difficult to see how antiviral drugs could compete with vaccines in the control of many virus diseases. One may cite smallpox, yellow fever, polio, and recently measles among human diseases, Newcastle disease, Marek's disease, and infectious bronchitis among poultry diseases—an area of veterinary disease control where vaccines have been particularly important. Research into the treatment of virus diseases by drugs is at present directed toward three general areas: (1) attempts to stimulate the defense mechanism of the host animal, (2) large screening programs to find drugs which directly block some virus-specific process, and (3) alleviation of the symptoms of the disease. The treatment of the symptoms, rather than the cause of a disease, has been the mainstay of medical practice from time immemorial, and this is still the case with most virus disease. The short incubation period of many virus diseases will inevitably restrict the therapeutic use of antiviral drugs and in cases where symptoms have already appeared. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7172480/ doi: 10.1016/s1054-3589(08)60460-3 id: cord-278377-jgq3dz3u author: Busson, L. title: Prospective evaluation of diagnostic tools for respiratory viruses in children and adults date: 2019-01-15 words: 4155.0 sentences: 199.0 pages: flesch: 48.0 cache: ./cache/cord-278377-jgq3dz3u.txt txt: ./txt/cord-278377-jgq3dz3u.txt summary: METHODS: Two hundred ninety-nine respiratory samples were prospectively explored using multiplex molecular techniques (FilmArray Respiratory Panel, Clart Pneumovir), immunological techniques (direct fluorescent assay, lateral flow chromatography) and cell cultures. Meanwhile, important questions concerning these ''new'' expensive rapid molecular techniques remain unanswered, such as their cost-effectiveness in terms of patient''s management, or the clinical significance of detecting nucleic acids of micro-organisms that could be non-infectious at the time the sample is collected. The objective of this work was to compare the performances of antigen detection and cell cultures techniques routinely used since years for the diagnosis of respiratory viral infections in the setting of a tertiary care hospital to those of newer molecular techniques (Clart Pneumovir, Genomica, Coslada, Spain and FilmArray Respiratory Panel, Biofire, Biomérieux, Marcy L''Etoile, France). False negative results with molecular techniques were significantly more frequent in samples with codetections compared to those with only one pathogen: 12% vs 3% for the FilmArray test (p = 0.034) and 76% vs 11% for the Clart Pneumovir test (p < 0.001). abstract: AIM: To compare the performances of molecular and non-molecular tests to diagnose respiratory viral infections and to evaluate the pros and contras of each technique. METHODS: Two hundred ninety-nine respiratory samples were prospectively explored using multiplex molecular techniques (FilmArray Respiratory Panel, Clart Pneumovir), immunological techniques (direct fluorescent assay, lateral flow chromatography) and cell cultures. FINDINGS: Molecular techniques permitted the recovery of up to 50% more respiratory pathogens in comparison to non-molecular methods. FilmArray detected at least 30% more pathogens than Clart Pneumovir which could be explained by the differences in their technical designs. The turnaround time under 2 hours for the FilmArray permitted delivery of results when patients were still in the emergency room. url: https://api.elsevier.com/content/article/pii/S0166093418303203 doi: 10.1016/j.jviromet.2019.01.006 id: cord-271920-1dzkgt6w author: Carpenter, Christopher R. title: Diagnosing COVID‐19 in the Emergency Department: A Scoping Review of Clinical Exam, Labs, Imaging Accuracy and Biases date: 2020-06-16 words: 7248.0 sentences: 523.0 pages: flesch: 48.0 cache: ./cache/cord-271920-1dzkgt6w.txt txt: ./txt/cord-271920-1dzkgt6w.txt summary: 3 As waves of COVID-19 patients present to ED''s in coming months with symptoms or potential exposures, understanding the diagnostic accuracy and reliability of history, physical exam, routine labs, advanced imaging, and an evolving array of COVID-19 diagnostics will be essential knowledge to inform the timing of testing, optimal specimen and test selection, shared decision-making, and ultimately derivation of clinical instruments to guide disposition, follow-up, and shared The search strategy used a combination of standardized terms and key words, including but not limited to (Covid-19 OR Novel Coronavirus OR SARS-COV-2) AND (diagnosis OR polymerase chain reaction OR serology OR CRISPR-CAS OR sensitivity/specificity) (Appendix). 40,42 It is known, however, that false negatives are frequent, so current recommendations advise incorporating patient''s exposure risk, clinical signs and symptoms, routine lab and imaging findings, serology, and (when available) CT results into real-time determination of COVID-19 status. abstract: In December 2019 a novel viral respiratory pathogen emerged in China, ultimately named severe acute respiratory syndrome coronavirus 2 (SARS‐Co‐V‐2) with the clinical illness dubbed coronavirus disease (COVID‐19). COVID‐19 became a global pandemic in early 2020 forcing governments worldwide to enact social isolation policies with dire economic ramifications. Emergency departments (ED) encountered decreased patient volumes before some in Seattle, New York City, New Orleans, and Detroit experienced waves of COVID‐19 patients mixed with asymptomatic patients or those concerned about potential exposures. Diagnosing COVID‐19 was hampered by inadequate supplies of reagents and kits, which was compounded by clinical and radiographic features that overlap with numerous seasonal viral respiratory infections. url: https://doi.org/10.1111/acem.14048 doi: 10.1111/acem.14048 id: cord-330721-hmnrnem6 author: Chambliss, Allison B title: Contingency planning in the clinical laboratory: lessons learned amidst COVID-19 date: 2020-04-21 words: 1248.0 sentences: 84.0 pages: flesch: 55.0 cache: ./cache/cord-330721-hmnrnem6.txt txt: ./txt/cord-330721-hmnrnem6.txt summary: The laboratory should begin contingency planning by assessing baseline operational status, which benches can be offered less frequently (batched as sample stability allows), which can be closed altogether, and the resultant minimum number of staff required to support emergent testing ( Tests that will need to be maintained include complete blood counts, metabolic panels, routine coagulation, troponin, liver function tests, blood gases, and inflammatory markers such as C-reactive protein, lactate dehydrogenase, and procalcitonin (4, 5) . In times of particularly critical shortages of staff and/or reagents, with proper agreement of hospital leadership and use of mass notification mechanisms, non-emergent tests could be temporarily masked from providers in the test ordering system and eliminate the laboratory from receiving them in the first place. Using the Chemistry section as an example, a similar contingency planning tool can be used across core clinical lab specialties to assess benches/testing that can be performed depending upon available staffing. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32603440/ doi: 10.1093/jalm/jfaa068 id: cord-281495-beb164oy author: Charpentier, Charlotte title: Performance evaluation of two SARS-CoV-2 IgG/IgM rapid tests (Covid-Presto and NG-Test) and one IgG automated immunoassay (Abbott) date: 2020-09-03 words: 2375.0 sentences: 122.0 pages: flesch: 59.0 cache: ./cache/cord-281495-beb164oy.txt txt: ./txt/cord-281495-beb164oy.txt summary: title: Performance evaluation of two SARS-CoV-2 IgG/IgM rapid tests (Covid-Presto and NG-Test) and one IgG automated immunoassay (Abbott) The aim of this study was to assess the analytical performances, sensitivity and specificity, of two rapid tests (CovidPresto® test rapid Covid-19 IgG/IgM and NG-Test® IgM-IgG COVID-19) and one automated immunoassay (Abbott SARS-CoV-2 IgG) for detecting antiSARS-CoV-2 antibodies. The aim of this study was to assess the analytical performances (sensitivity and specificity) and agreement of two rapid tests and one automated immunoassay for detecting antibodies against SARS-CoV-2. In the present study, we evaluated two different lateral flow tests (Covid-Presto ® and NG-Test ® ) and compared their performances to that of the automated Abbott immunoassay using the same samples panel. Sensitivity for IgG in samples collected later than 10 days after symptoms onset was excellent with the different tests being equal to 97.1%, 96.2% and 100% for Covid-Presto ® , NG-Test ® , and Abbott, respectively. abstract: The aim of this study was to assess the analytical performances, sensitivity and specificity, of two rapid tests (Covid- Presto® test rapid Covid-19 IgG/IgM and NG-Test® IgM-IgG COVID-19) and one automated immunoassay (Abbott SARS-CoV-2 IgG) for detecting anti- SARS-CoV-2 antibodies. This study was performed with: (i) a positive panel constituted of 88 SARS-CoV-2 specimens collected from patients with a positive SARS-CoV-2 RT-PCR, and (ii) a negative panel of 120 serum samples, all collected before November 2019, including 64 samples with a cross-reactivity panel. Sensitivity of Covid-Presto® test for IgM and IgG was 78.4% and 92.0%, respectively. Sensitivity of NG-Test® for IgM and IgG was 96.6% and 94.9%, respectively. Sensitivity of Abbott IgG assay was 96.5% showing an excellent agreement with the two rapid tests (κ = 0.947 and κ = 0.936 for NGTest ® and Covid-Presto® test, respectively). An excellent agreement was also observed between the two rapid tests (κ = 0.937). Specificity for IgM was 100% and 86.5% for Covid-Presto® test and NG-Test®, respectively. Specificity for IgG was 92.0%, 94.9% and 96.5% for Covid-Presto®, NGTest ®, and Abbott, respectively. Most of the false positive results observed with NG-Test® resulted from samples containing malarial antibodies. In conclusion, performances of these 2 rapid tests are very good and comparable to those obtained with automated immunoassay, except for IgM specificity with the NG-Test®. Thus, isolated IgM should be cautiously interpreted due to the possible false-positive reactions with this test. Finally, before their large use, the rapid tests must be reliably evaluated with adequate and large panel including early seroconversion and possible cross-reactive samples url: https://www.ncbi.nlm.nih.gov/pubmed/32919222/ doi: 10.1016/j.jcv.2020.104618 id: cord-119183-pbliko1k author: Cohen, Tomer title: A combination of ''pooling'' with a prediction model can reduce by 73% the number of COVID-19 (Corona-virus) tests date: 2020-05-03 words: 2706.0 sentences: 163.0 pages: flesch: 72.0 cache: ./cache/cord-119183-pbliko1k.txt txt: ./txt/cord-119183-pbliko1k.txt summary: In appendices A -C, we survey three different ways to use this data -the first-of-which is a known method due to Dorfman [3] -which we''ll call here ''single pooling'' (Appendix A): according to this method, if the pool turns out to be positive, all samples in that pool need to be re-tested individually, as shown in the following diagram: The expected number of tests can be calculated, based on the probability of the samples in the pool to be positive, and the size of the pool (see Appendix A for details). Appendix D includes a table comparing the required number of tests per patient with the various methods, as a function of , and also a comparison to a recently introduced method called double-pooling [4] . As before, is the probability for a positive test, is the size of the population, and , in this case, is the number of columns/rows in the matrix. abstract: We show that combining a prediction model (based on neural networks), with a new method of test pooling (better than the original Dorfman method, and better than double-pooling) called 'Grid', we can reduce the number of Covid-19 tests by 73%. url: https://arxiv.org/pdf/2005.03453v3.pdf doi: nan id: cord-283517-7gd0f06m author: Deak, Eszter title: Right-Sizing Technology in the Era of Consumer-Driven Health Care date: 2017-08-01 words: 6857.0 sentences: 331.0 pages: flesch: 45.0 cache: ./cache/cord-283517-7gd0f06m.txt txt: ./txt/cord-283517-7gd0f06m.txt summary: Today, we have molecular point-ofcare (mPOC) devices that can provide a rapid diagnostic answer within 20 minutes in a clinic, multiplex PCR sample-to-answer devices that can screen for >20 analytes in a single specimen in about an hour, high-volume automation that can enhance throughput and efficiency in the clinical microbiology laboratory with digital imaging, and next-generation sequencing (NGS) that can reveal a treasure trove of information in a single test. Factors may include syndrome-specific diagnostic needs, ease of use, the need for rapid results, improved sensitivity and specificity, operational needs (such as staffing and expertise), laboratory design (such as centralized versus decentralized models), cost, consumer demand, and the potential for improved patient outcomes. Considerations that go into the selection of a test or instrument platform for implementation include perceived turnaround time needs for improved patient care, sample volume requirements, number of tests expected, suitability for the intended laboratory based on available expertise and desired workflow, as well as cost. abstract: Abstract Technology for modern clinical and public health microbiology laboratories has evolved at an impressive rate over the last two decades. Contemporary diagnostics can rapidly provide powerful data that can impact patient lives and support infectious disease outbreak investigations. At the same time, dramatic changes to health care delivery are putting new pressures on a system that is now focusing on patient-centric, value-driven, convenient care. For laboratories, balancing all these demands in a cost-contained environment remains a challenge. This article explores the current and future directions of diagnostics in our dynamic health care environment. url: https://www.sciencedirect.com/science/article/pii/S0196439917300491 doi: 10.1016/j.clinmicnews.2017.07.001 id: cord-339122-7vvqtk84 author: Deb, Chaarushena title: Covid-19, Single-Sourced Diagnostic Tests, and Innovation Policy date: 2020-07-07 words: 3117.0 sentences: 167.0 pages: flesch: 49.0 cache: ./cache/cord-339122-7vvqtk84.txt txt: ./txt/cord-339122-7vvqtk84.txt summary: 16 An appropriate model for diagnostic testing development, including innovation incentives, should go beyond simply discouraging test monopolies and promoting confirmatory testing, by also allowing for low R&D costs for test development and yielding fast delivery of high quality tests-preventing the errors highlighted in the Covid-19 testing response from occurring in both emergency and non-emergency situations. And thus any sort of incentive model that relies on granting market exclusivity -such as the traditional patent system, FDA approval exclusivity, or trade secret protection -raises the same sorts of issues, if on a smaller scale, as those grimly demonstrated by the failure of U.S. SARS-CoV-2 testing at the onset of the Covid-19 pandemic, which ultimately resulted in the loss of many lives. But for diagnostic tests which rely on confirmatory testing, innovative improvements, and robust access to supply, single-sourcing creates a host of serious problems. abstract: The United States’ disastrous response to the onset of the Covid-19 pandemic has arisen in large part by an utter failure to provide adequate diagnostic tests for the presence of SARS-CoV-2. The Centers for Disease Control were the sole testing source authorized by the Food and Drug Administration, and when the CDC failed to provide reliable tests in sufficient volume, it took weeks for other providers to be approved and to ramp up testing. Revised policies should decrease the likelihood of sole-sourcing tests in pandemic contexts, which results in a fragile system. The pandemic sole-sourcing failure, however, not only accelerated the pandemic, but also provides lessons for innovation policy about diagnostic testing more generally. Sole-sourcing hurts clinical practice by limiting confirmatory testing and systemic robustness, whether in a pandemic or in regular practice. We thus argue against relying too heavily on exclusivity-creating patents as innovation incentive for diagnostic tests—including the proposed Coons-Tillis patent reform bill which would increase patentability for many such tests. Instead, we propose the use of reformed reimbursement to create better incentives for diagnostic test innovation. In both pandemics and elsewhere, single-sourcing creates too great a point of failure, but targeted innovation policy can help url: https://www.ncbi.nlm.nih.gov/pubmed/32908672/ doi: 10.1093/jlb/lsaa053 id: cord-311766-m9yv4qkm author: Demey, Baptiste title: Dynamic profile for the detection of anti-SARS-CoV-2 antibodies using four immunochromatographic assays date: 2020-05-07 words: 1754.0 sentences: 92.0 pages: flesch: 49.0 cache: ./cache/cord-311766-m9yv4qkm.txt txt: ./txt/cord-311766-m9yv4qkm.txt summary: Thus, the objective of our study was to evaluate four immunochromatographic assays for the detection of IgM and IgG antibodies to SARS-CoV-2 and to evaluate the kinetics of their detection by these LFA. We evaluated 4 immunochromatographic tests for the detection of IgM and IgG directed against SARS-CoV-2 ( Figure 1 ). Longitudinal immunochromatographic testing in all patients shows heterogeneity in the time to detection of antibodies after symptom reporting (Figure 2 ). With either IgM or IgG detection for a patient on days 5, 10 and 15 since onset of symptom, we calculated a clinical sensitivity between 9 and 24%, 67 and 82% and 100% respectively ( Figure 3B and Table 1 ). In conclusion, we described the kinetics of detection of post-symptom antibodies in 22 patients using immunochromatographic rapid tests and demonstrated the good performance of these tests for the detection of antibodies after SARS-CoV-2 infection. abstract: In order to fight the SARS-CoV-2 pandemic infection, there is a growing need and demand for diagnostic tools that are complementary and different from the RT-PCR currently in use. Multiple serological tests are or will be very soon available but need to be evaluated and validated. We have thus tested 4 immunochromatographic tests for the detection of antibodies to SARS-CoV-2. In addition, we assessed the kinetics of antibody appearance using these assays in 22 patients after they were tested positive by RT-PCR. We observed great heterogeneity in antiboy detection post-symptom onset. The median antibody detection time was between 8 and 10 days according to the manufacturers. All the tests showed a sensitivity of 60 to 80% on day 10 and 100% on day 15. In addition, a single cross-reaction was observed with other human coronavirus infections. Thus, immunochromatographic tests for the detection of anti-SARS-CoV-2 antibodies may have their place for the diagnostic panel of COVID-19. url: https://api.elsevier.com/content/article/pii/S0163445320302449 doi: 10.1016/j.jinf.2020.04.033 id: cord-328294-gii1b7s7 author: Doty, Richard L. title: Olfaction and Its Alteration by Nasal Obstruction, Rhinitis, and Rhinosinusitis date: 2009-01-02 words: 10862.0 sentences: 531.0 pages: flesch: 41.0 cache: ./cache/cord-328294-gii1b7s7.txt txt: ./txt/cord-328294-gii1b7s7.txt summary: The development and proliferation of easy-to-use, self-administered "scratch and sniff" tests of odor identification have significantly increased our understanding of smell function in humans, including the influences of such factors as age, gender, exposure to toxic agents, smoking behavior, and various disease states. 40 In this work, systemic prednisone 50 mg was administered each day for 7 days to 20 anosmic or severely hyposmic patients of several types whose olfactory function was monitored using butanol thresholds and odor identification tests. 43 reported that 28 patients with chronic rhinitis and no associated polyposis or rhinosinusitis had an average olfactory test score (based on a composite of odor identification and detection tests) indicative of moderate hyposmia. The comparatively few studies that have employed modern psychophysical tests to patients with rhinitis or rhinosinusitis have generally found an association between the degree of smell loss and the severity of nasal disease, although, except in cases of marked obstruction, no relationship is apparent between airway patency and olfactory dysfunction. abstract: The sense of smell has been largely ignored by otorhinolaryngologists, even though 1) its medical stewardship falls within their specialty's purview, 2) olfactory dysfunction is not uncommon in the general population, and 3) disorders of olfaction have significant quality of life, nutritional, and safety consequences. This report provides a succinct overview of the major intranasal neural systems present in humans (namely, cranial nerves O, I, and V, and the nonfunctional accessory [vomeronasal] organ system), along with a summary of notable findings resulting from the application of modern olfactory tests to patient populations, emphasizing diseases of the nose. Such tests have led to the discovery of significant influences of age, gender, smoking, toxic exposure, and genetics on the ability to smell. Within the field of otorhinolaryngology, they have revealed that 1) surgical and medical interventions in patients with rhinosinusitis do not, on average, lead to complete recovery of olfactory function, despite common beliefs to the contrary, and 2) associations are generally lacking between measures of airway patency and olfactory function in such cases. These findings have thrown into question the dogma that olfactory loss in rhinosinusitis is attributable primarily to blockage of airflow to the receptors and have led to histopathological studies demonstrating significant olfactory epithelial compromise in sinonasal syndromes. url: https://www.ncbi.nlm.nih.gov/pubmed/11224769/ doi: 10.1097/00005537-200103000-00008 id: cord-289461-bnusv816 author: Droste, M. C. title: Economic Benefits of COVID-19 Screening Tests date: 2020-10-27 words: 7911.0 sentences: 444.0 pages: flesch: 54.0 cache: ./cache/cord-289461-bnusv816.txt txt: ./txt/cord-289461-bnusv816.txt summary: The analysis is undertaken using a behavioral SIR model for the United States with 5 age groups, 66 economic sectors, screening and diagnostic testing, and partial adherence to instructions to quarantine or to isolate. Using our epidemiological-economic model, we project 66,000 deaths averted, an increase in GDP of $248 billion, and an increase in federal tax revenues of $68 billion over the counterfactual period of the program, June 1 -December 31, 2020, relative to a baseline with diagnostic but not screening testing. Testing costs are somewhat higher, but because the effective adherence rate is higher under this program than in Panel A, deaths averted rise to 153,000 and the increase in GDP is larger, $544 billion, for weekly testing. Relative to this literature, our main contribution is to provide carefully calibrated and estimated model for assessing the net economic, fiscal, and total (including mortality) benefits of multistep imperfect screening testing in conjunction with diagnostic testing. abstract: We assess the economic value of screening testing programs as a policy response to the ongoing COVID-19 pandemic. We find that the fiscal, macroeconomic, and health benefits of rapid SARS-CoV-2 screening testing programs far exceed their costs, with the ratio of economic benefits to costs typically in the range of 4-15 (depending on program details), not counting the monetized value of lives saved. Unless the screening test is highly specific, however, the signal value of the screening test alone is low, leading to concerns about adherence. Confirmatory testing increases the net economic benefits of screening tests by reducing the number of healthy workers in quarantine and by increasing adherence to quarantine measures. The analysis is undertaken using a behavioral SIR model for the United States with 5 age groups, 66 economic sectors, screening and diagnostic testing, and partial adherence to instructions to quarantine or to isolate. url: https://doi.org/10.1101/2020.10.22.20217984 doi: 10.1101/2020.10.22.20217984 id: cord-270935-t9pym9k0 author: Dumyati, Ghinwa title: Does Universal Testing for COVID-19 Work for Everyone? date: 2020-08-15 words: 2681.0 sentences: 179.0 pages: flesch: 55.0 cache: ./cache/cord-270935-t9pym9k0.txt txt: ./txt/cord-270935-t9pym9k0.txt summary: Strategies to address COVID-19 infections among nursing home residents vary based on the availability for SARS-CoV-2 tests, the incorporation of tests into broader surveillance efforts, and using results to help mitigate the spread of COVID-19 by identifying asymptomatic and presymptomatic infections. Dr. Jump reports support for this work in part through the Cleveland Geriatric Research 50 While there is general agreement that increased access to testing is important for personal and 23 public health, the selection and use of diagnostic tests to mitigate COVID-19 infections in post-24 acute and long-term care settings is complex and should be tailored to individual sites. Because he met the nursing 36 home''s enhanced screening criteria for COVID-19 (Table 1) , 1 he was placed on transmission-37 based precautions and a laboratory test for SARS-CoV-2 was ordered. abstract: Abstract The COVID-19 pandemic has been especially devastating among nursing home residents, with both the health circumstances of individual residents as well as communal living settings contributing to increased morbidity and mortality. Preventing the spread of COVID-19 infection requires a multipronged approach that includes early identification of infected residents and healthcare personnel, compliance with infection prevention and control measures, cohorting infected residents, and furlough of infected staff. Strategies to address COVID-19 infections among nursing home residents vary based on the availability for SARS-CoV-2 tests, the incorporation of tests into broader surveillance efforts, and using results to help mitigate the spread of COVID-19 by identifying asymptomatic and presymptomatic infections. We review the tests available to diagnose COVID-19 infections, the implications of universal testing for nursing home staff and residents, interpretation of test results, issues around repeat testing, and incorporation of test results as part of a long-term response to the COVID-19 pandemic. We propose a structured approach for facility-wide testing of resident and staff and provide alternatives if testing capacity is limited, emphasizing contact tracing. Nursing homes with strong screening protocols for residents and staff, that engage in contact tracing for new cases, and that continue to remain vigilant about infection prevent and control practices, may better serve their residents and staff by thoughtful use of symptom- and risk-based testing strategies. url: https://www.sciencedirect.com/science/article/pii/S1525861020307039?v=s5 doi: 10.1016/j.jamda.2020.08.013 id: cord-281241-k1adcls8 author: Döhla, M. title: Rapid point-of-care testing for SARS-CoV-2 in a community screening setting shows low sensitivity date: 2020-04-18 words: 1991.0 sentences: 127.0 pages: flesch: 59.0 cache: ./cache/cord-281241-k1adcls8.txt txt: ./txt/cord-281241-k1adcls8.txt summary: Objective: With the current SARS-CoV2 outbreak, countless tests need to be performed on potential symptomatic individuals, contacts and travellers. Objective: With the current SARS-CoV2 outbreak, countless tests need to be performed on potential symptomatic individuals, contacts and travellers. We therefore evaluated a rapid antibody IgG/IgMebased testing system in the community setting for its ability, specificity and sensitivity to reliably identify infected individuals. Thirty-nine randomly selected individuals at the centre were tested simultaneously using the SARS-CoV-2 rapid test and the gold standard RT-qPCR method (Altona Diagnostics). The rapid test used for evaluation is a qualitative IgG/IgM detection system to test for a current or past infection of SARS-CoV-2. abstract: OBJECTIVE: With the current SARS-CoV2 outbreak, countless tests need to be performed on potential symptomatic individuals, contacts and travellers. The gold standard is a quantitative polymerase chain reaction (qPCR)–based system taking several hours to confirm positivity. For effective public health containment measures, this time span is too long. We therefore evaluated a rapid test in a high-prevalence community setting. STUDY DESIGN: Thirty-nine randomly selected individuals at a COVID-19 screening centre were simultaneously tested via qPCR and a rapid test. Ten previously diagnosed individuals with known SARS-CoV-2 infection were also analysed. METHODS: The evaluated rapid test is an IgG/IgM–based test for SARS-CoV-2 with a time to result of 20 min. Two drops of blood are needed for the test performance. RESULTS: Of 49 individuals, 22 tested positive by repeated qPCR. In contrast, the rapid test detected only eight of those positive correctly (sensitivity: 36.4%). Of the 27 qPCR-negative individuals, 24 were detected correctly (specificity: 88.9%). CONCLUSION: Given the low sensitivity, we recommend not to rely on an antibody-based rapid test for public health measures such as community screenings. url: https://www.sciencedirect.com/science/article/pii/S0033350620301141 doi: 10.1016/j.puhe.2020.04.009 id: cord-027445-bpx4qr0i author: Eisty, Nasir U. title: Testing Research Software: A Case Study date: 2020-05-25 words: 2642.0 sentences: 143.0 pages: flesch: 48.0 cache: ./cache/cord-027445-bpx4qr0i.txt txt: ./txt/cord-027445-bpx4qr0i.txt summary: Method: Using the ParSplice research software project as a case, we implemented a testing framework based on a statistical testing approach called Multinomial Test. 2.1), the non-determinism stems from (1) the use of stochastic differential equations to model the physics and (2) the order in which communication between the procedures occurs (note however that even though the results from each execution depends upon message ordering, each valid order produces a statistically accurate result, which is the key requirement for the validity of ParSplice simulations). In this paper, we describe a case study of the ParSplice project in which we followed the PSIP methodology to develop a testing framework to address the difficulties of testing non-deterministic parallel research software. The approach we followed to develop the test framework can be a model for other research software projects. abstract: Background: The increasing importance of software for the conduct of various types of research raises the necessity of proper testing to ensure correctness. The unique characteristics of the research software produce challenges in the testing process that require attention. Aims: Therefore, the goal of this paper is to share the experience of implementing a testing framework using a statistical approach for a specific type of research software, i.e. non-deterministic software. Method: Using the ParSplice research software project as a case, we implemented a testing framework based on a statistical testing approach called Multinomial Test. Results: Using the new framework, we were able to test the ParSplice project and demonstrate correctness in a situation where traditional methodical testing approaches were not feasible. Conclusions: This study opens up the possibilities of using statistical testing approaches for research software that can overcome some of the inherent challenges involved in testing non-deterministic research software. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7304767/ doi: 10.1007/978-3-030-50436-6_33 id: cord-292274-upwn9o2m author: Ghaffari, Abdi title: COVID-19 Serological Tests: How Well Do They Actually Perform? date: 2020-07-04 words: 4648.0 sentences: 244.0 pages: flesch: 44.0 cache: ./cache/cord-292274-upwn9o2m.txt txt: ./txt/cord-292274-upwn9o2m.txt summary: While IgM and IgG antibodies have been the leading candidates in COVID-19 serological test development, recent studies show that IgA, predominately present in the mucosal tissue, may also play a critical role in the immune response and disease progression [12] . While IgM and IgG antibodies have been the leading candidates in COVID-19 serological test development, recent studies show that IgA, predominately present in the mucosal tissue, may also play a critical role in the immune response and disease progression [12] . Typically, RDT test strips use a drop of blood to detect the presence of patient antibodies (IgG, IgM, or IgA) produced against a specific SARS-CoV-2 antigen ( Figure 2 ). Critics point to gaps in our understanding of immune response to COVID-19 infection, including the ability of serological tests to detect neutralizing antibodies and the capacity of the immune system to provide long-term immunity against SARS-CoV-2. abstract: In only a few months after initial discovery in Wuhan, China, SARS-CoV-2 and the associated coronavirus disease 2019 (COVID-19) have become a global pandemic causing significant mortality and morbidity and implementation of strict isolation measures. In the absence of vaccines and effective therapeutics, reliable serological testing must be a key element of public health policy to control further spread of the disease and gradually remove quarantine measures. Serological diagnostic tests are being increasingly used to provide a broader understanding of COVID-19 incidence and to assess immunity status in the population. However, there are discrepancies between claimed and actual performance data for serological diagnostic tests on the market. In this study, we conducted a review of independent studies evaluating the performance of SARS-CoV-2 serological tests. We found significant variability in the accuracy of marketed tests and highlight several lab-based and point-of-care rapid serological tests with high levels of performance. The findings of this review highlight the need for ongoing independent evaluations of commercialized COVID-19 diagnostic tests. url: https://www.ncbi.nlm.nih.gov/pubmed/32635444/ doi: 10.3390/diagnostics10070453 id: cord-280571-ntgt5hy9 author: Ginocchio, Christine C. title: Strengths and Weaknesses of FDA-Approved/Cleared Diagnostic Devices for the Molecular Detection of Respiratory Pathogens date: 2011-05-01 words: 7521.0 sentences: 341.0 pages: flesch: 39.0 cache: ./cache/cord-280571-ntgt5hy9.txt txt: ./txt/cord-280571-ntgt5hy9.txt summary: In addition to RADTs, there are U.S. Food and Drug Administration (FDA)-approved/cleared nonmolecular-based viral diagnostic methods with a more rapid time to result, compared with traditional viral tube culture, eg, direct fluorescent antibody (DFA) testing and rapid cell culture. Although these 8 viruses are responsible for a large number of respiratory tract infections, bocavirus, selected coronaviruses (229E, OC43, NL63, and HKU-1), parainfluenza 4, and rhinovirus are also important causes of respiratory disease and are generally only detected using NAATs. Because antiviral therapies are currently limited to the treatment of influenza A, influenza B, cytomegalovirus pneumonia, and varicella zoster virus pneumonia, it is often argued that the specific identification of other viruses is not relevant, because the information would not change patient management. With clinical integration of real-time polymerase chain reaction (PCR) and FDA-approved/cleared simple cartridge-based NAATs, laboratories of all sizes are now able to perform molecular diagnostic tests. abstract: The rapid, sensitive, and specific identification of the microbial etiological characteristics of respiratory tract infections enhances the appropriate use of both antibiotics and antiviral agents and reduces the risk of nosocomial transmission. This article reviews the current nucleic acid amplification tests approved by the U.S. Food and Drug Administration (FDA) for the detection of respiratory pathogens. In addition, Emergency Use Authorization tests for the detection of 2009 influenza A H1N1 are discussed. The advantages and limitations of the current FDA-approved/cleared tests are reviewed. url: https://doi.org/10.1093/cid/cir046 doi: 10.1093/cid/cir046 id: cord-316047-d9cpe9yl author: Gonzalez, T. title: Influence of COVID-19 confinement on students’ performance in higher education date: 2020-10-09 words: 8517.0 sentences: 451.0 pages: flesch: 60.0 cache: ./cache/cord-316047-d9cpe9yl.txt txt: ./txt/cord-316047-d9cpe9yl.txt summary: This study analyzes the effects of COVID-19 confinement on the autonomous learning performance of students in higher education. We present a study that involves more than 450 students enrolled in 3 subjects from different degrees from the Universidad Autónoma de Madrid (Spain) during three academic years, including data obtained in the 2019/2020 academic year, when the restrictions due to the COVID-19 pandemic have been in force. In the case of "Design of Water Treatment Facilities", a longitudinal study has been performed in academic year 2017/2018 to analyse the effect of rewards in the students'' learning strategies, especially those related to time management. The second stage corresponds to the period of COVID-19 confinement (after March 11), where some measurable activities were performed in a different format and statistical differences can be found by comparing experimental and control groups. abstract: This study analyzes the effects of COVID-19 confinement on the autonomous learning performance of students in higher education. Using a field experiment with 458 students from three different subjects at Universidad Autónoma de Madrid (Spain), we study the differences in assessments by dividing students into two groups. The first group (control) corresponds to academic years 2017/2018 and 2018/2019. The second group (experimental) corresponds to students from 2019/2020, which is the group of students that had their face-to-face activities interrupted because of the confinement. The results show that there is a significant positive effect of the COVID-19 confinement on students’ performance. This effect is also significant in activities that did not change their format when performed after the confinement. We find that this effect is significant both in subjects that increased the number of assessment activities and subjects that did not change the student workload. Additionally, an analysis of students’ learning strategies before confinement shows that students did not study on a continuous basis. Based on these results, we conclude that COVID-19 confinement changed students’ learning strategies to a more continuous habit, improving their efficiency. For these reasons, better scores in students’ assessment are expected due to COVID-19 confinement that can be explained by an improvement in their learning performance. url: https://doi.org/10.1371/journal.pone.0239490 doi: 10.1371/journal.pone.0239490 id: cord-303539-gimz41yb author: Goudouris, Ekaterini S. title: Laboratory diagnosis of COVID-19() date: 2020-08-31 words: 3605.0 sentences: 220.0 pages: flesch: 45.0 cache: ./cache/cord-303539-gimz41yb.txt txt: ./txt/cord-303539-gimz41yb.txt summary: DATA SOURCES: Searches in PubMed and Google Scholar for articles made available in 2020, using the terms "diagnosis" OR "diagnostic" OR "diagnostic tests" OR "tests" AND "COVID-19" OR "SARS-CoV-2" in the title. 25 Some studies report patients with mild (or even asymptomatic) COVID-19 present lower levels of SARS-CoV-2-specific antibodies or may even do not develop detectable levels, while patients with more severe conditions have higher levels of these. 38 The data presented suggest that the diagnosis of COVID-19 should be based on clinical manifestations, contact history, imaging tests, laboratory tests, and not only on serological tests and the search for the genetic material of the virus. The gold standard for the diagnosis of SARS-CoV-2 infection is the identification of viral genetic material by RT-PCR, in different samples, with greater sensitivity in bronchoalveolar lavage and nasopharyngeal swab. abstract: OBJECTIVES: This was a non-systematic review of the literature on the laboratory diagnosis of COVID-19. DATA SOURCES: Searches in PubMed and Google Scholar for articles made available in 2020, using the terms "diagnosis" OR "diagnostic” OR "diagnostic tests" OR "tests" AND "COVID-19" OR "SARS-CoV-2" in the title. SUMMARY OF FINDINGS: Tests for the etiological agent identify genetic material of SARS-CoV-2 or humoral responses to it. The gold standard for diagnosis is the identification of viral genome targets by real-time polymerase chain reaction (RT-PCR) in respiratory tract materials during the first week of symptoms. Serological tests should be indicated from the second week of symptoms onwards. A wide range of different tests is available, with variable sensitivity and specificity, most of which require validation. Laboratory tests such as complete blood count, C-reactive protein (CRP), D-dimer, clotting tests, lactic dehydrogenase (LDH), ferritin, and procalcitonin identify risk of disease with greater severity, thromboembolic complications, myocardial damage, and/or worse prognosis. Imaging tests may be useful for diagnosis, especially when there is a compatible clinical picture, and other tests presented negative results or were unavailable. CONCLUSIONS: The identification of genetic material of the virus by RT-PCR is the gold standard test, but its sensitivity is not satisfactory. The diagnosis of COVID-19 should be based on clinical data, epidemiological history, tests for etiological diagnosis, and tests to support the diagnosis of the disease and/or its complications. New diagnostic methods with higher sensitivity and specificity, as well as faster results, are necessary. url: https://api.elsevier.com/content/article/pii/S0021755720301996 doi: 10.1016/j.jped.2020.08.001 id: cord-262846-1mhimfsf author: Gray, Nicholas title: Is “no test is better than a bad test”? Impact of diagnostic uncertainty in mass testing on the spread of COVID-19 date: 2020-10-21 words: 6023.0 sentences: 337.0 pages: flesch: 55.0 cache: ./cache/cord-262846-1mhimfsf.txt txt: ./txt/cord-262846-1mhimfsf.txt summary: This strategy would involve detecting those who have successfully overcome the virus, and are likely to have some level of immunity (or at least reduced susceptibility to more serious illness if they are infected again), so are relatively safe to relax their personal lockdown measures. To explore the effect of imperfect testing on the disease dynamics when strategies testing regimes are employed to relax lockdown measures, three new classes were added to the model. implement quarantine in their model but do not incorporate the effects on the dynamics from imperfect testing, nor do they consider how the quality and scale of an available test affect the spread of a disease. Wide-scale screening for antibodies in the general population promises significant scientific value, and targeted antibody testing is likely to have value for reducing risks to NHS and care-sector staff, and other key workers who will need to have close contact with COVID-19 sufferers. abstract: Testing is viewed as a critical aspect of any strategy to tackle epidemics. Much of the dialogue around testing has concentrated on how countries can scale up capacity, but the uncertainty in testing has not received nearly as much attention beyond asking if a test is accurate enough to be used. Even for highly accurate tests, false positives and false negatives will accumulate as mass testing strategies are employed under pressure, and these misdiagnoses could have major implications on the ability of governments to suppress the virus. The present analysis uses a modified SIR model to understand the implication and magnitude of misdiagnosis in the context of ending lockdown measures. The results indicate that increased testing capacity alone will not provide a solution to lockdown measures. The progression of the epidemic and peak infections is shown to depend heavily on test characteristics, test targeting, and prevalence of the infection. Antibody based immunity passports are rejected as a solution to ending lockdown, as they can put the population at risk if poorly targeted. Similarly, mass screening for active viral infection may only be beneficial if it can be sufficiently well targeted, otherwise reliance on this approach for protection of the population can again put them at risk. A well targeted active viral test combined with a slow release rate is a viable strategy for continuous suppression of the virus. url: https://doi.org/10.1371/journal.pone.0240775 doi: 10.1371/journal.pone.0240775 id: cord-307500-2jwuzfan author: Gray, Nicholas title: "No test is better than a bad test": Impact of diagnostic uncertainty in mass testing on the spread of Covid-19 date: 2020-04-22 words: 6478.0 sentences: 361.0 pages: flesch: 57.0 cache: ./cache/cord-307500-2jwuzfan.txt txt: ./txt/cord-307500-2jwuzfan.txt summary: Three scenarios for cessation of lock-down measures are explored: (1) immediate end of lock-down measures, (2) continued lock-down with antibody testing based immunity passports, and (3) incremental relaxation of lock-down measures with active viral testing. Sensitivity, specifcity, prevalence and test capacity are modified for both active viral and antibody testing to determine their population level effect on the continuing epidemic. This strategy would involve detecting those who have successfully overcome the virus, and are likely to have some level of immunity (or at least reduced susceptibility to more serious illness if they are infected again), so are relatively safe to relax their personal social distancing measures. To explore the effect of imperfect testing on the disease dynamics when strategies are employed to relax the current social distancing measures the SIR model described in the supplimentary material was modified. In order to explore the possible impact of testing strategies on the relaxation of current social distancing measures several scenarios have been analysed. abstract: Background: The cessation of lock-down measures will require an effective testing strategy. Much focus at the beginning of the UK's Covid-19 epidemic was directed to deficiencies in the national testing capacity. The quantity of tests may seem an important focus, but other characteristics are likely more germane. False positive tests are more probable than positive tests when the overall population has a low prevalence of the disease, even with highly accurate tests. Methods: We modify an SIR model to include quarantines states and test performance using publicly accessible estimates for the current situation. Three scenarios for cessation of lock-down measures are explored: (1) immediate end of lock-down measures, (2) continued lock-down with antibody testing based immunity passports, and (3) incremental relaxation of lock-down measures with active viral testing. Sensitivity, specifcity, prevalence and test capacity are modified for both active viral and antibody testing to determine their population level effect on the continuing epidemic. Findings: Diagnostic uncertainty can have a large effect on the epidemic dynamics of Covid-19 within the UK. The dynamics of the epidemic are more sensitive to test performance and targeting than test capacity. The quantity of tests is not a substitute for an effective strategy. Poorly targeted testing has the propensity to exacerbate the peak in infections. Interpretation: The assessment that 'no test is better than a bad test' is broadly supported by the present analysis. Antibody testing is unlikely to be a solution to the lock-down, regardless of test quality or capacity. A well designed active viral testing strategy combined with incremental relaxation of the lock-down measures is shown to be a potential strategy to restore some social activity whilst continuing to keep infections low. url: http://medrxiv.org/cgi/content/short/2020.04.16.20067884v1?rss=1 doi: 10.1101/2020.04.16.20067884 id: cord-026215-neqsup40 author: Grzegorzewski, Przemyslaw title: Two-Sample Dispersion Problem for Fuzzy Data date: 2020-05-16 words: 4713.0 sentences: 335.0 pages: flesch: 67.0 cache: ./cache/cord-026215-neqsup40.txt txt: ./txt/cord-026215-neqsup40.txt summary: A new permutation two-sample test for dispersion based on fuzzy random variables is proposed. At least some of the problems associated with the lack of a satisfying difference in constructing statistical tools for reasoning based on fuzzy observations could be overcome by using adequate metrics defined in F(R) -for the general overview see [2] . For instance, in most cases we are not able to find the null distribution of a test statistic based on fuzzy data and, consequently, to find either the critical value or to compute the p-value required for rejection or acceptance of the hypothesis under study. All these reasons indicate that the permutation test applied to fuzzy random variables might be also a competitive tool useful in statistical inference for imprecise data. On the other hand, in Fig. 2 we have a histogram made for the test statistic (11) null distribution obtained for two fuzzy samples of the same samle sizes as before but which differ in dispersion. abstract: The problem of comparing variability of two populations with fuzzy data is considered. A new permutation two-sample test for dispersion based on fuzzy random variables is proposed. A case-study illustrating the applicability of the suggested testing procedure is also presented. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7274660/ doi: 10.1007/978-3-030-50153-2_7 id: cord-150218-javbnjrg author: Gupta, Prateek title: COVI-AgentSim: an Agent-based Model for Evaluating Methods of Digital Contact Tracing date: 2020-10-30 words: 13386.0 sentences: 673.0 pages: flesch: 54.0 cache: ./cache/cord-150218-javbnjrg.txt txt: ./txt/cord-150218-javbnjrg.txt summary: We use COVI-AgentSim to perform cost-benefit analyses comparing no DCT to: 1) standard binary contact tracing (BCT) that assigns binary recommendations based on binary test results; and 2) a rule-based method for feature-based contact tracing (FCT) that assigns a graded level of recommendation based on diverse individual features. We call these methods feature-based contact tracing (FCT), and hypothesize they could provide an important and effective means of reducing the spread of the disease, perhaps even more effectively than BCT at lower adoption rates. Recognizing this potential, we propose COVI-AgentSim -a software testbed 2 to design, evaluate and benchmark DCT methods using cost-benefit analysis in terms of lives saved, reduction in effective reproductive number (R t ) of the virus, disability-adjusted life years (DALYs) averted, and productive hours lost. A key difference in our simulator is the rich set of individual-level features (including e.g. pre-existing medical conditions), which allow us to benchmark feature-based contact tracing methods, and also allow for stratification over a larger variety of subgroups. abstract: The rapid global spread of COVID-19 has led to an unprecedented demand for effective methods to mitigate the spread of the disease, and various digital contact tracing (DCT) methods have emerged as a component of the solution. In order to make informed public health choices, there is a need for tools which allow evaluation and comparison of DCT methods. We introduce an agent-based compartmental simulator we call COVI-AgentSim, integrating detailed consideration of virology, disease progression, social contact networks, and mobility patterns, based on parameters derived from empirical research. We verify by comparing to real data that COVI-AgentSim is able to reproduce realistic COVID-19 spread dynamics, and perform a sensitivity analysis to verify that the relative performance of contact tracing methods are consistent across a range of settings. We use COVI-AgentSim to perform cost-benefit analyses comparing no DCT to: 1) standard binary contact tracing (BCT) that assigns binary recommendations based on binary test results; and 2) a rule-based method for feature-based contact tracing (FCT) that assigns a graded level of recommendation based on diverse individual features. We find all DCT methods consistently reduce the spread of the disease, and that the advantage of FCT over BCT is maintained over a wide range of adoption rates. Feature-based methods of contact tracing avert more disability-adjusted life years (DALYs) per socioeconomic cost (measured by productive hours lost). Our results suggest any DCT method can help save lives, support re-opening of economies, and prevent second-wave outbreaks, and that FCT methods are a promising direction for enriching BCT using self-reported symptoms, yielding earlier warning signals and a significantly reduced spread of the virus per socioeconomic cost. url: https://arxiv.org/pdf/2010.16004v1.pdf doi: nan id: cord-296588-q2716lda author: Hanson, Kimberly E title: Infectious Diseases Society of America Guidelines on the Diagnosis of COVID-19 date: 2020-06-16 words: 10179.0 sentences: 681.0 pages: flesch: 47.0 cache: ./cache/cord-296588-q2716lda.txt txt: ./txt/cord-296588-q2716lda.txt summary: OBJECTIVE: The IDSA''s goal was to develop an evidence-based diagnostic guideline to assists clinicians, clinical laboratorians, patients and policymakers in decisions related to the optimal use of SARS-CoV-2 nucleic acid amplification tests. It is important to note as well, that not all specimens were collected from the same patient at the same time, the time of collection from symptom onset was not provided in all studies and various approaches for establishing SARS-CoV-2 positivity were used to define positive results (i.e., clinical evaluation, detection different gene targets versus nucleic acid sequencing). While NP swab collection is widely used and the primary specimen type for commercial direct SARS-CoV-2 test platforms, based on current available evidence, clinical practice, and availability of testing resources, the panel believes there are comparable alternative methods for sampling the nasal passages. abstract: BACKGROUND: Accurate molecular diagnostic tests are necessary for confirming a diagnosis of coronavirus disease 2019 (COVID-19). Direct detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleic acids in respiratory tract specimens informs patient, healthcare institution and public health level decision-making. The numbers of available SARS-CoV-2 nucleic acid detection tests are rapidly increasing, as is the COVID-19 diagnostic literature. Thus, the Infectious Diseases Society of America (IDSA) recognized a significant need for frequently updated systematic reviews of the literature to inform evidence-based best practice guidance. OBJECTIVE: The IDSA’s goal was to develop an evidence-based diagnostic guideline to assists clinicians, clinical laboratorians, patients and policymakers in decisions related to the optimal use of SARS-CoV-2 nucleic acid amplification tests. In addition, we provide a conceptual framework for understanding molecular diagnostic test performance, discuss the nuance of test result interpretation in a variety of practice settings, and highlight important unmet research needs in the COVID-19 diagnostic testing space. METHODS: IDSA convened a multidisciplinary panel of infectious diseases clinicians, clinical microbiologists, and experts in systematic literature review to identify and prioritize clinical questions and outcomes related to the use of SARS-CoV-2 molecular diagnostics. Grading of Recommendations Assessment, Development and Evaluation (GRADE) methodology was used to assess the certainty of evidence and make testing recommendations. RESULTS: The panel agreed on 15 diagnostic recommendations. CONCLUSIONS: Universal access to accurate SARS-CoV-2 nucleic acid testing is critical for patient care, hospital infection prevention and the public response to the COVID-19 pandemic. Information on the clinical performance of available tests is rapidly emerging, but the quality of evidence of the current literature is considered low to very low. Recognizing these limitations, the IDSA panel weighed available diagnostic evidence and recommends nucleic acid testing for all symptomatic individuals suspected of having COVID-19. In addition, testing is recommended for asymptomatic individuals with known or suspected contact with a COVID-19 case. Testing asymptomatic individuals without known exposure is suggested when the results will impact isolation/quarantine/personal protective equipment (PPE) usage decisions, dictate eligibility for surgery, or inform administration of immunosuppressive therapy. Ultimately, prioritization of testing will depend on institutional-specific resources and the needs of different patient populations. url: https://www.ncbi.nlm.nih.gov/pubmed/32556191/ doi: 10.1093/cid/ciaa760 id: cord-012934-c6pbr64i author: Hao, Weiming title: Vestibular prognosis in idiopathic sudden sensorineural hearing loss with vestibular dysfunction treated with oral or intratympanic glucocorticoids: a protocol for randomized controlled trial date: 2020-07-22 words: 5443.0 sentences: 280.0 pages: flesch: 43.0 cache: ./cache/cord-012934-c6pbr64i.txt txt: ./txt/cord-012934-c6pbr64i.txt summary: title: Vestibular prognosis in idiopathic sudden sensorineural hearing loss with vestibular dysfunction treated with oral or intratympanic glucocorticoids: a protocol for randomized controlled trial The primary outcomes will be vestibular function outcomes assessed by sensory organization test, caloric test, video head impulse test, cervical vestibular evoked myogenic potential, and ocular vestibular evoked myogenic potential; the secondary outcomes include self-reported vestibular dysfunction symptoms; dizziness-related handicap, visual analogue scale for vertigo and tinnitus; and pure tone audiometry. To evaluate the recovery of vestibular function, we set the recovery rates of the whole battery of vestibular function tests (SOT/caloric test/vHIT/VEMPs) as the primary outcome, which is the proportion of patients whose abnormal results of vestibular function tests at baseline recover to normal at 4-/8-week follow-up: in this study, we define a 10-dB PTA criterion as clinically significant difference based on a previous RCT [9] . abstract: BACKGROUND: Idiopathic sudden sensorineural hearing loss (ISSNHL) is a rapid-onset sensorineural hearing impairment with unclear etiology and unsatisfying treatment effects. Vestibular dysfunction has been considered as a poor indicator in the clinical manifestations and prognosis of ISSNHL, which occurred in approximately 28–57% cases. Glucocorticoids, administered through oral or intratympanic way, are currently regularly and standardly applied for ISSNHL to improve the hearing outcome. However, the vestibular prognosis of ISSNHL after routine treatments remains seldom explored. This study aims to compare the effectiveness of oral and intratympanic glucocorticoids in ISSNHL with vestibular dysfunction in terms of the pattern and trajectory of possible process of vestibular function recovery. METHODS/DESIGN: A randomized, outcome-assessor- and analyst-blinded, controlled, clinical trial (RCT) will be carried out. Seventy-two patients with ISSNHL complaining of vestibular dysfunction appearing as vertigo or imbalance will be recruited and randomized into either oral or intratympanic glucocorticoid therapy group with a 1:1 allocation ratio. The primary outcomes will be vestibular function outcomes assessed by sensory organization test, caloric test, video head impulse test, cervical vestibular evoked myogenic potential, and ocular vestibular evoked myogenic potential; the secondary outcomes include self-reported vestibular dysfunction symptoms; dizziness-related handicap, visual analogue scale for vertigo and tinnitus; and pure tone audiometry. Assessments of primary outcomes will be performed at baseline and at 4 and 8 weeks post-randomization, while assessments of secondary outcomes will be performed at baseline and 1, 2, 4, and 8 weeks post-randomization. DISCUSSION: Previous intervention studies of ISSNHL included only hearing outcomes, with little attention paid on the prognosis of vestibular dysfunction. This trial will be the first RCT study focusing on the progress and prognosis of vestibular dysfunction in ISSNHL. The efficacy of two commonly used therapies of glucocorticoids will be compared in both auditory and vestibular function fields, rather than in the hearing outcome alone. TRIAL REGISTRATION: ClinicalTrials.gov NCT03974867. Registered on 23 July 2019 url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7477872/ doi: 10.1186/s13063-020-04579-6 id: cord-290251-ihq8gdwj author: Hasell, Joe title: A cross-country database of COVID-19 testing date: 2020-10-08 words: 3805.0 sentences: 196.0 pages: flesch: 52.0 cache: ./cache/cord-290251-ihq8gdwj.txt txt: ./txt/cord-290251-ihq8gdwj.txt summary: The database consists of two parts, provided for each included country: (1) a time series for the cumulative and daily number of tests performed, or people tested, plus derived variables (discussed below); (2) metadata including a detailed description of the source and any available information on data quality or comparability issues needed for the interpretation of the time series. Firstly, for a number of countries, figures reported in official sources -including press releases, government websites, dedicated dashboards, and social media accounts of national authorities -are recorded manually as they are released. The time series for cumulative and daily testing for each country-series is then provided in the covid-testing-all-observations.csv file. In covid-testing-all-observations.csv, for those sources only providing daily testing figures, this field is derived as the running total of the raw daily data, and is also provided per thousand people of the country''s 2020 population. abstract: Our understanding of the evolution of the COVID-19 pandemic is built upon data concerning confirmed cases and deaths. This data, however, can only be meaningfully interpreted alongside an accurate understanding of the extent of virus testing in different countries. This new database brings together official data on the extent of PCR testing over time for 94 countries. We provide a time series for the daily number of tests performed, or people tested, together with metadata describing data quality and comparability issues needed for the interpretation of the time series. The database is updated regularly through a combination of automated scraping and manual collection and verification, and is entirely replicable, with sources provided for each observation. In providing accessible cross-country data on testing output, it aims to facilitate the incorporation of this crucial information into epidemiological studies, as well as track a key component of countries’ responses to COVID-19. url: https://doi.org/10.1038/s41597-020-00688-8 doi: 10.1038/s41597-020-00688-8 id: cord-292209-d1ty9etr author: Horta, Bernardo L title: Prevalence of antibodies against SARS-CoV-2 according to socioeconomic and ethnic status in a nationwide Brazilian survey date: 2020-10-29 words: 4330.0 sentences: 247.0 pages: flesch: 53.0 cache: ./cache/cord-292209-d1ty9etr.txt txt: ./txt/cord-292209-d1ty9etr.txt summary: Subjects answered a questionnaire on household assets, schooling and self-reported skin color/ethnicity using the standard Brazilian classification in five categories: white, black, brown, Asian or indigenous. The present analyses were aimed at assessing socioeconomic and ethnic group inequalities in prevalence of antibodies against SARS-CoV-2 in 133 sentinel cities throughout Brazil, as part of the EPICOVID-19 study (www.epicovid19brasil.org). In summary, the analyses of the three waves of national serological surveys in Brazil showed important inequalities in the prevalence of antibodies against SARS-CoV-2 according to family wealth, education and ethnic groups. Yet, even after adjustment for region, indigenous individuals were about twice as likely as whites to present antibodies against SARS-CoV-2, and in the national analyses including adjustment for region of the country and socioeconomic status, the prevalence ratio remained at around two. abstract: OBJECTIVES. To investigate socioeconomic and ethnic group inequalities in prevalence of antibodies against SARS-CoV-2 in the 27 federative units of Brazil. METHODS. In this cross-sectional study, three household surveys were carried out on May 14-21, June 4-7, and June 21-24, 2020 in 133 Brazilian urban areas. Multi-stage sampling was used to select 250 individuals in each city to undergo a rapid antibody test. Subjects answered a questionnaire on household assets, schooling and self-reported skin color/ethnicity using the standard Brazilian classification in five categories: white, black, brown, Asian or indigenous. Principal component analyses of assets was used to classify socioeconomic position into five wealth quintiles. Poisson regression was used for the analyses. RESULTS. 25 025 subjects were tested in the first, 31 165 in the second, and 33 207 in the third wave of the survey, with prevalence of positive results equal to 1.4%, 2.4%, and 2.9% respectively. Individuals in the poorest quintile were 2.16 times (95% confidence interval 1.86; 2.51) more likely to test positive than those in the wealthiest quintile, and those with 12 or more years of schooling had lower prevalence than subjects with less education. Indigenous individuals had 4.71 (3.65; 6.08) times higher prevalence than whites, as did those with black or brown skin color. Adjustment for region of the country reduced the prevalence ratios according to wealth, education and ethnicity, but results remained statistically significant. CONCLUSIONS. The prevalence of antibodies against SARS-CoV-2 in Brazil shows steep class and ethnic gradients, with lowest risks among white, educated and wealthy individuals. url: https://doi.org/10.26633/rpsp.2020.135 doi: 10.26633/rpsp.2020.135 id: cord-331617-1ytcd0ax author: Horvath, Karl title: Antikörpertests bei COVID-19 - Was uns die Ergebnisse sagen date: 2020-05-15 words: 2635.0 sentences: 331.0 pages: flesch: 55.0 cache: ./cache/cord-331617-1ytcd0ax.txt txt: ./txt/cord-331617-1ytcd0ax.txt summary: Da weitgehend alle zur Diagnose eingesetzten Tests nicht vollständig fehlerfrei funktionieren, ist auch bei der Testung auf Vorliegen von SARS-CoV-2 spezifischen AK damit zu rechnen, dass es einen Anteil von Personen gibt, der vom Test falsch klassifiziert wird. Wie groß dieser jeweilig falsch klassifizierte Anteil an allen getesteten Personen ist, d.h. wie sicher ein positives oder negatives Testresultat ist, ist abhängig von der Sensitivität und Spezifität des jeweiligen Tests sowie von der gegebenen Vortestwahrscheinlichkeit. Mit anderen Worten beschreibt die Vortestwahrscheinlichkeit das Risiko, dass bei einer bisher ungetesteten Person eine SARS-CoV-2 Infektion vorliegt bzw. Zu bedenken ist auch, dass sich die Prävalenz einer SARS-CoV-2 Infektion und damit die Vortestwahrscheinlichkeit mit Fortschreiten der Pandemie ändern wird. Auch bei nahezu idealen Testeigenschaften sind bei geringer Vortestwahrscheinlichkeit (wie sie bei der Testung von Personen ohne Symptome und Risikofaktoren für eine SARS-CoV-2 Infektion besteht) positive Testresultate häufig falsch. abstract: INTRODUCTION: In the context of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, the detection of virus-specific antibodies (AB) will play an increasing role. The presence or absence of such antibodies can potentially lead to considerations regarding immunity and infection. ISSUE: How reliable are inferences from positive or negative test results regarding the actual presence of SARS-CoV-2 specific antibodies? METHODS: Calculation of the probability that, depending on the pretest probability (prevalence of SARS-CoV-2 infection) and test properties, antibodies are present or absent in the case of positive or negative test results. RESULTS: Sensitivity and specificity of different SARS-CoV-2 AB test systems vary between 53 % and 94 % and between 91 % and 99.5 %, respectively. When using a test with high test quality, the positive predictive value (PPV) is 42 % and 7 9%, respectively, with a pre-test probability of 1 % to 5 %, as can currently be assumed for the general population in Austria or Germany. For persons with an increased pre-test probability of 20 %, e. g. persons from high-risk professions, the PPW is 95 %, with a pre-test probability of 80 % the PPW is almost 100 %. The negative predictive value (NPV) is at least 99.7 % for persons with a low pre-test probability of up to 5 % and 79.1 % for persons with a pre-test probability of 80 %. When using test systems with lower sensitivity and specificity, the reliability of the results decreases considerably. The PPV is 5.9 % with a pre-test probability of 1 %. CONCLUSIONS: A sufficiently high sensitivity and specificity are prerequisites for the application of antibody test systems. Positive test results are often false if the pre-test probability is low. Depending on the assumed prevalence of a SARS-CoV-2 infection, there are substantial differences in the significance of a concrete test result for the respective affected persons. url: https://doi.org/10.1016/j.zefq.2020.05.005 doi: 10.1016/j.zefq.2020.05.005 id: cord-256568-mbkrg98v author: Jantzen, R. title: Epidemiological and socio-economic characteristics of the COVID-19 spring outbreak in Quebec, Canada: A population-based study date: 2020-09-01 words: 7907.0 sentences: 419.0 pages: flesch: 54.0 cache: ./cache/cord-256568-mbkrg98v.txt txt: ./txt/cord-256568-mbkrg98v.txt summary: 7.6% of the participants declared that they have experienced at least one of the four COVID-related symptoms chosen by the Public Health authorities (fever, cough, dyspnea, anosmia) but were not tested. Results from the tree-based model analyzes adjusted on exposure factors show that the combination of dyspnea, dry cough and fever was highly associated with being tested whereas anosmia, fever, and headache were the most discriminant factors for having a positive test among those tested. A multiple logistic regression analyzis showed that place of residence, dweling, risk exposure (medical worker, contact with a COVID-19 positive patient, international travel), having at least one pre-existing condition were independent factors associated with the outcome ( Table 1) . Taking into account socio-demographic, medical and exposure factors (place of residence, dweling, medical worker, contact with a COVID-19 positive patient, international travel, pre-existing condition) as confounding factors and COVID-related symptoms as explanatory variables, we performed a GPLTR analyzis for identifying the combinations of symptoms leading to the most homogeneous sub-groups with respect to being tested. abstract: Background: By mid-July 2020, more than 108,000 COVID-19 cases had been diagnosed in Canada with more than half in the province of Quebec. To be prepared for a potential second wave of COVID-19 in the fall, it seems of utmost importance to analyze the epidemiological and socio-economic characteristics of the spring outbreak in the population. Method: We conducted an online survey of the participants of the CARTaGENE population-based cohort, composed of middle-aged and older adults. We collected information on socio-demographic, lifestyle, health condition, COVID-related symptoms and COVID-19 testing. We studied the association between these factors and two outcomes: the status of having been tested for SARS-CoV-2 and the status of having received a positive test when having been tested. These associations were evaluated with univariate and multivariate analyzes using a hybrid tree-based regression model. Results: Among the 8,129 respondents from the CARTaGENE cohort, 649 were tested for COVID-19 and 41 were positive. Medical workers and individuals having a contact with a COVID-19 patient had the highest probabilities of being tested (32% and 42.4%, respectively) and of being positive (17.2% and 13.0%, respectively) among those tested. 7.6% of the participants declared that they have experienced at least one of the four COVID-related symptoms chosen by the Public Health authorities (fever, cough, dyspnea, anosmia) but were not tested. Results from the tree-based model analyzes adjusted on exposure factors show that the combination of dyspnea, dry cough and fever was highly associated with being tested whereas anosmia, fever, and headache were the most discriminant factors for having a positive test among those tested. During the spring outbreak, more than one third of the participants have experienced a decrease in access to health services. There were sex and age differences in the socio-economic and emotional impacts of the pandemic. Conclusion: We have shown some discrepancies between the symptoms associated with being tested and being positive. In particular, the anosmia is a major discriminant symptom for positivity whereas ear-nose-throat symptoms seem not to be COVID-related. The results also emphasize the need of increasing the accessibility of testing for the general population. url: https://doi.org/10.1101/2020.08.26.20182675 doi: 10.1101/2020.08.26.20182675 id: cord-033420-pjtyv0pv author: Kalokairinou, Louiza title: The promise of direct-to-consumer COVID-19 testing: ethical and regulatory issues date: 2020-09-23 words: 6322.0 sentences: 310.0 pages: flesch: 48.0 cache: ./cache/cord-033420-pjtyv0pv.txt txt: ./txt/cord-033420-pjtyv0pv.txt summary: Although the provision of DTC tests has potential benefits—such as expanding access to testing and reducing the risk of exposure for consumers and medical personnel—it also raises significant ethical and regulatory concerns. The second part discusses five primary issues for DTC COVID-19 tests: test accuracy; potential misinterpretation of results; misleading claims and other misinformation; privacy concerns; and fair allocation of scarce resources. The second part identifies five primary ethical and regulatory issues for DTC COVID-19 tests: uncertainty over the accuracy of test results; potential misinterpretation of test results by users; misleading product promotion and misinformation; privacy concerns; and fair allocation of scarce resources. We conclude with recommendations for regulators, companies, and other relevant stakeholders that can help ensure high-quality, accurate, and equitably distributed COVID-19 tests, and inform the ethical provision of DTC health tests during public health crises. abstract: Widespread diagnostic and serological (antibody) testing is one key to mitigating the COVID-19 pandemic. While at first, the majority of COVID-19 diagnostic testing in the USA took place in healthcare settings, quickly a direct-to-consumer (DTC) testing market also emerged. In these DTC provision models, the test is initiated by a consumer and the sample collection occurs at home or in a commercial laboratory. Although the provision of DTC tests has potential benefits—such as expanding access to testing and reducing the risk of exposure for consumers and medical personnel—it also raises significant ethical and regulatory concerns. This article reviews these challenges and shows how they parallel and also diverge from prior concerns raised in the DTC health testing arena. The first part of this paper provides an overview of the landscape of diagnostic and serological tests for COVID-19, anticipating how provision models are likely to evolve in the future. The second part discusses five primary issues for DTC COVID-19 tests: test accuracy; potential misinterpretation of results; misleading claims and other misinformation; privacy concerns; and fair allocation of scarce resources. We conclude with recommendations for regulators and companies that aim to ensure ethically marketed DTC COVID-19 tests. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7543538/ doi: 10.1093/jlb/lsaa069 id: cord-002626-jzwwses4 author: Kaul, Karen L. title: The Case for Laboratory Developed Procedures: Quality and Positive Impact on Patient Care date: 2017-07-16 words: 14822.0 sentences: 754.0 pages: flesch: 40.0 cache: ./cache/cord-002626-jzwwses4.txt txt: ./txt/cord-002626-jzwwses4.txt summary: Clinical laboratories have thus had to develop new assays or modified the existing FDA-approved ones to detect high-risk HPV genotypes in head and neck cancer specimens. The vast majority of reporting laboratories utilized LDPs. 57 KRAS and RAS family gene mutation analysis is also critical in the management of patients with non-small-cell lung cancer (NSCLC) and other tumors, 58 for which FDA approval of kits has not occurred; LDPs or off-label use of kits is required. 74, 75 The FDA approval of anti-EGFR therapies based on clinical trial outcomes data resulted in the need for clinical laboratories to test tumor tissue for the EGFR-sensitizing mutations in order for patients to be eligible for treatment. During those ground-breaking first 15 years of the targeted cancer therapy era, if the laboratory community had been prohibited from providing high-quality, standardized LDP-based testing under existing CLIA guidelines, the negative consequences to patient care in the past and the future would have been substantial. abstract: An explosion of knowledge and technology is revolutionizing medicine and patient care. Novel testing must be brought to the clinic with safety and accuracy, but also in a timely and cost-effective manner, so that patients can benefit and laboratories can offer testing consistent with current guidelines. Under the oversight provided by the Clinical Laboratory Improvement Amendments, laboratories have been able to develop and optimize laboratory procedures for use in-house. Quality improvement programs, interlaboratory comparisons, and the ability of laboratories to adjust assays as needed to improve results, utilize new sample types, or incorporate new mutations, information, or technologies are positive aspects of Clinical Laboratory Improvement Amendments oversight of laboratory-developed procedures. Laboratories have a long history of successful service to patients operating under Clinical Laboratory Improvement Amendments. A series of detailed clinical examples illustrating the quality and positive impact of laboratory-developed procedures on patient care is provided. These examples also demonstrate how Clinical Laboratory Improvement Amendments oversight ensures accurate, reliable, and reproducible testing in clinical laboratories. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5528950/ doi: 10.1177/2374289517708309 id: cord-018335-4l7scdqk author: Kiechle, Frederick L. title: Utilization Management in a Large Community Hospital date: 2016-12-01 words: 11062.0 sentences: 549.0 pages: flesch: 40.0 cache: ./cache/cord-018335-4l7scdqk.txt txt: ./txt/cord-018335-4l7scdqk.txt summary: In preparation for the shift from fee-for-service to a valuebased payment system [ 15 ] large community hospitals have been actively engaged in three enterprises which will impact laboratory test utilization: buying physician practices, increasing the use of hospitalists and consolidation of hospitals. Certainly, utilization management of POCT programs will require investigations to determine the relationship between total laboratory turn-around time for results, patient outcome and hospital costs using cost effectiveness analyses [ 36 ] . As technology advances, the traditionally " agrarian society " of the laboratory is becoming more industrialized with the implementation of automation, molecular based testing, and use of mass spectrometry ( MALDI-TOF -Matrix-Assisted Laser Desorption Ionization-Time of Flight). However, all of these technological advances are shortening the time for a laboratory diagnosis and ultimately maximizing the impact to patient care and how physicians at a large community hospital will utilize the more rapid microbiology laboratory services. abstract: The utilization management of laboratory tests in a large community hospital is similar to academic and smaller community hospitals. There are numerous factors that influence laboratory utilization. Outside influences like hospitals buying physician practices, increasing numbers of hospitalists, and hospital consolidation will influence the number and complexity of the test menu that will need to be monitored for over and/or under utilization in the central laboratory and reference laboratory. CLIA’88 outlines the four test categories including point-of-care testing (waived) and provider-performed microscopy that need laboratory test utilization management. Incremental cost analysis is the most efficient method for evaluating utilization reduction cost savings. Economies of scale define reduced unit cost per test as test volume increases. Outreach programs in large community hospitals provide additional laboratory tests from non-patients in physician offices, nursing homes, and other hospitals. Disruptive innovations are changing the present paradigms in clinical diagnostics, like wearable sensors, MALDI-TOF, multiplex infectious disease panels, cell-free DNA, and others. Obsolete tests need to be universally defined and accepted by manufacturers, physicians, laboratories, and hospitals, to eliminate access to their reagents and testing platforms. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123185/ doi: 10.1007/978-3-319-34199-6_14 id: cord-307123-h48uwj93 author: Kiechle, Frederick L. title: Establishing benchmarks and metrics for disruptive technologies, inappropriate and obsolete tests in the clinical laboratory date: 2014-01-01 words: 5416.0 sentences: 298.0 pages: flesch: 40.0 cache: ./cache/cord-307123-h48uwj93.txt txt: ./txt/cord-307123-h48uwj93.txt summary: Examples include guidelines for hypothyroidism in adults from the American Association of Clinical Endocrinologists and the American Thyroid Association [30] , definition of myocardial infarction from the American College of Cardiology Foundation and American Heart Association [31] , definition of diabetes mellitus from the American Diabetes Association [32] , pharmacogenetics as well as follow-up testing for metabolic diseases identified by expanded newborn screening using tandem mass spectrometry from the National Academy of Clinical Biochemistry [33, 34] , and use of bone metabolic markers from the Japan Osteoporosis Society [35] . This is an example of testing that was removed from the market based on recommendations from the Centers for Disease Control (CDC) stating that the rapid antigen detection tests for GBS are not sensitive enough to replace the culture based prenatal screening or to use in place of the risk-based approach when culture results are unknown at the time of labor [51] . abstract: Benchmarks and metrics related to laboratory test utilization are based on evidence-based medical literature that may suffer from a positive publication bias. Guidelines are only as good as the data reviewed to create them. Disruptive technologies require time for appropriate use to be established before utilization review will be meaningful. Metrics include monitoring the use of obsolete tests and the inappropriate use of lab tests. Test utilization by clients in a hospital outreach program can be used to monitor the impact of new clients on lab workload. A multi-disciplinary laboratory utilization committee is the most effective tool for modifying bad habits, and reviewing and approving new tests for the lab formulary or by sending them out to a reference lab. url: https://doi.org/10.1016/j.cca.2013.05.024 doi: 10.1016/j.cca.2013.05.024 id: cord-328320-1f3r80r5 author: Kim, Edward title: Drawing on Israel’s Experience Organizing Volunteers to Operationalize Drive-Through Coronavirus Testing Centers date: 2020-04-16 words: 1432.0 sentences: 76.0 pages: flesch: 51.0 cache: ./cache/cord-328320-1f3r80r5.txt txt: ./txt/cord-328320-1f3r80r5.txt summary: title: Drawing on Israel''s Experience Organizing Volunteers to Operationalize Drive-Through Coronavirus Testing Centers To increase the country''s capacity to test and track suspected coronavirus disease 2019 (COVID-19) cases, Israel launched drive-through testing centers in key cities, including Tel Aviv, Jerusalem, Be''er Sheva, and Haifa. This article examines the challenges that the national emergency medical services and volunteers faced in the process of implementing drive-through testing centers to offer lessons learned and direction to health-care professionals in other countries. 5 Working alongside the Ministry of Health, Magen David Adom (MDA)-Israel''s emergency medical, disaster, ambulance, and blood bank service-operationalized drive-through coronavirus testing centers, mirroring the models used by China and South Korea. The testing centers are staffed with medical teams, police officers, security personnel, and volunteer students, and can process 6 lanes of cars in parallel, taking on average 3-5 min per car. To quickly operationalize "drive and test" facilities while allowing for process improvements, MDA used the Plan-Do-Check-Act methodology. abstract: To increase the country’s capacity to test and track suspected coronavirus disease 2019 (COVID-19) cases, Israel launched drive-through testing centers in key cities, including Tel Aviv, Jerusalem, Be’er Sheva, and Haifa. This article examines the challenges that the national emergency medical services and volunteers faced in the process of implementing drive-through testing centers to offer lessons learned and direction to health-care professionals in other countries. url: https://doi.org/10.1017/dmp.2020.104 doi: 10.1017/dmp.2020.104 id: cord-308021-cnf4xljc author: Kohns Vasconcelos, Malte title: SARS-CoV-2 testing and infection control strategies in European paediatric emergency departments during the first wave of the pandemic date: 2020-10-13 words: 1981.0 sentences: 99.0 pages: flesch: 47.0 cache: ./cache/cord-308021-cnf4xljc.txt txt: ./txt/cord-308021-cnf4xljc.txt summary: Between February and May 2020, during the first wave of the COVID-19 pandemic, paediatric emergency departments in 12 European countries were prospectively surveyed on their implementation of SARS-CoV-2 disease (COVID-19) testing and infection control strategies. All participating departments (23) implemented standardised case definitions, testing guidelines, early triage and infection control strategies early in the outbreak. Paediatric departments of 23 mostly tertiary care hospitals in 12 European countries (Belgium, Germany, France, Italy, Poland, Portugal, the UK, the Netherlands, Greece, Spain, Lithuania and Switzerland) participated in the surveys (response rate 29%). This changed by April at all three sites, so that afterwards detection of another pathogen that could explain the respiratory symptoms no longer excluded a patient from being a suspect case and from undergoing SARS-CoV-2 testing. In the early stages of the COVID-19 pandemic, paediatric emergency departments implemented standardised case definitions, testing guidelines and infection control measures rapidly. abstract: Between February and May 2020, during the first wave of the COVID-19 pandemic, paediatric emergency departments in 12 European countries were prospectively surveyed on their implementation of SARS-CoV-2 disease (COVID-19) testing and infection control strategies. All participating departments (23) implemented standardised case definitions, testing guidelines, early triage and infection control strategies early in the outbreak. Patient testing criteria initially focused on suspect cases and later began to include screening, mainly for hospital admissions. Long turnaround times for test results likely put additional strain on healthcare resources. Conclusion: Shortening turnaround times for SARS-CoV-2 tests should be a priority. Specific paediatric testing criteria are needed. url: https://www.ncbi.nlm.nih.gov/pubmed/33051714/ doi: 10.1007/s00431-020-03843-w id: cord-034948-w59wxu8i author: Kuriyama, Akira title: Performance of the cuff leak test in adults in predicting post-extubation airway complications: a systematic review and meta-analysis date: 2020-11-07 words: 4775.0 sentences: 268.0 pages: flesch: 49.0 cache: ./cache/cord-034948-w59wxu8i.txt txt: ./txt/cord-034948-w59wxu8i.txt summary: We conducted a systematic review and meta-analysis to assess the diagnostic accuracy of the cuff leak test for predicting post-extubation airway complications in intubated adult patients in critical care settings. We included studies that examined the diagnostic accuracy of cuff leak test if post-extubation airway obstruction after extubation or reintubation was explicitly reported as the reference standard. Subgroup analyses suggested that the type of cuff leak test and length of intubation might be the cause of statistical heterogeneity of sensitivity and specificity, respectively, for post-extubation airway obstruction. Consequently, we conducted a systematic review and meta-analysis to assess the diagnostic accuracy of the cuff leak test for predicting post-extubation airway obstruction and subsequent reintubation. We included observational studies (cross-sectional and cohort studies) that examined the diagnostic accuracy of cuff leak test in critical care settings if: (1) the data were extractable into a 2 × 2 table from the reported data, (2) post-extubation airway obstruction after extubation or reintubation was explicitly reported as the reference standard. abstract: BACKGROUND: Clinical practice guidelines recommend performing a cuff leak test in mechanically ventilated adults who meet extubation criteria to screen those at high risk for post-extubation stridor. Previous systematic reviews demonstrated excellent specificity of the cuff leak test but disagreed with respect to sensitivity. We conducted a systematic review and meta-analysis to assess the diagnostic accuracy of the cuff leak test for predicting post-extubation airway complications in intubated adult patients in critical care settings. METHODS: We searched Medline, EMBASE, Scopus, ISI Web of Science, the Cochrane Library for eligible studies from inception to March 16, 2020, without language restrictions. We included studies that examined the diagnostic accuracy of cuff leak test if post-extubation airway obstruction after extubation or reintubation was explicitly reported as the reference standard. Two authors in duplicate and independently assessed the risk of bias using the Quality Assessment for Diagnostic Accuracy Studies-2 tool. We pooled sensitivities and specificities using generalized linear mixed model approach to bivariate random-effects meta-analysis. Our primary outcomes were post-extubation airway obstruction and reintubation. RESULTS: We included 28 studies involving 4493 extubations. Three studies were at low risk for all QUADAS-2 risk of bias domains. The pooled sensitivity and specificity of cuff leak test for post-extubation airway obstruction were 0.62 (95% CI 0.49–0.73; I(2) = 81.6%) and 0.87 (95% CI 0.82–0.90; I(2) = 97.8%), respectively. The pooled sensitivity and specificity of the cuff leak test for reintubation were 0.66 (95% CI 0.46–0.81; I(2) = 48.9%) and 0.88 (95% CI 0.83–0.92; I(2) = 87.4%), respectively. Subgroup analyses suggested that the type of cuff leak test and length of intubation might be the cause of statistical heterogeneity of sensitivity and specificity, respectively, for post-extubation airway obstruction. CONCLUSIONS: The cuff leak test has excellent specificity but moderate sensitivity for post-extubation airway obstruction. The high specificity suggests that clinicians should consider intervening in patients with a positive test, but the low sensitivity suggests that patients still need to be closely monitored post-extubation. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7648377/ doi: 10.1186/s13054-020-03358-8 id: cord-273324-xhpv783y author: Land, Kevin J. title: REASSURED diagnostics to inform disease control strategies, strengthen health systems and improve patient outcomes date: 2018-12-13 words: 7423.0 sentences: 298.0 pages: flesch: 41.0 cache: ./cache/cord-273324-xhpv783y.txt txt: ./txt/cord-273324-xhpv783y.txt summary: For example, as POC technologies for HIV viral load and early infant diagnosis were being developed, there was tremendous emphasis on quality, given the complexity of the test and lessons learned from HIV RDTs. Malaria is estimated to be the cause of at least a million deaths a year worldwide, most of which are in sub-Saharan Africa. Although national TB programmes provide a robust architecture for the implementation of new technologies, challenges associated with the near-POC NAT assay remain as barriers -affordability (molecular assays are device-based and costly, even with subsidy), expertise (more technically demanding than lateral flow RDTs) and sustainability 46 , in addition to power and per-test time. Such tests can only be created by forming strong collaborative partnerships across many disciplinary boundaries, and we look toward a future when data connectivity linking cost-effective ASSURED diagnostics to laboratory systems will form the backbone of health care systems and provide real-time data for evidence-based disease control and prevention strategies, more efficient health systems and improved patient outcomes. abstract: Lack of access to quality diagnostics remains a major contributor to health burden in resource-limited settings. It has been more than 10 years since ASSURED (affordable, sensitive, specific, user-friendly, rapid, equipment-free, delivered) was coined to describe the ideal test to meet the needs of the developing world. Since its initial publication, technological innovations have led to the development of diagnostics that address the ASSURED criteria, but challenges remain. From this perspective, we assess factors contributing to the success and failure of ASSURED diagnostics, lessons learnt in the implementation of ASSURED tests over the past decade, and highlight additional conditions that should be considered in addressing point-of-care needs. With rapid advances in digital technology and mobile health (m-health), future diagnostics should incorporate these elements to give us REASSURED diagnostic systems that can inform disease control strategies in real-time, strengthen the efficiency of health care systems and improve patient outcomes. url: https://www.ncbi.nlm.nih.gov/pubmed/30546093/ doi: 10.1038/s41564-018-0295-3 id: cord-345454-r1ymzk6n author: Levesque, J. title: A note on COVID-19 seroprevalence studies: a meta-analysis using hierarchical modelling date: 2020-05-06 words: 3631.0 sentences: 230.0 pages: flesch: 61.0 cache: ./cache/cord-345454-r1ymzk6n.txt txt: ./txt/cord-345454-r1ymzk6n.txt summary: Many of these studies find an antibody prevalence comparable to the false positive rate of their respective serology tests and the relatively low statistical power associated with each study has invited criticism. To determine the strength of the signal, we perform a meta-analysis on the publicly available seroprevalence data based on Bayesian hierarchical modelling with Markov Chain Monte Carlo and Generalized Linear Mixed Modelling with prediction sampling. The Santa Clara study shows a density function consistent with a high probability of a non-zero antibody prevalence, with a mean and a mode slightly greater than 1%, although we note that the posterior distribution does include zero. Figure 2 : The two dimensional marginal posterior distribution functions for antibody prevalence with the false positive rate at each study location from Bayesian hierarchical model. Figure 7 shows the resulting density functions for the antibody prevalence in each location from the GLMM prediction sampling. abstract: In recent weeks, several seroprevalence studies have appeared which attempt to determine the prevalence of antibodies against SARS-CoV-2 in the population of certain European and American locations. Many of these studies find an antibody prevalence comparable to the false positive rate of their respective serology tests and the relatively low statistical power associated with each study has invited criticism. To determine the strength of the signal, we perform a meta-analysis on the publicly available seroprevalence data based on Bayesian hierarchical modelling with Markov Chain Monte Carlo and Generalized Linear Mixed Modelling with prediction sampling. We examine studies with results from Santa Clara County (CA), Los Angeles County (CA), San Miguel County (CO), Chelsea (MA), the comte de Geneve (Switzerland), and Gangelt (Germany). Our results are in broad agreement with the conclusions of the studies; we find that there is evidence for non-trivial levels of antibody prevalence across all study locations. However, we also find that a significant probability mass exists for antibody prevalence at levels lower than the reported figures. The results of our meta-analysis on the recent seroprevalence studies point to an important and strongly suggestive signal. url: https://doi.org/10.1101/2020.05.03.20089201 doi: 10.1101/2020.05.03.20089201 id: cord-252959-ktet18wl author: Lim, Jong-Min title: Ingestion of Exopolymers from Aureobasidium pullulans Reduces the Duration of Cold and Flu Symptoms: A Randomized, Placebo-Controlled Intervention Study date: 2018-05-30 words: 6389.0 sentences: 278.0 pages: flesch: 45.0 cache: ./cache/cord-252959-ktet18wl.txt txt: ./txt/cord-252959-ktet18wl.txt summary: Subjects for whom the following criteria were applicable were excluded from the experiment: individuals with a body mass index (BMI) under 18 or over 35; individuals who exceeded the normal maximum alanine transaminase and aspartate transaminase levels by 2-fold; females who were pregnant or were breast-feeding; females of childbearing age who did not agree to use contraceptives via medically proven methods (e.g., condoms, lubricant, and femidom) during the test period; individuals with a fasting plasma dextrose concentration over 126 mg/dL; individuals with high blood pressure (systolic blood pressure of 160 mm Hg or diastolic blood pressure of 100 mm Hg); individuals continuously using medicine that could affect the effectiveness assessment (hyperlipidemia medicine, steroid medicines, hormone medicines, immunosuppressants, and antibiotics); individuals who require continuous treatment for psychiatric disorders such as anorexia, depression, and manic depression; individuals with systemic diseases such as immunity-related diseases, serious hepatic and renal insufficiencies, malignant tumors, pulmonary disease, collagenosis, multiple sclerosis, allergic skin conditions, and other autoimmune diseases; individuals with a medical history of drugs and clinically significant allergic reactions; individuals with a history of gastrointestinal disorders that could affect the absorption of the test foods or a history of gastrointestinal surgery (excluding a simple appendectomy or hernia operation); individuals who consumed medicine or herbal medicines within a month of participation in the experiment which could affect immunity; individuals who participated in a different human study or clinical test and took experimental products within 3 months of participation in this experiment (excluding human studies with cosmetics); and individuals whom the researchers otherwise determined might have difficulty completing the experiment. abstract: AIM: The objective of the study was to assess the efficacy of exopolymers from Aureobasidium pullulans (EAP) on the incidence of colds and flu in healthy adults. METHODS: We conducted a randomized, double-blind, placebo-controlled study at the onset of the influenza season. A total of 76 subjects (30–70 years of age) were recruited from the general population. The subjects were instructed to take one capsule per day of either EAP or a placebo for a period of 8 weeks. The duration of cold and flu symptoms, a primary variable in assessing effectiveness, and serum cytokine levels as well as WBC counts as secondary variables were also evaluated. RESULTS: EAP was associated with a statistically significant decrease in the duration of cold and flu symptoms, a primary variable in assessing effectiveness. Although cold and flu symptom levels were not significantly different at a significance level of 5%, the cold and flu symptom levels of the EAP group were less severe compared to the placebo group. No statistically significant changes of serum cytokine levels as well as WBC counts were observed. CONCLUSION: The results showed that EAP is a useful pharmaceutical and functional food material for preventing and treating colds and flu. url: https://doi.org/10.1155/2018/9024295 doi: 10.1155/2018/9024295 id: cord-332481-y0rd70ry author: Ljubic, T. title: The effect of serological screening for SARS-CoV-2 antibodies to participants'' attitudes and risk behaviour: a study on a tested population sample of industry workers in Split-Dalmatia County, Croatia date: 2020-06-17 words: 3846.0 sentences: 190.0 pages: flesch: 47.0 cache: ./cache/cord-332481-y0rd70ry.txt txt: ./txt/cord-332481-y0rd70ry.txt summary: title: The effect of serological screening for SARS-CoV-2 antibodies to participants'' attitudes and risk behaviour: a study on a tested population sample of industry workers in Split-Dalmatia County, Croatia Rapid serological tests for SARS-CoV-2 antibodies have been questioned by scientists and the public because of unexplored effects of negative test results on behaviour and attitudes, that could lower the level of adherence to protective measures. Thus, this study aims at investigating the changes in personal attitudes and behaviour of DIV Group industry workers before and after receiving negative serological test results for SARS-CoV-2 antibodies. The results of this study indicate that the levels of fear of being infected or infecting others with COVID-19, as well as behaviours regarding adherence to protective measure, changed significantly in the timeframe after receiving negative test results. abstract: Rapid serological tests for SARS-CoV-2 antibodies have been questioned by scientists and the public because of unexplored effects of negative test results on behaviour and attitudes, that could lower the level of adherence to protective measures. Therefore, our study aimed to investigate the changes in personal attitudes and behaviour before and after negative serological test results for SARS-CoV-2 antibodies. We conducted a survey questionnaire on 200 industry workers (69% males and 31% females) that have been previously tested negative. The survey examined participants' self-reported general attitudes towards COVID-19, sense of fear, as well as their behaviour related to protective measures before and after the testing. The participants perceived the disease as a severe health threat and acknowledged the protective measures as appropriate. They reported a high level of adherence to measures and low level of fear both before and after the testing. Although those indicators were statistically significantly reduced after the test (P < 0.004), they did not result in risk behaviour. Therefore, the serological tests are not an additional threat regarding the risk behaviour in an environment where protective measures are efficient. In contrast, they might contribute to reducing the fear in the society and working environment. url: https://doi.org/10.1101/2020.06.15.20131482 doi: 10.1101/2020.06.15.20131482 id: cord-298441-77w86l8q author: Lombardi, Andrea title: Characteristics of 1,573 healthcare workers who underwent nasopharyngeal swab for SARS-CoV-2 in Milano, Lombardy, Italy date: 2020-06-20 words: 1438.0 sentences: 67.0 pages: flesch: 52.0 cache: ./cache/cord-298441-77w86l8q.txt txt: ./txt/cord-298441-77w86l8q.txt summary: To answer this question, we reviewed all the 59 nasopharyngeal swab performed in HCWs exposed to confirmed cases of COVID-19 at the 60 Foundation IRCCS Ca'' Granda Ospedale Maggiore Policlinico located in Milan, the capital 61 of Lombardy, by large the Italian region mostly affected by We assessed 62 frequency of positive tests among symptomatic and asymptomatic HCWs and evaluated the 63 association between occupation, symptoms (type and number), and presence of the infection. Therefore, in middle-and high-resource settings a mass screening for all 163 HCWs exposed to confirmed COVID-19 cases appears the best approach to limit the spread When stratified according to occupation, test-positive frequencies were clearly higher among 177 subsets with direct contact with patients (physicians including residents, nurses and 178 midwives, healthcare assistants and health technicians) than those without (clerical works and 179 technicians). abstract: OBJECTIVES: The management of healthcare workers (HCWs) exposed to confirmed cases of COVID-19 is still a matter of debate. We aimed to assess in this group the attack rate of asymptomatic carriers and the symptoms most frequently associated with the infection. METHODS: Occupational and clinical characteristics of HCWs who performed a nasopharyngeal swab for the detection of SARS-CoV-2 in a University Hospital from February 24, to March 31, 2020, were collected. For those who tested positive and for the asymptomatic positives we checked laboratory and clinical data as of May 22 to calculate the time necessary to become test-negative and to verify whether symptoms developed thereafter. Frequencies of positive tests were compared according to selected variables using multivariable logistic regression models. RESULTS: Positive tests were 139 among 1,573 HCWs (8.8%, 95% confidence interval [CI]: 7.5-10.3), with a marked difference between symptomatic (122/503, 24.2%) and asymptomatic (17/1,070, 1.6%) workers (p<0.001). Physicians were the group with the highest frequency of positive tests (61/582, 10.5%), whereas clerical workers and technicians displayed the lowest frequency (5/137, 3.6%). The likelihood of being positive increased with the number of reported symptoms and the strongest predictors were taste and smell alterations (odds ratio [OR]= 76.9) and fever (OR = 9.12). The median time from first positive test to a negative test was 27 days (95% CI: 24-30). CONCLUSIONS: A relevant number of HCWs can be infected by SARS-CoV-2 without displaying any symptom. Among symptomatic workers, the key symptoms to guide diagnosis are taste and smell alterations and fever. In median, almost four weeks are necessary to achieve negativity of nasopharyngeal swab. url: https://www.ncbi.nlm.nih.gov/pubmed/32569835/ doi: 10.1016/j.cmi.2020.06.013 id: cord-102817-m1l1t0e1 author: Lucas, T. C. title: Responsible modelling: Unit testing for infectious disease epidemiology date: 2020-08-16 words: 6076.0 sentences: 412.0 pages: flesch: 66.0 cache: ./cache/cord-102817-m1l1t0e1.txt txt: ./txt/cord-102817-m1l1t0e1.txt summary: At the time of writing, infectious disease modellers are playing a central role in the interpretation of available data on the COVID-19 pandemic to inform policy design and evaluation [1] [2] [3] . We do not know of high profile cases of infectious disease models being found to have bugs once published, but as code is not always shared and little post-publication testing of code occurs, this likely represents a failure of detection. It is also notable that there are few texts available which demonstrate the use of unit testing to check infectious disease models. Unit testing is a formally-defined, principled framework that compares comprehensive output scenarios from code to what the programmer expected to happen ( [22] Chapter 7, [23] , [24] ). Instead we devise tests that cover standard usage as well as corner case scenarios: what do we want our function to do if given a negative number e.g. sqrt(-1), or a vector argument containing strings or missing values e.g. sqrt(c(4,"melon",NA))? abstract: Infectious disease epidemiology is increasingly reliant on large-scale computation and inference. Models have guided health policy for epidemics including COVID- 19 and Ebola and endemic diseases such as malaria and tuberculosis. Yet a single coding bug may bias results, leading to incorrect conclusions and wrong actions that could cause avoidable harm. We are ethically obliged to ensure our code is as free of error as possible. Unit testing is a coding method to avoid such bugs, but unit testing is rarely used in epidemiology. We demonstrate through simple examples how unit testing can handle the particular quirks of infectious disease models. url: http://medrxiv.org/cgi/content/short/2020.08.14.20175216v1?rss=1 doi: 10.1101/2020.08.14.20175216 id: cord-298086-pbfi5c8e author: Lyngse, F. P. title: COVID-19 Transmission Within Danish Households: A Nationwide Study from Lockdown to Reopening date: 2020-09-09 words: 7792.0 sentences: 547.0 pages: flesch: 63.0 cache: ./cache/cord-298086-pbfi5c8e.txt txt: ./txt/cord-298086-pbfi5c8e.txt summary: Methods We used comprehensive administrative register data from Denmark, comprising the full population and all COVID-19 tests, to estimate household transmission risk and attack rate. To our knowledge, this is the first nationwide study that uses estimates of household attack rates and transmission risks that exploit SARS-CoV-2 test data from an entire population. We defined the attack rate as the proportion of additional household members that tested positive, whereas the transmission risk was the proportion of secondary cases per primary case. To estimate the attack rate, we estimated the proportion of potential secondary household members who received a positive test within 14 days after the test date of the primary case. (In Appendix D, we illustrate changes over all three periods.) Figure 1 panel (a) shows that after receiving a positive test result in the household (t = 0), 36% of potential secondary cases were tested (blue) the day after the positive test result (t = 1) of the primary case was available and 13% of these 36% were positive (red). abstract: Background The Covid-19 pandemic is one of the most serious global public health threats in recent times. Understanding transmission of SARS-CoV-2 is of utmost importance to be able to respond to outbreaks and take action against spread of the disease. Transmission within the household is a concern, especially because infection control is difficult to apply within the household domain. Methods We used comprehensive administrative register data from Denmark, comprising the full population and all COVID-19 tests, to estimate household transmission risk and attack rate. Results We studied the testing dynamics for COVID-19 and found that the day after receiving a positive test result within the household, 35% of potential secondary cases were tested and 13% of these were positive. After a primary case in 6,782 households, 82% of potential secondary cases were tested within 14 days, of which 17% tested positive as secondary cases, implying an attack rate of 17%. Among primary cases, those aged 0-24 were underrepresented when compared with the total population. We found an approximately linearly increasing relationship between attack rate and age. We investigated the transmission risk from primary cases by age, and found an increasing risk with age of primary cases for adults, while the risk seems to decrease with age for children. Conclusions Although there is an increasing attack rate and transmission risk of SARS-CoV-2 with age, children are also able to transmit SARS-CoV-2 within the household. url: http://medrxiv.org/cgi/content/short/2020.09.09.20191239v1?rss=1 doi: 10.1101/2020.09.09.20191239 id: cord-121057-986xoy22 author: Mahdi, Esam title: Simultaneous Diagnostic Testing for Linear-Nonlinear Dependence in Time Series date: 2020-08-18 words: 4230.0 sentences: 213.0 pages: flesch: 57.0 cache: ./cache/cord-121057-986xoy22.txt txt: ./txt/cord-121057-986xoy22.txt summary: In this respect, Engle (1982) showed that the classical portmanteau tests proposed by Box and Pierce (1970) and Ljung and Box (1978) , based on the autocorrelation function of the residuals, fail to detect the presence of the Autoregressive Conditional Heteroscedasticity, arch , in many financial time series models. In Section 2 we discuss the generalized correlations of residuals and review some test statistics that have been commonly used to detect nonlinearity structure in stationary time series models. In Section 3, we propose new goodness-of-fit (auto-and-cross-correlated) tests that can be used to detect, simultaneously, linear, bilinear, and nonlinear dependency in time series models, and derive their asymptotic distribution as a chi-squared distribution. In this article, we propose four goodness-of-fit tests to detect various types of linear and nonlinear dependency in stationary time series models. abstract: Several goodness-of-fit tests have been proposed to detect linearity in stationary time series based on the autocorrelations of the residuals. Others have been developed based on the autocorrelations of the square residuals or based on the cross-correlations between residuals and their squares to test for nonlinearity. In this paper, we propose omnibus portmanteau tests that can be used for detecting, simultaneously, many linear, bilinear, and nonlinear dependence structures in stationary time series based on combining all these correlations. An extensive simulation study is conducted to examine the finite sample performance of the proposed tests. The simulation results show that the proposed tests successfully control the Type I error probability and tend to be more powerful than other tests in most cases. The efficacy of the proposed tests is demonstrated through the analysis of Amazon.com, Inc., daily log-returns. url: https://arxiv.org/pdf/2008.08176v1.pdf doi: nan id: cord-337458-dc90ecfe author: Markwalter, Christine F. title: Inorganic Complexes and Metal-Based Nanomaterials for Infectious Disease Diagnostics date: 2018-12-04 words: 40568.0 sentences: 2391.0 pages: flesch: 40.0 cache: ./cache/cord-337458-dc90ecfe.txt txt: ./txt/cord-337458-dc90ecfe.txt summary: In this review, we define the components of a diagnostic to include: (1) the target biomarker, an endogenous indicator of a disease state, which is most often a pathogen or host protein, carbohydrate, or nucleic acid sequence, (2) sample preparation, which allows for biomarker isolation, purification, and/or concentration from complex biological matrices, (3) molecular recognition elements, which specifically capture and detect the target biomarker, (4) signal generation and amplification, and (5) instrumentation for signal read-out. 113, 114 In subsequent studies, the group developed and optimized a hand-held, easy-to-use device 85, 115 (Figure 8A ) in which HRP2-bound, IMAC-functionalized magnetic beads were directly transferred to the sample pad of commercial malaria lateral flow assays. If combined with one of the sample preparation strategies discussed previously (section 3) or integrated with paper or another field-ready substrate, this Ir(III)-based detection strategy could produce a robust and sensitive assay that is applicable in low-resource diagnostic settings. abstract: [Image: see text] Infectious diseases claim millions of lives each year. Robust and accurate diagnostics are essential tools for identifying those who are at risk and in need of treatment in low-resource settings. Inorganic complexes and metal-based nanomaterials continue to drive the development of diagnostic platforms and strategies that enable infectious disease detection in low-resource settings. In this review, we highlight works from the past 20 years in which inorganic chemistry and nanotechnology were implemented in each of the core components that make up a diagnostic test. First, we present how inorganic biomarkers and their properties are leveraged for infectious disease detection. In the following section, we detail metal-based technologies that have been employed for sample preparation and biomarker isolation from sample matrices. We then describe how inorganic- and nanomaterial-based probes have been utilized in point-of-care diagnostics for signal generation. The following section discusses instrumentation for signal readout in resource-limited settings. Next, we highlight the detection of nucleic acids at the point of care as an emerging application of inorganic chemistry. Lastly, we consider the challenges that remain for translation of the aforementioned diagnostic platforms to low-resource settings. url: https://doi.org/10.1021/acs.chemrev.8b00136 doi: 10.1021/acs.chemrev.8b00136 id: cord-286539-3sr4djft author: Mentus, Cassidy title: Analysis and Applications of Adaptive Group Testing Methods for COVID-19 date: 2020-04-07 words: 5533.0 sentences: 379.0 pages: flesch: 65.0 cache: ./cache/cord-286539-3sr4djft.txt txt: ./txt/cord-286539-3sr4djft.txt summary: If a population has a low prevalence of COVID-19 then it is likely for groups of individuals to not have any positive cases. We are therefore able to design a strategy to use less tests to determine whether each individual is positive or negative for the disease by testing mixtures of samples from groups. For each level of prevalence we specify a xed number of individuals to test their combined samples, performing binary search if it is positive. https://doi.org/10.1101/2020.04.05.20050245 doi: medRxiv preprint 9 Performance of group testing methods at dierent prevalences For our performance analysis, we sample populations of sizes N = 100, 1000 at prevelance levels p = .001, .01, .02, .03, .04, .05, .1, .15, .2, and .25. https://doi.org/10.1101/2020.04.05.20050245 doi: medRxiv preprint Figure 11 .1: For GBS32 we sample a population of size 10,000 and record the number of times each case is tested. abstract: Abstract Testing strategies for Covid-19 to maximize number of people tested is urgently needed. Recently, it has been demonstrated that RT-PCR has the sensitivity to detect one positive case in a mixed sample 32 cases [9]. In this paper we propose non-adaptive and adaptive group testing strategies based on generalized binary splitting (GBS) [2] where we restrict the group test to the largest group that can be used. The method starts by choosing a group from the population to be tested, performing a test on the combined sample from the entire group and progressively splitting the group further into subgroups. Compared to individual testing at 4% prevalence we save 74% at 1% we save 91% and at 1% we save 97% of tests. We analyze the number of times each sample is used and show the method is still efficient if we resort to testing a case individually if the sample is running low. Abstract In addition we recommend clinical screening to filter out individuals with symptoms and show this leaves us with a population with lower prevalence. Our approach is particularly applicable to vulnerable confined populations such as nursing homes, prisons, military ships and cruise ships. url: https://doi.org/10.1101/2020.04.05.20050245 doi: 10.1101/2020.04.05.20050245 id: cord-102704-wfuzk2dp author: Meza, Diana K. title: Predicting the presence and titer of rabies virus neutralizing antibodies from low-volume serum samples in low-containment facilities date: 2020-04-30 words: 3183.0 sentences: 192.0 pages: flesch: 43.0 cache: ./cache/cord-102704-wfuzk2dp.txt txt: ./txt/cord-102704-wfuzk2dp.txt summary: Despite small conflicts, titer predictions were correlated across tests repeated on different dates both for dog samples (r = 0.93), and for a second dataset of sera from wild common vampire bats (r = 0.72, N = 41), indicating repeatability. The pmRFFIT enables high-throughput detection of rabies virus neutralizing antibodies in low-biocontainment settings and is suited to studies in wild or captive animals where large serum volumes cannot be obtained. The binomial and log-normal models fit to 193 this data subset included only the fixed effect of the virus-infected N2A cell counts, but the random 194 effects were identical to those explained above (i.e. test date and field). A final distinction is that 316 instead of scoring microscope field or wells as virus positive or negative, the pmRFFIT predicts 317 serological status and RVNA titer from infected cell counts in a single serum dilution using statistical 318 abstract: Serology is a core component of the surveillance and management of viral zoonoses. Virus neutralization tests are a gold standard serological diagnostic, but requirements for large volumes of serum and high biosafety containment can limit widespread use. Here, focusing on Rabies lyssavirus, a globally important zoonosis, we developed a pseudotype micro-neutralization rapid fluorescent focus inhibition test (pmRFFIT) that overcomes these limitations. Specifically, we adapted an existing micro-neutralization test to use a green fluorescent protein–tagged murine leukemia virus pseudotype in lieu of pathogenic rabies virus, reducing the need for specialized reagents for antigen detection and enabling use in low-containment laboratories. We further used statistical analysis to generate rapid, quantitative predictions of the probability and titer of rabies virus neutralizing antibodies from microscopic imaging of neutralization outcomes. Using 47 serum samples from domestic dogs with neutralizing antibody titers estimated using the fluorescent antibody virus neutralization test (FAVN), pmRFFIT showed moderate sensitivity (78.79%) and high specificity (84.62%). Despite small conflicts, titer predictions were correlated across tests repeated on different dates both for dog samples (r = 0.93), and for a second dataset of sera from wild common vampire bats (r = 0.72, N = 41), indicating repeatability. Our test uses a starting volume of 3.5 μL of serum, estimates titers from a single dilution of serum rather than requiring multiple dilutions and end point titration, and may be adapted to target neutralizing antibodies against alternative lyssavirus species. The pmRFFIT enables high-throughput detection of rabies virus neutralizing antibodies in low-biocontainment settings and is suited to studies in wild or captive animals where large serum volumes cannot be obtained. url: https://doi.org/10.1101/2020.04.24.060095 doi: 10.1101/2020.04.24.060095 id: cord-307187-5blsjicu author: Missel, Malene title: A stoic and altruistic orientation towards their work: a qualitative study of healthcare professionals’ experiences of awaiting a COVID-19 test result date: 2020-11-11 words: 5818.0 sentences: 286.0 pages: flesch: 48.0 cache: ./cache/cord-307187-5blsjicu.txt txt: ./txt/cord-307187-5blsjicu.txt summary: title: A stoic and altruistic orientation towards their work: a qualitative study of healthcare professionals'' experiences of awaiting a COVID-19 test result The purpose of this study was to explore healthcare professionals'' experiences of awaiting a test result for a potential COVID-19 infection. RESULTS: The participating healthcare professionals'' experiences of awaiting a COVID-19 test result were found to be associated with a stoic and altruistic orientation towards their work. Therefore, this study aim to shed light on HCPs'' experiences of awaiting a test result for a potential COVID-19 infection through individual interviews. The comprehensive understanding illuminated the meaning of the participants'' experiences of awaiting a COVID-19 test result as a stoic and altruistic orientation towards their work. abstract: BACKGROUND: Extensive measures to reduce person-to-person transmission of COVID-19 are required to control the current outbreak. Special attention is directed at healthcare professionals as reducing the risk of infection in healthcare is essential. The purpose of this study was to explore healthcare professionals’ experiences of awaiting a test result for a potential COVID-19 infection. METHODS: Qualitative interviews with 15 healthcare professionals were performed, underpinned by a phenomenological hermeneutical analytical framework. RESULTS: The participating healthcare professionals’ experiences of awaiting a COVID-19 test result were found to be associated with a stoic and altruistic orientation towards their work. These healthcare professionals presented a strong professional identity overriding most concerns about their own health. The result of the coronavirus test was a decisive parameter for whether healthcare professionals could return to work. The healthcare professionals were aware that their family and friends were having a hard time knowing that the COVID-19 infection risk was part of their jobs. This concern did not, however, cause the healthcare professionals to falter in their belief that they were doing the right thing by focusing on their core area. The threat to own health ran through the minds of the healthcare professionals occasionally, which makes access to testing particularly important. CONCLUSION: The participating healthcare professionals had a strong professional identity. However, a discrepancy between an altruistic role as a healthcare professional and the expectations that come from the community was illuminated. A mental health coronavirus hotline for healthcare professionals is suggested. url: https://doi.org/10.1186/s12913-020-05904-0 doi: 10.1186/s12913-020-05904-0 id: cord-324944-ixh3ykrc author: Mitsakakis, Konstantinos title: Diagnostic tools for tackling febrile illness and enhancing patient management date: 2018-12-05 words: 20805.0 sentences: 961.0 pages: flesch: 45.0 cache: ./cache/cord-324944-ixh3ykrc.txt txt: ./txt/cord-324944-ixh3ykrc.txt summary: This review gives an overview of diagnostic technologies featuring a platform based approach: (i) assay (nucleic acid amplification technologies are examined); (ii) cartridge (microfluidic technologies are presented); (iii) instrument (various detection technologies are discussed); and at the end proposes a way that such technologies can be interfaced with electronic clinical decision-making algorithms towards a broad and complete diagnostic ecosystem. In studies that have recorded the clinical presentation of patients (and not only their laboratory results), the causes of fever in outpatients could be classified into four main syndromes: 1) acute respiratory infections (ARI, of any type); 2) diarrhea (gastroenteritis); 3) fever with another clear focus (e.g. meningitis or skin infection); and 4) non-specific fevers [13] (each diagnostic platform described in Section 5 focuses on at least one of the aforementioned cases). abstract: Most patients with acute infectious diseases develop fever, which is frequently a reason to visit health facilities in resource-limited settings. The symptomatic overlap between febrile diseases impedes their diagnosis on clinical grounds. Therefore, the World Health Organization promotes an integrated management of febrile illness. Along this line, we present an overview of endemic and epidemic etiologies of fever and state-of-the-art diagnostic tools used in the field. It becomes evident that there is an urgent need for the development of novel technologies to fulfill end-users' requirements. This need can be met with point-of-care and near-patient diagnostic platforms, as well as e-Health clinical algorithms, which co-assess test results with key clinical elements and biosensors, assisting clinicians in patient triage and management, thus enhancing disease surveillance and outbreak alerts. This review gives an overview of diagnostic technologies featuring a platform based approach: (i) assay (nucleic acid amplification technologies are examined); (ii) cartridge (microfluidic technologies are presented); (iii) instrument (various detection technologies are discussed); and at the end proposes a way that such technologies can be interfaced with electronic clinical decision-making algorithms towards a broad and complete diagnostic ecosystem. url: https://www.sciencedirect.com/science/article/pii/S0167931718304556 doi: 10.1016/j.mee.2018.10.001 id: cord-312477-2y88gzji author: Mlcochova, P. title: Combined point of care nucleic acid and antibody testing for SARS-CoV-2: a prospective cohort study in suspected moderate to severe COVID-19 disease. date: 2020-06-18 words: 4920.0 sentences: 281.0 pages: flesch: 52.0 cache: ./cache/cord-312477-2y88gzji.txt txt: ./txt/cord-312477-2y88gzji.txt summary: title: Combined point of care nucleic acid and antibody testing for SARS-CoV-2: a prospective cohort study in suspected moderate to severe COVID-19 disease. Methods We developed (i) an in vitro neutralization assay using a lentivirus expressing a genome encoding luciferase and pseudotyped with spike protein and (ii) an ELISA test to detect IgG antibodies to nucleocapsid (N) and spike (S) proteins from SARS-CoV-2. We then prospectively recruited participants with suspected moderate to severe COVID-19 and tested for SARS-CoV-2 nucleic acid in a combined nasal/throat swab using the standard laboratory RT-PCR and a validated rapid nucleic acid test. We then prospectively recruited participants with suspected moderate to severe COVID-19 and tested for SARS-CoV-2 nucleic acid in a combined nasal/throat swab using the standard laboratory RT-PCR and a validated rapid nucleic acid test. abstract: Abstract Background Rapid COVID-19 diagnosis in hospital is essential for patient management and identification of infectious patients to limit the potential for nosocomial transmission. The diagnosis is complicated by 30-50% of COVID-19 hospital admissions with negative nose/throat swabs negative for SARS-CoV-2 nucleic acid, frequently after the first week of illness when SARS-CoV-2 antibody responses become detectable. We assessed the diagnostic accuracy of combined rapid antibody point of care (POC) and nucleic acid assays for suspected COVID-19 disease in the emergency department. Methods We developed (i) an in vitro neutralization assay using a lentivirus expressing a genome encoding luciferase and pseudotyped with spike protein and (ii) an ELISA test to detect IgG antibodies to nucleocapsid (N) and spike (S) proteins from SARS-CoV-2. We tested two promising candidate lateral flow rapid fingerprick test with bands for IgG and IgM. We then prospectively recruited participants with suspected moderate to severe COVID-19 and tested for SARS-CoV-2 nucleic acid in a combined nasal/throat swab using the standard laboratory RT-PCR and a validated rapid nucleic acid test. Additionally, serum collected at admission was retrospectively tested by in vitro neutralization, ELISA and the candidate POC antibody tests. We determined the sensitivity and specificity of the individual and combined rapid POC diagnostic tests against a composite gold standard of neutralisation and the standard laboratory RT-PCR. Results 45 participants had specimens tested for nucleic acid in nose/throat swabs as well as stored sera for antibodies. Serum neutralisation assay, SARS-CoV-2 Spike IgG ELISA and the POC antibody test results were concordant. Using the composite gold standard, prevalence of COVID-19 disease was 53.3% (24/45). Median age was 73.5 (IQR 54.0-86.5) years in those with COVID-19 disease by our gold standard and 63.0 (IQR 41.0-72.0) years in those without disease. Median duration of symptoms was 7 days (IQR 1-8) in those with infection. The overall sensitivity of rapid NAAT diagnosis was 79.2% (95CI 57.8-92.9%) and 50.0% (11.8-88.2) at days 8-28. Sensitivity and specificity of the combined rapid POC diagnostic tests reached 100% (95CI 85.8-100) and 94.7% (95CI 74.0-99.0) overall. Conclusions Dual point of care SARS-CoV-2 testing can significantly improve diagnostic sensitivity, whilst maintaining high specificity. Rapid combined tests have the potential to transform our management of COVID-19, including inflammatory manifestations where nucleic acid test results are negative. A rapid combined approach will also aid recruitment into clinical trials and in prescribing therapeutics, particularly where potentially harmful immune modulators (including steroids) are used. url: http://medrxiv.org/cgi/content/short/2020.06.16.20133157v1?rss=1 doi: 10.1101/2020.06.16.20133157 id: cord-001253-3jnkki5z author: Mohammad, Fahim title: Advantages and Limitations of Anticipating Laboratory Test Results from Regression- and Tree-Based Rules Derived from Electronic Health-Record Data date: 2014-04-14 words: 3850.0 sentences: 178.0 pages: flesch: 55.0 cache: ./cache/cord-001253-3jnkki5z.txt txt: ./txt/cord-001253-3jnkki5z.txt summary: We used four types of input-age, gender, diagnoses (three-digit ICD-9 codes), and results of laboratory tests on blood samples added to the record in the seven days before a given test was ordered-to build simple, robust models for whether the result of a test would be within the reference interval (''''normal'''') or outside of it in a given direction (''''abnormal''''), treating high and low results separately. To determine how well sendout and in-house test results can be anticipated based on basic information available in the medical record, we used two independent methods-generalized linear modeling (GLM) and classification and regression trees (CART)to build simple, robust test-result predictors and then evaluated the performance of these predictors according to the standard clinical metrics of positive predictive value (PPV) and negative predictive value (NPV), as well as sensitivity and specificity via the receiveroperator curve (ROC) area under the curve (AUC). abstract: Laboratory testing is the single highest-volume medical activity, making it useful to ask how well one can anticipate whether a given test result will be high, low, or within the reference interval (“normal”). We analyzed 10 years of electronic health records—a total of 69.4 million blood tests—to see how well standard rule-mining techniques can anticipate test results based on patient age and gender, recent diagnoses, and recent laboratory test results. We evaluated rules according to their positive and negative predictive value (PPV and NPV) and area under the receiver-operator characteristic curve (ROC AUCs). Using a stringent cutoff of PPV and/or NPV≥0.95, standard techniques yield few rules for sendout tests but several for in-house tests, mostly for repeat laboratory tests that are part of the complete blood count and basic metabolic panel. Most rules were clinically and pathophysiologically plausible, and several seemed clinically useful for informing pre-test probability of a given result. But overall, rules were unlikely to be able to function as a general substitute for actually ordering a test. Improving laboratory utilization will likely require different input data and/or alternative methods. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3986061/ doi: 10.1371/journal.pone.0092199 id: cord-354006-j1y42oxu author: Ozdemir, Vural title: Shifting emphasis from pharmacogenomics to theragnostics date: 2006 words: 4200.0 sentences: 142.0 pages: flesch: 29.0 cache: ./cache/cord-354006-j1y42oxu.txt txt: ./txt/cord-354006-j1y42oxu.txt summary: As biomarker applications move towards point-of-care to individualize drug therapy, a number of qualitatively different concerns arise relating to gene patents and ethical and therapeutic policy aspects of theragnostic testing 4, 8, 9 . In the present analyses, we ''unpack'' and contrast the motivations at play that are driving the pursuit for theragnostic patents and its bioethical corollaries in: (1) fundamental upstream basic research oriented to the discovery of genes for human diseases; and (2) downstream clinical applications at point-of-care as theragnostic tests to stratify patient populations for individualization of pharmacotherapy. While genetic tests hold the promise of a more rational clinical forecast and management of disease risk in the future, they are also raising concerns about the provision of public healthcare services (reduced access) and the impact of market forces on the products of research (commercialization of technologies) and academic freedom. abstract: What will be the role of theragnostic patents in upstream and downstream biomarker research? url: https://www.ncbi.nlm.nih.gov/pubmed/16900136/ doi: 10.1038/nbt0806-942 id: cord-320970-ru2iw0py author: Peeling, Rosanna W title: Serology testing in the COVID-19 pandemic response date: 2020-07-17 words: 3669.0 sentences: 186.0 pages: flesch: 49.0 cache: ./cache/cord-320970-ru2iw0py.txt txt: ./txt/cord-320970-ru2iw0py.txt summary: On the basis of our knowledge and understanding of viral infectivity and host response, we urge countries without the capacity to do molecular testing at scale to research the use of serology tests to triage symptomatic patients in community settings, to test contacts of confirmed cases, and in situational analysis and surveillance. Point-of-care molecular assays for SARS-CoV-2 detection are now available to enable community-based testing for COVID-19 in LMICs. Unfortunately, the production of these test cartridges takes time and, again, global demand has outstripped supply, leaving LMICs struggling for access. On the basis of our current knowledge and understanding of viral infectivity and host response, we urge countries with restricted capacity for molecular testing to embark on research into the use of serology tests in triaging symptomatic patients in community settings, testing contacts of confirmed cases, and in situational analysis and surveillance. abstract: The collapse of global cooperation and a failure of international solidarity have led to many low-income and middle-income countries being denied access to molecular diagnostics in the COVID-19 pandemic response. Yet the scarcity of knowledge on the dynamics of the immune response to infection has led to hesitation on recommending the use of rapid immunodiagnostic tests, even though rapid serology tests are commercially available and scalable. On the basis of our knowledge and understanding of viral infectivity and host response, we urge countries without the capacity to do molecular testing at scale to research the use of serology tests to triage symptomatic patients in community settings, to test contacts of confirmed cases, and in situational analysis and surveillance. The WHO R&D Blue Print expert group identified eight priorities for research and development, of which the highest is to mobilise research on rapid point-of-care diagnostics for use at the community level. This research should inform control programmes of the required performance and utility of rapid serology tests, which, when applied specifically for appropriate public health measures to then be put in place, can make a huge difference. url: https://www.sciencedirect.com/science/article/pii/S147330992030517X doi: 10.1016/s1473-3099(20)30517-x id: cord-288982-63ddlh20 author: Peeling, Rosanna W. title: Diagnostics in a digital age: an opportunity to strengthen health systems and improve health outcomes date: 2015-11-09 words: 4391.0 sentences: 216.0 pages: flesch: 44.0 cache: ./cache/cord-288982-63ddlh20.txt txt: ./txt/cord-288982-63ddlh20.txt summary: Rapid point-of-care (POC) tests for infectious diseases can improve access to diagnosis and patient management, but the quality of these tests vary, quality of testing is often not assured and there are few mechanisms to capture test results for surveillance when the testing is so decentralised. In a digital age, it is possible to link data from diagnostic laboratories and POC test readers and devices to provide data on testing coverage, disease trends and timely information for early warning of infectious disease outbreaks to inform design or optimisation of disease control and elimination programmes. In the last decade, rapid point-of-care (POC) diagnostic tests fulfilling the ASSURED criteria (Affordable, Sensitive, Specific, User-friendly, Rapid and robust, Equipment-free and Deliverable) have become commercially available and are widely used for infectious diseases such as malaria, HIV and syphilis. abstract: Diagnostics play a critical role in clinical decision making, and in disease control and prevention. Rapid point-of-care (POC) tests for infectious diseases can improve access to diagnosis and patient management, but the quality of these tests vary, quality of testing is often not assured and there are few mechanisms to capture test results for surveillance when the testing is so decentralised. A new generation of POC molecular tests that are highly sensitive and specific, robust and easy to use are now available for deployment in low resource settings. Decentralisation of testing outside of the laboratory can put tremendous stress on the healthcare system and presents challenges for training and quality assurance. A feature of many of these POC molecular devices is that they are equipped with data transmission capacities. In a digital age, it is possible to link data from diagnostic laboratories and POC test readers and devices to provide data on testing coverage, disease trends and timely information for early warning of infectious disease outbreaks to inform design or optimisation of disease control and elimination programmes. Data connectivity also allows control programmes to monitor the quality of tests and testing, and optimise supply chain management; thus, increasing the efficiency of healthcare systems and improving patient outcomes. url: https://www.ncbi.nlm.nih.gov/pubmed/26553825/ doi: 10.1093/inthealth/ihv062 id: cord-017359-zr0bo9el author: Pfannschmidt, Karlson title: Evaluating Tests in Medical Diagnosis: Combining Machine Learning with Game-Theoretical Concepts date: 2016-05-10 words: 3335.0 sentences: 214.0 pages: flesch: 56.0 cache: ./cache/cord-017359-zr0bo9el.txt txt: ./txt/cord-017359-zr0bo9el.txt summary: Our approach is motivated and illustrated by a concrete case study in veterinary medicine, namely the diagnosis of a disease in cats called feline infectious peritonitis. An important special case is the use of semi-supervised learning to exploit "unlabeled" data coming from individuals for which tests have been made but the true health condition is unknown. Our approach is motivated by a concrete case study in veterinary medicine, namely the diagnosis of a disease in cats called feline infectious peritonitis (FIP). In addition to the use of (semi-supervised) machine learning methodology in medical diagnosis, we propose a game-theoretical approach for measuring the usefulness of individual tests as well as model-based combinations of such tests. More specifically, what can be estimated in this way is the generalization performance of a model that is trained on a combination A and data in the form of L labeled and U unlabeled examples. Performances of different diagnostic tests for feline infectious peritonitis in challenging clinical cases abstract: In medical diagnosis, information about the health state of a patient can often be obtained through different tests, which may perhaps be combined into an overall decision rule. Practically, this leads to several important questions. For example, which test or which subset of tests should be selected, taking into account the effectiveness of individual tests, synergies and redundancies between them, as well as their cost. How to produce an optimal decision rule on the basis of the data given, which typically consists of test results for patients with or without confirmed health condition. To address questions of this kind, we develop an approach that combines (semi-supervised) machine learning methodology with concepts from (cooperative) game theory. Roughly speaking, while the former is responsible for optimally combining single tests into decision rules, the latter is used to judge the influence and importance of individual tests as well as the interaction between them. Our approach is motivated and illustrated by a concrete case study in veterinary medicine, namely the diagnosis of a disease in cats called feline infectious peritonitis. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121901/ doi: 10.1007/978-3-319-40596-4_38 id: cord-323476-rb9n5wc0 author: Poole, Stephen title: How are rapid diagnostic tests for infectious diseases used in clinical practice: a global survey by the International Society of Antimicrobial Chemotherapy (ISAC) date: 2020-09-09 words: 1908.0 sentences: 111.0 pages: flesch: 47.0 cache: ./cache/cord-323476-rb9n5wc0.txt txt: ./txt/cord-323476-rb9n5wc0.txt summary: title: How are rapid diagnostic tests for infectious diseases used in clinical practice: a global survey by the International Society of Antimicrobial Chemotherapy (ISAC) Novel rapid diagnostic tests (RDTs) offer huge potential to optimise clinical care and improve patient outcomes. An electronic survey was devised by the International Society of Antimicrobial Chemotherapy (ISAC) Rapid Diagnostics and Biomarkers working group focussing on the availability, structure and impact of RDTs around the world. The International Society of Antimicrobial Chemotherapy (ISAC)''s Rapid Diagnostics and Biomarkers Working Group conducted this international survey aiming to identify and highlight some key issues related to RDTs and their impacts in clinical practice and provide a number of key points to consider while adopting a RDT. Our survey highlights the availability of these tests in different resource settings, as well as the current models for governance, quality control and reporting. abstract: Novel rapid diagnostic tests (RDTs) offer huge potential to optimise clinical care and improve patient outcomes. In this study, we aim to assess the current patterns of use around the world, identify issues for successful implementation and suggest best practice advice on how to introduce new tests. An electronic survey was devised by the International Society of Antimicrobial Chemotherapy (ISAC) Rapid Diagnostics and Biomarkers working group focussing on the availability, structure and impact of RDTs around the world. It was circulated to ISAC members in December 2019. Results were collated according to the UN human development index (HDI). 81 responses were gathered from 31 different countries. 84% of institutions reported the availability of any test 24/7. In more developed countries, this was more for respiratory viruses, whereas in high and medium/low developed countries, it was for HIV and viral hepatitis. Only 37% of those carrying out rapid tests measured the impact. There is no ‘one-size fits all’ solution to RDTs: the requirements must be tailored to the healthcare setting in which they are deployed and there are many factors that should be considered prior to this. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s10096-020-04031-2) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1007/s10096-020-04031-2 doi: 10.1007/s10096-020-04031-2 id: cord-017072-qwe1ne3q author: Poritz, Mark A. title: Multiplex PCR for Detection and Identification of Microbial Pathogens date: 2018-11-10 words: 7205.0 sentences: 299.0 pages: flesch: 41.0 cache: ./cache/cord-017072-qwe1ne3q.txt txt: ./txt/cord-017072-qwe1ne3q.txt summary: Multiplex respiratory panels have the potential to improve patient management and lower overall healthcare costs by improving use of influenza antivirals, reducing inappropriate use of antibiotics and antivirals, reducing use of healthcare resource (e.g., additional laboratory or imaging procedures), informing appropriate infection control practices, and reducing length of hospital, emergency department, and intensive care unit (ICU) stay. In another study evaluating adult patients with a positive influenza result on a multiplex respiratory panel, Rappo [21] reported a significantly lower odds ratio for hospital admission (p = 0.046), a reduced length of stay (p = 0.040), reductions in antimicrobial duration (p = 0.032), and a reduction in the number of chest radiographs (p = 0.005). As with the individual molecular assays and the MALDI-TOF identification, numerous studies have shown that use of multiplex molecular blood culture panels dramatically reduces the time to organism identification [29] [30] [31] [32] which drives more appropriate pathogen-directed therapy. A retrospective study of the impact of rapid diagnostic testing on time to pathogen identification and antibiotic use for children with positive blood cultures abstract: Multiplexed nucleic acid-based tests for infectious disease have become a standard part of clinical laboratory practice. These tests provide a comprehensive syndrome-based approach to determine the etiological agent of disease. The technology underlying these different systems is reviewed here with a special focus on the BioFire FilmArray® platform. The literature on the clinical utility and cost-effectiveness of these platforms for respiratory, blood culture, and gastrointestinal infections is discussed. Although there are reports showing a clear benefit to the patient or to the healthcare system from adopting a syndromic molecular approach, it is also apparent that clinical laboratories and healthcare providers are still learning how to take full advantage of the new systems. Finally, some improvements to this technology that should appear in the next few years are discussed. These include automated pathogen-specific surveillance based on aggregating the data from these systems, a move toward point-of-care syndromic testing, and further decreases in time to result of the tests. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121544/ doi: 10.1007/978-3-319-95111-9_19 id: cord-325956-1kxxg0s9 author: Potluri, Rahul title: Making sense of the Global Coronavirus Data: The role of testing rates in understanding the pandemic and our exit strategy date: 2020-04-11 words: 3967.0 sentences: 217.0 pages: flesch: 62.0 cache: ./cache/cord-325956-1kxxg0s9.txt txt: ./txt/cord-325956-1kxxg0s9.txt summary: We analysed the number of diagnostic tests performed in proportion to the number of cases and subsequently deaths across different countries and projected pandemic outcomes. Country wise population level pandemic projections were extrapolated utilising three models 1) inherent case per test and death per test rates at the time of obtaining the data (4/4/2020 0900 BST) for each country; 2) rates adjusted according to the countries who conducted at least 100000 tests and 3) rates adjusted according to South Korea. https://doi.org/10.1101/2020.04.06.20054239 doi: medRxiv preprint Discussion COVID-19 statistics are complex and comparing different countries based on number of total cases, deaths and/or case fatality rate does not show the complete picture (Table 1) . In our analyses we showed the deaths and cases in relation to the number of tests performed and presented population level pandemic projections based on these. abstract: The Coronavirus disease 2019(COVID-19) outbreak has caused havoc across the world. Subsequently, research on COVID-19 has focused on number of cases and deaths and predicted projections have focused on these parameters. We propose that the number of tests performed is a very important denominator in understanding the COVID-19 data. We analysed the number of diagnostic tests performed in proportion to the number of cases and subsequently deaths across different countries and projected pandemic outcomes. We obtained real time COVID-19 data from the reference website Worldometer at 0900 BST on Saturday 4th April, 2020 and collated the information obtained on the top 50 countries with the highest number of COVID 19 cases. We analysed this data according to the number of tests performed as the main denominator. Country wise population level pandemic projections were extrapolated utilising three models - 1) inherent case per test and death per test rates at the time of obtaining the data (4/4/2020 0900 BST) for each country; 2) rates adjusted according to the countries who conducted at least 100000 tests and 3) rates adjusted according to South Korea. We showed that testing rates impact on the number of cases and deaths and ultimately on future projections for the pandemic across different countries. We found that countries with the highest testing rates per population have the lowest death rates and give us an early indication of an eventual COVID-19 mortality rate. It is only by continued testing on a large scale that will enable us to know if the increasing number of patients who are seriously unwell in hospitals across the world are the tip of the iceberg or not. Accordingly, obtaining this information through a rapid increase in testing globally is the only way which will enable us to exit the COVID-19 pandemic and reduce economic and social instability. url: https://doi.org/10.1101/2020.04.06.20054239 doi: 10.1101/2020.04.06.20054239 id: cord-284945-837qlk8y author: Rahmandad, H. title: Estimating the global spread of COVID-19 date: 2020-06-26 words: 16602.0 sentences: 1376.0 pages: flesch: 54.0 cache: ./cache/cord-284945-837qlk8y.txt txt: ./txt/cord-284945-837qlk8y.txt summary: Using data for all 84 countries with reliable testing data (spanning 4.75 billion people) we develop a dynamic epidemiological model integrating data on cases, deaths, excess mortality and other factors to estimate how asymptomatic transmission, disease acuity, hospitalization, and behavioral and policy responses to risk condition prevalence and IFR across nations and over time. Our model captures transmission dynamics for the disease, as well as how, at the country level, transmission rates vary in response to risk perception and weather, testing rates condition infection and death data, and fatality rates depend on demographics and hospitalization. Using testing rate time series and various country-level data points (e.g. population, hospital capacity, comorbidities, age distribution), the model endogenously simulates confirmed new daily cases and deaths over time and matches them against observed data by maximizing the likelihood of observing those data given the model parameters. abstract: Limited and inconsistent testing and differences in age distribution, health care resources, social distancing, and policies have caused large variations in the extent and dynamics of the COVID-19 pandemic across nations, complicating the estimation of prevalence, the infection fatality rate (IFR), and other factors important to care providers and policymakers. Using data for all 84 countries with reliable testing data (spanning 4.75 billion people) we develop a dynamic epidemiological model integrating data on cases, deaths, excess mortality and other factors to estimate how asymptomatic transmission, disease acuity, hospitalization, and behavioral and policy responses to risk condition prevalence and IFR across nations and over time. For these nations we estimate IFR averages 0.68% (0.64%-0.7%). Cases and deaths through June 18, 2020 are estimated to be 11.8 and 1.48 times official reports, respectively, at 88.5 (85-95.3) million and 600 (586-622) thousand. Prevalence and IFR vary substantially, e.g., Ecuador (18%; 0.61%), Chile (15.5%; 0.57%), Mexico (8.8%; 0.69%), Iran (7.9%; 0.44%), USA (5.3%; 0.99%), UK (5.2%; 1.59%), Iceland (1.65%, 0.56%), New Zealand (0.1%, 0.64%), but all nations remain well below the level needed for herd immunity. By alerting the public earlier and reducing contacts, extensive testing when the pandemic was declared could have averted 35.3 (32.7-42.7) million cases and 197 (171-232) thousand deaths. However, future outcomes are less dependent on testing and more contingent on the willingness of communities and governments to reduce transmission. Absent breakthroughs in treatment or vaccination and with mildly improved responses we project 249 (186-586) million cases and 1.75 (1.40-3.67) million deaths in the 84 countries by Spring 2021. url: https://doi.org/10.1101/2020.06.24.20139451 doi: 10.1101/2020.06.24.20139451 id: cord-007047-7ty9mxa9 author: Reller, L. Barth title: Implications of New Technology for Infectious Diseases Practice date: 2006-11-15 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: New assays for the diagnosis of infectious diseases—particularly those that use molecular technologies—will revolutionize infectious diseases practices, but the fulfillment of the promise is several years away. Problems with currently available molecular assays include a lack of knowledge about the extent of microbial nucleic acid in “normal” hosts, concentration of agent material in small volume samples, lack of microbiologist expertise, lack of adequate reimbursement, and difficulty with validation based on conventional methods. Clinicians must appreciate the shortcomings of new technology to use it effectively and appropriately. However, we are realizing tangible progress in our ability to detect new etiological agents; the availability of rapid, accurate diagnostic tests for previously difficult infections; and advances into new, human response—based paradigms for diagnostic testing. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7107913/ doi: 10.1086/508536 id: cord-320864-k9zksbyt author: Remes-Troche, J. M. title: Recommendations for the reopening and activity resumption of the neurogastroenterology units in the face of the COVID-19 pandemic. Position of the Sociedad Latinoamericana de Neurogastroenterología date: 2020-11-01 words: 4669.0 sentences: 256.0 pages: flesch: 46.0 cache: ./cache/cord-320864-k9zksbyt.txt txt: ./txt/cord-320864-k9zksbyt.txt summary: When health authorities allow a return to normalcy and in the absence of effective treatment or a preventive vaccine for COVID 19 infection, we recommend a strict protocol to classify patients according to their infectious-contagious status through the appropriate use of tests to detect the virus and its immune response, as well as the use of protective measures to be followed by health personnel to avoid contagion during the performance of a gastrointestinal motility test. Positions have already been established on how to work and/or resume activities at those units (e.g., those issued by the American Neurogastroenterology and Motility Society [ANMS] 4 and the Grupo Español de Motilidad Digestiva [GEMD]) 5 but due to the fact that the epidemiologic behavior, protective equipment avail-ability, serologic diagnostic test performance capacity for corroborating immunity, and socioeconomic context are different throughout Latin America, a group of experts that are members of the Sociedad Latinoamericana de Neurogastroenterología (SLNG) had a virtual meeting to formulate a consensus document with recommendations for the performance of gastrointestinal motility tests. abstract: The COVID 19 pandemic has forced the establishment of measures to avoid contagion during diagnostic and therapeutic tests in gastroenterology. Gastrointestinal motility studies involve a high and intermediate risk of transmission of infection by this virus. Given its elective or non-urgent indication in most cases, we recommend deferring the performance of these tests until there is a significant control of the infection rate in each country, during the pandemic. When health authorities allow a return to normalcy and in the absence of effective treatment or a preventive vaccine for COVID 19 infection, we recommend a strict protocol to classify patients according to their infectious-contagious status through the appropriate use of tests to detect the virus and its immune response, as well as the use of protective measures to be followed by health personnel to avoid contagion during the performance of a gastrointestinal motility test. url: https://api.elsevier.com/content/article/pii/S2255534X2030092X doi: 10.1016/j.rgmxen.2020.07.004 id: cord-354005-q5nj0ku1 author: Richaud, M. title: Specific testing of textiles for transportation date: 2017-09-29 words: 11220.0 sentences: 561.0 pages: flesch: 48.0 cache: ./cache/cord-354005-q5nj0ku1.txt txt: ./txt/cord-354005-q5nj0ku1.txt summary: Then, different aspects of textile testing relevant to the transportation industry are discussed: safety, flammability, hygiene, performance of composite parts, and durability. For instance, the FAA standard on airworthiness of airplanes (FAR/CS 25.853) includes several flammability test methods that apply to textile components: EASA for its part is currently reviewing its legislation on civil aircrafts to take into account the increased air traffic and arrival of new technologies such as drones (Juul, 2016) . A series of test methods for textile-reinforced composites has also been developed by various standardization organizations (Table 14 .9). This includes performance related to safety for airbags, seat belts, tires, and slings; flammability, smoke generation, and toxicity, with test methods and specific requirements for each type of application; hygiene for filters and antimicrobial textiles; destructive and nondestructive tests conducted on textile-reinforced composites at the textile and composite level; and durability. Standard guide for testing fabric-reinforced "Textile" composite materials abstract: The use of textiles in transportation may be associated with the need to combine comfort and functionality. The evolution of each mean of transportation along with the increased awareness about the importance of passengers' safety pushed research and development forward towards a larger use of lightweight, fire-resistant, nontoxic, and durable textiles in transportation. This in turn led to the development of test methods assessing the different aspects of textiles in transportation. This chapter starts with a presentation of the transportation textile market. Then, different aspects of textile testing relevant to the transportation industry are discussed: safety, flammability, hygiene, performance of composite parts, and durability. The chapter ends with considerations regarding future trends for textiles in transportation. url: https://www.sciencedirect.com/science/article/pii/B9780081004531000155 doi: 10.1016/b978-0-08-100453-1.00015-5 id: cord-296306-xcomjvaa author: Rivett, Lucy title: Screening of healthcare workers for SARS-CoV-2 highlights the role of asymptomatic carriage in COVID-19 transmission date: 2020-05-11 words: 6500.0 sentences: 350.0 pages: flesch: 48.0 cache: ./cache/cord-296306-xcomjvaa.txt txt: ./txt/cord-296306-xcomjvaa.txt summary: Significant differences exist in the availability of healthcare worker (HCW) SARS-CoV-2 testing between countries, and existing programmes focus on screening symptomatic rather than asymptomatic staff. Table 3 outlines the total number of SARS-CoV-2 tests performed in each screening group (HCW asymptomatic, HCW symptomatic, and HCW symptomatic household contact) categorised according to the ward with the highest anticipated risk of exposure to high; ''amber'', medium; ''green'', low; . Three subgroups of SARS-CoV-2 positive asymptomatic HCW Each individual in the HCW asymptomatic screening group was contacted by telephone to establish a clinical history, and COVID-19 probability criteria ( Table 1) were retrospectively applied to categorise any symptoms in the month prior to testing ( Figure 2 ). 12/30 (40%) individuals from the HCW asymptomatic screening group reported symptoms > 7 days prior to testing, and the majority experiencing symptoms consistent with a high probability of COVID-19 had appropriately self-isolated during that period. abstract: Significant differences exist in the availability of healthcare worker (HCW) SARS-CoV-2 testing between countries, and existing programmes focus on screening symptomatic rather than asymptomatic staff. Over a 3 week period (April 2020), 1032 asymptomatic HCWs were screened for SARS-CoV-2 in a large UK teaching hospital. Symptomatic staff and symptomatic household contacts were additionally tested. Real-time RT-PCR was used to detect viral RNA from a throat+nose self-swab. 3% of HCWs in the asymptomatic screening group tested positive for SARS-CoV-2. 17/30 (57%) were truly asymptomatic/pauci-symptomatic. 12/30 (40%) had experienced symptoms compatible with coronavirus disease 2019 (COVID-19)>7 days prior to testing, most self-isolating, returning well. Clusters of HCW infection were discovered on two independent wards. Viral genome sequencing showed that the majority of HCWs had the dominant lineage B∙1. Our data demonstrates the utility of comprehensive screening of HCWs with minimal or no symptoms. This approach will be critical for protecting patients and hospital staff. url: https://www.ncbi.nlm.nih.gov/pubmed/32392129/ doi: 10.7554/elife.58728 id: cord-030341-uora9qcb author: Ruland, Sebastian title: HybridTiger: Hybrid Model Checking and Domination-based Partitioning for Efficient Multi-Goal Test-Suite Generation (Competition Contribution) date: 2020-03-13 words: 1259.0 sentences: 73.0 pages: flesch: 49.0 cache: ./cache/cord-030341-uora9qcb.txt txt: ./txt/cord-030341-uora9qcb.txt summary: title: HybridTiger: Hybrid Model Checking and Domination-based Partitioning for Efficient Multi-Goal Test-Suite Generation (Competition Contribution) In Test-Comp 2019, we applied a random partitioning strategy and used predicate analysis as model checking technique. HybridTiger uses the CoVeriTest [3] algorithm to sequentially combine test-case generation runs utilizing different verification techniques. Each test-case generation run applies the CPA/Tiger-MGP 4 (Tiger Multi-Goal-Partitioning) algorithm, which utilizes the CEGAR algorithm. HybridTiger first extracts test goals from input programs and repeatedly executes reachability analyses provided by CPAchecker until every reachable test goal is covered by at least one test case. HybridTiger receives as inputs a C program and a property specification (i.e., a set of test goals). Second, HybridTiger uses control-flow information to partition test goals which potentially enhances efficiency of test-case generation due to information reuse among similar test goals. Configurable Software Verification: Concretizing the Convergence of Model Checking and Program Analysis abstract: In theory, software model checkers are well-suited for automated test-case generation. The idea is to perform (non-)reachability queries for the test goals and extract test cases from resulting counterexamples. However, in case of realistic programs, even simple coverage criteria (e.g., branch coverage) force model checkers to deal with several hundreds or even thousands of test goals. Processing each of these test goals in isolation with model checking techniques does not scale. Therefore, our tool HybridTiger builds on recent ideas on multi-property verification. However, since every additional property (i.e., test goal) reduces the model checker’s abstraction possibilities, we split the set of all test goals into different partitions. In Test-Comp 2019, we applied a random partitioning strategy and used predicate analysis as model checking technique. In Test-Comp 2020, we improved our technique in two ways. First, we exploit domination information among control-flow locations in our partitioning strategy to group test goals being located on (preferably) similar paths. Second, we account to inherent weaknesses of the predicate analysis by applying a hybrid software model-checking approach that switches between explicit model checking and predicate-based model checking on-the-fly. Our tool HybridTiger is integrated into the software analysis framework CPAchecker. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7418130/ doi: 10.1007/978-3-030-45234-6_26 id: cord-031567-w2676lrz author: Sabit, Maureen title: Pollen allergen skin test and specific IgE reactivity among Filipinos: a community-based study date: 2020-08-12 words: 4280.0 sentences: 234.0 pages: flesch: 50.0 cache: ./cache/cord-031567-w2676lrz.txt txt: ./txt/cord-031567-w2676lrz.txt summary: Data characteristics of test subjects (cases and controls) and positive reactions to different pollen allergens using skin prick test and specific IgE ELISA were presented as frequency (percentage) and compared using the Chi square test of homogeneity or Fisher''s Exact test or z-test for two sample proportions. Of the 11 species of arboreal plants used for SPT, most of the study subjects tested positive to three pollen sources: Mangifera indica (MAN), Acacia auriculiformis (ACA), and Lantana camara (LAN) as shown in Table 2 . Skin prick tests (SPT), which is an essential procedure to confirm sensitization in IgE-mediated allergic disease in subjects with allergic rhinitis, asthma, and atopic dermatitis, can be performed from infancy to old age [24] . A high percentage of test subjects in this study reported a history of rhinitis and asthma, which, are allergic diseases often associated with sensitization to aeroallergens [46] . abstract: BACKGROUND: Despite the clinical importance of pollen allergens among Filipinos, few studies delve into the sensitization profiles of Filipinos against pollen allergens. This study determined the sensitization profile of Filipinos to pollen using skin prick test (SPT) and pollen-specific ELISA. METHODS: Pollen from fifteen selected plant sources was collected and extracted for use in sensitization tests. Volunteers were interviewed for their clinical history prior to blood sampling and SPT. The blood samples collected were assessed using Enzyme-Linked Immunosorbent Assay (ELISA). RESULTS: The best panel of pollen allergens for the skin prick test was Mangifera indica (64%), Acacia auriculiformis (28%), Mimosa spp. (25%) Amaranthus spinosus (22%), Lantana camara (20%), Pilea microphylla (16%) and Dichanthium aristatum (15%). Young adults had more sensitizations to pollen than among early childhood and elderly. There were more allergic subjects that have rhinitis (61%) than asthma (42%) and atopic dermatitis (35%). Pollen-specific IgE levels show low percent reactivity as compared to the skin test with Cocos nucifera obtaining the highest IgE reactivity (21%). CONCLUSIONS: Pollen allergens from both arboreal and herbaceous plants used in this study yielded positive reactivities for both skin tests and specific IgE tests. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7477877/ doi: 10.1186/s13223-020-00471-9 id: cord-179749-qdbmpi7j author: Sacks, Daniel W. title: What can we learn about SARS-CoV-2 prevalence from testing and hospital data? date: 2020-08-01 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Measuring the prevalence of active SARS-CoV-2 infections is difficult because tests are conducted on a small and non-random segment of the population. But people admitted to the hospital for non-COVID reasons are tested at very high rates, even though they do not appear to be at elevated risk of infection. This sub-population may provide valuable evidence on prevalence in the general population. We estimate upper and lower bounds on the prevalence of the virus in the general population and the population of non-COVID hospital patients under weak assumptions on who gets tested, using Indiana data on hospital inpatient records linked to SARS-CoV-2 virological tests. The non-COVID hospital population is tested fifty times as often as the general population. By mid-June, we estimate that prevalence was between 0.01 and 4.1 percent in the general population and between 0.6 to 2.6 percent in the non-COVID hospital population. We provide and test conditions under which this non-COVID hospitalization bound is valid for the general population. The combination of clinical testing data and hospital records may contain much more information about the state of the epidemic than has been previously appreciated. The bounds we calculate for Indiana could be constructed at relatively low cost in many other states. url: https://arxiv.org/pdf/2008.00298v1.pdf doi: nan id: cord-276577-06boh550 author: Schanzer, Dena L. title: Estimating Sensitivity of Laboratory Testing for Influenza in Canada through Modelling date: 2009-08-18 words: 3960.0 sentences: 175.0 pages: flesch: 38.0 cache: ./cache/cord-276577-06boh550.txt txt: ./txt/cord-276577-06boh550.txt summary: METHODS AND FINDINGS: The weekly number of influenza-negative tests from 1999 to 2006 was modelled as a function of laboratory-confirmed positive tests for influenza, respiratory syncytial virus (RSV), adenovirus and parainfluenza viruses, seasonality, and trend using Poisson regression. The RVDSS collects, collates, and reports weekly data from participating laboratories on the number of tests performed and the number of specimens confirmed positive for influenza, respiratory syncytial virus (RSV), para-influenza virus (PIV), and adenovirus. The overall model fit, and the general consistency of the sensitivity estimates, suggests that these many respiratory viruses were reasonably accounted for by the seasonal baseline and that the strong association between the number of influenza positive and influenza negative tests on a weekly basis is indicative of a significant number of false negative results, rather than the activity of another virus or viruses exactly synchronous with influenza. abstract: BACKGROUND: The weekly proportion of laboratory tests that are positive for influenza is used in public health surveillance systems to identify periods of influenza activity. We aimed to estimate the sensitivity of influenza testing in Canada based on results of a national respiratory virus surveillance system. METHODS AND FINDINGS: The weekly number of influenza-negative tests from 1999 to 2006 was modelled as a function of laboratory-confirmed positive tests for influenza, respiratory syncytial virus (RSV), adenovirus and parainfluenza viruses, seasonality, and trend using Poisson regression. Sensitivity was calculated as the number of influenza positive tests divided by the number of influenza positive tests plus the model-estimated number of false negative tests. The sensitivity of influenza testing was estimated to be 33% (95%CI 32–34%), varying from 30–40% depending on the season and region. CONCLUSIONS: The estimated sensitivity of influenza tests reported to this national laboratory surveillance system is considerably less than reported test characteristics for most laboratory tests. A number of factors may explain this difference, including sample quality and specimen procurement issues as well as test characteristics. Improved diagnosis would permit better estimation of the burden of influenza. url: https://doi.org/10.1371/journal.pone.0006681 doi: 10.1371/journal.pone.0006681 id: cord-350473-f47i7y5h author: Sen-Crowe, Brendon title: COVID-19 laboratory testing issues and capacities as we transition to surveillance testing and contact tracing date: 2020-05-27 words: 1099.0 sentences: 91.0 pages: flesch: 54.0 cache: ./cache/cord-350473-f47i7y5h.txt txt: ./txt/cord-350473-f47i7y5h.txt summary: The sensitivity of PCR tests have been estimated at 71%, resulting in ~30% of infected patients having a negative finding. The second type of test is serologic, which detects immunoglobulins (IgG and IgM) specific for SARS-CoV-2 and provides an estimation of population virus exposure 4 . Many FDA-approved serologic tests have high sensitivity and specificity. To address the development of a reliable test, the Department of Health & Human Services (HHS) provided funding for the development of Simplexa COVID-19 Direct Assay and to QIAGEN to accelerate development of their RPS2 test 15 . Additionally, HHS is purchasing the ID NOW COVID-19 rapid point-of-care test (Abbott Diagnostics Scarborough Inc.) for public health labs (Table 1) 16 . Saliva is more sensitive for SARS-CoV-2 detection in COVID-19 patients than nasopharyngeal swabs abstract: nan url: https://doi.org/10.1016/j.ajem.2020.05.071 doi: 10.1016/j.ajem.2020.05.071 id: cord-290978-e7imc11r author: Shevachman, M. title: A Long-Lasting Sanitizing Skin Protectant based on CAGE, a Choline and Geranic Acid Eutectic date: 2020-08-07 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The recent outbreak and rapid spread of coronavirus disease 2019 (COVID-19) is a global pandemic and a massive public health crisis. COVID-19 has also had a severe impact on the quality of life and mental health. While different health authorities such as WHO and CDC are encouraging adoption of strategies including hand washing and use of facemasks to reduce the spread of the pathogens and infections, adoption of these approaches requires substantial commitment. Current hand sanitizers based on ethanol provide immediate protection, however, the protection rendered by such sanitizers is very short-lived due to their rapid evaporation. A long-lasting sanitizing skin protectant that can effectively inactivate SARS-CoV-2 and provide persistent efficacy over several hours will provide people the freedom to carry on with their activities without constant concerns about the cleanliness of their hands. Herein, we describe a skin protectant, IonLASTTM, based on an ionic liquid/deep eutectic solvent, formed by GRAS materials, choline and geranic acid (CAGE, CG-101), that provides protection for at least 4h after a single application. IonLASTTM was formulated as a gel that facilitates easy application on the skin. Tolerance of CG-101 was substantiated through a study in human volunteers. In vitro studies confirmed that IonLASTTM effectively inactivates a human coronavirus hCoV229E. A second human clinical study established that a single application of IonLASTTM imparts protection against microbes that lasts up to several hours. url: http://medrxiv.org/cgi/content/short/2020.08.04.20161067v1?rss=1 doi: 10.1101/2020.08.04.20161067 id: cord-170195-lrg11s5n author: Stoye, Jorg title: A Critical Assessment of Some Recent Work on COVID-19 date: 2020-05-20 words: 2764.0 sentences: 166.0 pages: flesch: 61.0 cache: ./cache/cord-170195-lrg11s5n.txt txt: ./txt/cord-170195-lrg11s5n.txt summary: I tentatively re-analyze data from two well-publicized studies on COVID-19, namely the Charit''{e}"viral load in children"and the Bonn"seroprevalence in Heinsberg/Gangelt"study, from information available in the preprints. The authors focus on a hypothesis test as deliverable of their analysis; I would have recommended a nonparametric mean regression with error bands, resulting in some estimated age effect. To the statistically educated reader, the above headlines may suggest that the study tests, and fails to reject, H 0 : "Children have the same viral load as adults." It does not. To take an educated guess, I will now try to recover from the paper a test of H 0 : "Children have the same viral load as adults." To this purpose, I combine the first two and the remaining age bins of Figure 1 to find means of 4.74 and 5.21 with 95% confidence intervals of [4.42, 5.05] and [5.15, 5.27], respectively. abstract: I tentatively re-analyze data from two well-publicized studies on COVID-19, namely the Charit'{e}"viral load in children"and the Bonn"seroprevalence in Heinsberg/Gangelt"study, from information available in the preprints. The studies have the following in common: - They received worldwide attention and arguably had policy impact. - The thrusts of their findings align with the respective lead authors' (different) public stances on appropriate response to COVID-19. - Tentatively, my reading of the Gangelt study neutralizes its thrust, and my reading of the Charit'{e} study reverses it. The exercise may aid in placing these studies in the literature. With all caveats that apply to n=2 quickfire analyses based off preprints, one also wonders whether it illustrates inadvertent effects of"researcher degrees of freedom." url: https://arxiv.org/pdf/2005.10237v2.pdf doi: nan id: cord-025556-oyfx3ij5 author: THUNSTRÖM, LINDA title: Testing for COVID-19: willful ignorance or selfless behavior? date: 2020-05-08 words: 6776.0 sentences: 296.0 pages: flesch: 58.0 cache: ./cache/cord-025556-oyfx3ij5.txt txt: ./txt/cord-025556-oyfx3ij5.txt summary: Furthermore, willful ignorance often arises when selfish wants conflict with social benefits, which might be particularly likely for potential ''super-spreaders'' – people with many social interactions – given people who test positive are urged to self-isolate for two weeks. Furthermore, we expect those at the lowest risk of losing out financially (e.g., risk to labor income or health care costs) or emotionally from self-isolating (i.e., if they are introverts who attach a low value to social interactions) to be the most willing to get tested for COVID-19. We therefore conclude that the positive effect of being an extrovert on willingness to test for COVID-19 is likely due to social health benefits weighing more heavily in their decision than their private costs from potential self-isolation for 14 days, should the test come back positive. abstract: Widespread testing is key to controlling the spread of COVID-19. But should we worry about self-selection bias in the testing? The recent literature on willful ignorance says we should – people often avoid health information. In the context of COVID-19, such willful ignorance can bias testing data. Furthermore, willful ignorance often arises when selfish wants conflict with social benefits, which might be particularly likely for potential ‘super-spreaders’ – people with many social interactions – given people who test positive are urged to self-isolate for two weeks. We design a survey in which participants (n = 897) choose whether to take a costless COVID-19 test. We find that 70% would take a test. Surprisingly, the people most likely to widely spread COVID-19 – the extraverts, others who meet more people in their daily lives and younger people – are the most willing to take a test. People's ability to financially or emotionally sustain self-isolation does not matter to their decision. We conclude that people are selfless in their decision to test for COVID-19. Our results are encouraging – they imply that COVOD-19 testing may succeed in targeting those who generate the largest social benefits from self-isolation if infected, which strengthens the case for widespread testing. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7256418/ doi: 10.1017/bpp.2020.15 id: cord-342181-x14iywtr author: Taipale, J. title: Population-scale testing can suppress the spread of COVID-19 date: 2020-05-01 words: 7522.0 sentences: 359.0 pages: flesch: 50.0 cache: ./cache/cord-342181-x14iywtr.txt txt: ./txt/cord-342181-x14iywtr.txt summary: Our model also indicates that unlike sampling-based tests, population-scale testing does not need to be very accurate: false negative rates up to 15% could be tolerated if 80% comply with testing every ten days, and false positives can be almost arbitrarily high when a high fraction of the population is already effectively quarantined. Using the standard (continuous, deterministic) SIR model, the equations in Fig. 2A and Methods show that the optimal population-scale testing strategy will succeed if at least two thirds of all new COVID-19 cases are immediately identified and quarantined. Although a population-scale test does not need to be as accurate as a clinical-grade qRT-PCR test (see above), apart from a potential increase in errors due to sample collection, there is no theoretical reason why a self-test based on isothermal amplification would not achieve the false negative and positive rates that are equivalent to the current state-of-the-art methodology. abstract: We propose an additional intervention that would contribute to the control of the COVID-19 pandemic, offer more protection for people working in essential jobs, and help guide an eventual reopening of society. The intervention is based on: (1) testing every individual (2) repeatedly, and (3) self-quarantine of infected individuals. Using a standard epidemiological model (SIR), we show here that by identification and isolation of the majority of infectious individuals, including those who may be asymptomatic, the reproduction number R0 of SARS-CoV-2 would be reduced well below 1.0, and the epidemic would collapse. We replicate these observations in a more complex stochastic dynamic model on a social network graph. We also find that the testing regime would be additive to other interventions, and be effective at any level of prevalence. If adopted as a policy, any industrial society could sustain the regime for as long as it takes to find a safe and effective cure or vaccine. Our model also indicates that unlike sampling-based tests, population-scale testing does not need to be very accurate: false negative rates up to 15% could be tolerated if 80% comply with testing every ten days, and false positives can be almost arbitrarily high when a high fraction of the population is already effectively quarantined. Testing at the required scale would be feasible if existing qPCR-based methods are scaled up and multiplexed. A mass produced, low throughput field test kit could also be carried out at home. Economic analysis also supports the feasibility of the approach: current reagent costs for tests are in the range of a dollar or less, and the estimated benefits for population-scale testing are so large that the policy would be cost-effective even if the costs were larger by more than two orders of magnitude. To identify both active and previous infections, both viral RNA and antibodies could be tested. All technologies to build such test kits, and to produce them in the scale required to test the entire world's population exist already. Integrating them, scaling up production, and implementing the testing regime will require resources and planning, but at a scale that is very small compared to the effort that every nation would devote to defending itself against a more traditional foe. url: http://medrxiv.org/cgi/content/short/2020.04.27.20078329v1?rss=1 doi: 10.1101/2020.04.27.20078329 id: cord-144448-mqs502xm author: Theagarajan, Lakshmi N. title: Group Testing for COVID-19: How to Stop Worrying and Test More date: 2020-04-14 words: 7392.0 sentences: 473.0 pages: flesch: 71.0 cache: ./cache/cord-144448-mqs502xm.txt txt: ./txt/cord-144448-mqs502xm.txt summary: We present multiple group testing algorithms that could reduce the number of tests performed for COVID-19 diagnosis. • Combinatorial group testing (CGT): The combinatorial algorithms require the exact number (or an upper bound) of the infected samples D. • Probabilistic group testing (PGT): The probabilistic algorithms require an upper bound on α and identify all infected samples with certain probability P D . In general, if T is the number of tests for COVID that are to be performed on a swab with viral load V l with r replicates to achieve a sensitivity of 1 − γ * , then the maximum pool size can be derived as The GBS algorithm simply attempts to perform the BSP D times to identify at most D infected samples in a given pool of size N . abstract: The corona virus disease 2019 (COVID-19) caused by the novel corona virus has an exponential rate of infection. COVID-19 is particularly notorious as the onset of symptoms in infected patients are usually delayed and there exists a large number of asymptomatic carriers. In order to prevent overwhelming of medical facilities and large fatality rate, early stage testing and diagnosis are key requirements. In this article, we discuss the methodologies from the group testing literature and its relevance to COVID-19 diagnosis. Specifically, we investigate the efficiency of group testing using polymerase chain reaction (PCR) for COVID-19. Group testing is a method in which multiple samples are pooled together in groups and fewer tests are performed on these groups to discern all the infected samples. We study the effect of dilution due to pooling in group testing and show that group tests can perform well even in the presence of dilution effects. We present multiple group testing algorithms that could reduce the number of tests performed for COVID-19 diagnosis. We analyze the efficiency of these tests and provide insights on their practical relevance. With the use of algorithms described here, test plans can be developed that can enable testing centers to increase the number of diagnosis performed without increasing the number of PCR tests. The codes for generating test plans are available online at [1]. url: https://arxiv.org/pdf/2004.06306v2.pdf doi: nan id: cord-295126-lz2jbmcn author: Toresdahl, Brett G. title: Coronavirus Disease 2019 (COVID-19): Considerations for the Competitive Athlete date: 2020-04-06 words: 2405.0 sentences: 156.0 pages: flesch: 51.0 cache: ./cache/cord-295126-lz2jbmcn.txt txt: ./txt/cord-295126-lz2jbmcn.txt summary: First and foremost, preventing the transmission of COVID-19 is needed to reduce the risk of spread to individuals within a community who are most at risk of severe infection or death, which includes older individuals and the immunocompromised. Sports medicine providers can support athletes and teams during the COVID-19 pandemic by advocating the following preventative measures: With these limitations, testing algorithms offered preference to patients with symptoms (fever, cough, or shortness of breath), an immunocompromised state, or close contact with someone with COVID-19. In-home isolation is recommended for athletes with confirmed or suspected COVID-19 who do not show severe symptoms. If an athlete on a sports team develops symptoms consistent with COVID-19, teammates, coaches, and other staff who had close contact with the athlete (within 6 feet) in the preceding 14 days should begin in-home isolation. Correlation of chest CT and RT-PCR testing in coronavirus disease 2019 (COVID-19) in China: a report of 1014 cases abstract: nan url: https://doi.org/10.1177/1941738120918876 doi: 10.1177/1941738120918876 id: cord-326148-9wpxm5of author: Van Walle, I. title: Meta-analysis of the clinical performance of commercial SARS-CoV-2 nucleic acid, antigen and antibody tests up to 22 August 2020 date: 2020-09-18 words: 3790.0 sentences: 218.0 pages: flesch: 49.0 cache: ./cache/cord-326148-9wpxm5of.txt txt: ./txt/cord-326148-9wpxm5of.txt summary: title: Meta-analysis of the clinical performance of commercial SARS-CoV-2 nucleic acid, antigen and antibody tests up to 22 August 2020 We reviewed the clinical performance of SARS-CoV-2 nucleic acid, viral antigen and antibody tests based on 94739 test results from 157 published studies and 20205 new test results from 12 EU/EEA Member States. Pooling the results and considering only results with 95% confidence interval width [≤]5%, we found 4 nucleic acid tests, among which 1 point of care test, and 3 antibody tests with a clinical sensitivity [≤]95% for at least one target population (hospitalised, mild or asymptomatic, or unknown). Study heterogeneity was low for 8/14 (57.1%) sensitivity and 68/84 (81.0%) specificity results with confidence interval width [≤]5%, and lower for nucleic acid tests than antibody tests. Studies containing potentially usable data on clinical performance of SARS-CoV-2 nucleic acid, antigen and antibody tests were first extracted from systematic reviews on this topic. abstract: We reviewed the clinical performance of SARS-CoV-2 nucleic acid, viral antigen and antibody tests based on 94739 test results from 157 published studies and 20205 new test results from 12 EU/EEA Member States. Pooling the results and considering only results with 95% confidence interval width [≤]5%, we found 4 nucleic acid tests, among which 1 point of care test, and 3 antibody tests with a clinical sensitivity [≤]95% for at least one target population (hospitalised, mild or asymptomatic, or unknown). Analogously, 9 nucleic acid tests and 25 antibody tests, among which 12 point of care tests, had a clinical specificity of [≤]98%. Three antibody tests achieved both thresholds. Evidence for nucleic acid and antigen point of care tests remains scarce at present, and sensitivity varied substantially. Study heterogeneity was low for 8/14 (57.1%) sensitivity and 68/84 (81.0%) specificity results with confidence interval width [≤]5%, and lower for nucleic acid tests than antibody tests. Manufacturer reported clinical performance was significantly higher than independently assessed in 11/32 (34.4%) and 4/34 (11.8%) cases for sensitivity and specificity respectively, indicating a need for improvement in this area. Continuous monitoring of clinical performance within more clearly defined target populations is needed. url: http://medrxiv.org/cgi/content/short/2020.09.16.20195917v1?rss=1 doi: 10.1101/2020.09.16.20195917 id: cord-334274-4jee19hx author: Waelde, K. title: How to remove the testing bias in CoV-2 statistics date: 2020-10-16 words: 7041.0 sentences: 518.0 pages: flesch: 63.0 cache: ./cache/cord-334274-4jee19hx.txt txt: ./txt/cord-334274-4jee19hx.txt summary: Private and public decision making should not be based on time series of CoV-2-infections as the latter do not provide information about the true epidemic dynamics in a country. 3 We show that time series on the number of tests and time series on reported infections do not allow one to obtain information about the true state of an epidemic. It also studies the (lack of) informational content of time series on reported infections and time series on the number of tests, and the properties of the positive rate. Testing increases the positive rate if the number of tests undertaken due to symptoms 17 This paper is about conceptional issues related to the …nding an unbiased estimator for an unobserved time series. If we knew the number of Covid-19 cases, i.e. CoV-2 infections with severe acute respiratory symptoms (SARS), then we would know at least one part of epidemic dynamics (Ĩ symp (t) in our model). abstract: BACKGROUND. Public health measures and private behaviour are based on reported numbers of SARS-CoV-2 infections. Some argue that testing influences the confirmed number of infections. OBJECTIVES/METHODS. Do time series on reported infections and the number of tests allow one to draw conclusions about actual infection numbers? A SIR model is presented where the true numbers of susceptible, infectious and removed individuals are unobserved. Testing is also modelled. RESULTS. Official confirmed infection numbers are likely to be biased and cannot be compared over time. The bias occurs because of different reasons for testing (e.g. by symptoms, representative or testing travellers). The paper illustrates the bias and works out the effect of the number of tests on the number of reported cases. The paper also shows that the positive rate (the ratio of positive tests to the total number of tests) is uninformative in the presence of non-representative testing. CONCLUSIONS. A severity index for epidemics is proposed that is comparable over time. This index is based on Covid-19 cases and can be obtained if the reason for testing is known. url: https://doi.org/10.1101/2020.10.14.20212431 doi: 10.1101/2020.10.14.20212431 id: cord-310195-am3u7z76 author: Waller, J. title: Immunity Passports for SARS-CoV-2: an online experimental study of the impact of antibody test terminology on perceived risk and behaviour date: 2020-05-10 words: 4813.0 sentences: 281.0 pages: flesch: 55.0 cache: ./cache/cord-310195-am3u7z76.txt txt: ./txt/cord-310195-am3u7z76.txt summary: Objective: To assess the impact of describing an antibody-positive test result using the terms Immunity and Passport or Certificate, alone or in combination, on perceived risk of becoming infected with SARS-CoV-2 and intention to continue protective behaviours. Conclusions: Using the term Immunity (vs Antibody) to describe antibody tests for SARS-CoV-2 increases the proportion of people believing that an antibody-positive result means they have no risk of catching coronavirus in the future, a perception that may be associated with less frequent hand washing. This study was designed to test two hypotheses: describing a test indicating the presence of antibodies using the term Immunity (vs Antibody), and describing test results as Passports or Certificates (vs Test), increases the likelihood that those with this test result erroneously perceive they have no risk of becoming infected in the future with coronavirus. . https://doi.org/10.1101/2020.05.06.20093401 doi: medRxiv preprint Primary outcome Proportion of participants perceiving an antibody-positive test result to mean no risk of catching coronavirus in the future, assessed in response to a question with four response options. abstract: Objective: To assess the impact of describing an antibody-positive test result using the terms Immunity and Passport or Certificate, alone or in combination, on perceived risk of becoming infected with SARS-CoV-2 and intention to continue protective behaviours. Design: 2 by 3 experimental design. Setting: Online with data collected between 28th April and 1st May 2020. Participants: 1,204 adults registered with a UK research panel. Intervention: Participants were randomised to receive one of six descriptions of an antibody test and results showing SARS-CoV-2 antibodies, differing in the terms used to describe the type of test (Immunity vs Antibody) and the test result (Passport vs Certificate vs Test). Main outcome measures: The primary outcome was the proportion of participants perceiving no risk of becoming infected with SARS-CoV-2 given an antibody positive test result. Other outcomes include intended changes to frequency of hand washing and physical distancing. Results: When using the term Immunity (vs Antibody), 19.1% of participants [95% CI: 16.1 to 22.5] (vs 9.8% [95% CI: 7.5 to 12.4]) perceived no risk of catching coronavirus at some point in the future given an antibody-positive test result (AOR: 2.91 [95% CI: 1.52 to 5.55]). Using the terms Passport or Certificate, as opposed to Test, had no significant effect (AOR: 1.24 [95% CI: 0.62 to 2.48] and AOR: 0.96 [95% CI: 0.47 to 1.99] respectively). There was no significant interaction between the effects of the test and result terminology. Across groups, perceiving no risk of infection was associated with an intention to wash hands less frequently (AOR: 2.32 [95% CI: 1.25 to 4.28]) but there was no significant association with intended avoidance of physical contact with others outside of the home (AOR: 1.37 [95% CI: 0.93 to 2.03]). Conclusions: Using the term Immunity (vs Antibody) to describe antibody tests for SARS-CoV-2 increases the proportion of people believing that an antibody-positive result means they have no risk of catching coronavirus in the future, a perception that may be associated with less frequent hand washing. The way antibody testing is described may have implications for the likely impact of testing on transmission rates. url: https://doi.org/10.1101/2020.05.06.20093401 doi: 10.1101/2020.05.06.20093401 id: cord-021511-88xaynf7 author: Werner, Linda L. title: Immunologic and Plasma Protein Disorders date: 2009-05-15 words: 6195.0 sentences: 376.0 pages: flesch: 34.0 cache: ./cache/cord-021511-88xaynf7.txt txt: ./txt/cord-021511-88xaynf7.txt summary: Hypoalbuminemia associated with hepatomegaly; microhepatia; neurologic signs; icterus; decreased blood urea nitrogen (BUN) with or without increased alanine aminotransferase (ALT), serum alkaline phosphatase (SAP), or both; or abnormal hepatic function test results (e.g., serum bile acids) requires a diagnostic workup for hepatic insufficiency (see Chapter 9). Occasionally Indicated • Protein electrophoresis is performed when hyperglobulinemia is not caused by hemoconcentration and either (1) the globulin concentration is high enough to make monoclonal gammopathy a reasonable possibility or (2) humoral immunodeficiencies are suspected. Immunoelectrophoresis is the method of choice to detect urinary and serum Bence Jones protein, a monoclonal protein equivalent to immunoglobulin light chains which occasionally occurs in multiple myeloma and macroglobulinemia. Monoclonal immunoglobulin elevations are also called paraproteins or M proteins and are usually the result of lymphocyte and plasma cell neoplasias (e.g., multiple myeloma, macroglobulinemia, lymphosarcoma; see Table 12 -3). Diagnosis of multiple myeloma in dogs requires finding at least two of the following: lytic skeletal lesions, bone marrow plasmacytosis, Bence Jones proteinuria, or a monoclonal spike on serum protein electrophoresis. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7150071/ doi: 10.1016/b0-72-168903-5/50017-3 id: cord-349161-4899cq99 author: Whiting, Penny F title: Graphical presentation of diagnostic information date: 2008-04-11 words: 5807.0 sentences: 306.0 pages: flesch: 41.0 cache: ./cache/cord-349161-4899cq99.txt txt: ./txt/cord-349161-4899cq99.txt summary: For diagnostic accuracy studies, measures of test performance (sensitivity, specificity, predictive values, likelihood ratios or diagnostic odds ratio) are plotted on the horizontal axis. ROC plots can be used to present the results of diagnostic systematic reviews, but differ from those used in primary studies as each point typically represents a separate study or data set within a study (individual studies may contribute more than one point). A summary ROC (SROC) curve can be estimated using one of several methods [12] [13] [14] [15] and quantifies test accuracy and the association between sensitivity and specificity based on differences between studies. A number of graphical displays aim to put results of diagnostic test evaluations into clinical context, based either on primary studies or systematic reviews. The inclusion of graphical displays, such as SROC plots or forest plots, in systematic reviews of test accuracy studies allows a visual assessment of heterogeneity between studies by showing the results from each individual study included in the review. abstract: BACKGROUND: Graphical displays of results allow researchers to summarise and communicate the key findings of their study. Diagnostic information should be presented in an easily interpretable way, which conveys both test characteristics (diagnostic accuracy) and the potential for use in clinical practice (predictive value). METHODS: We discuss the types of graphical display commonly encountered in primary diagnostic accuracy studies and systematic reviews of such studies, and systematically review the use of graphical displays in recent diagnostic primary studies and systematic reviews. RESULTS: We identified 57 primary studies and 49 systematic reviews. Fifty-six percent of primary studies and 53% of systematic reviews used graphical displays to present results. Dot-plot or box-and- whisker plots were the most commonly used graph in primary studies and were included in 22 (39%) studies. ROC plots were the most common type of plot included in systematic reviews and were included in 22 (45%) reviews. One primary study and five systematic reviews included a probability-modifying plot. CONCLUSION: Graphical displays are currently underused in primary diagnostic accuracy studies and systematic reviews of such studies. Diagnostic accuracy studies need to include multiple types of graphic in order to provide both a detailed overview of the results (diagnostic accuracy) and to communicate information that can be used to inform clinical practice (predictive value). Work is required to improve graphical displays, to better communicate the utility of a test in clinical practice and the implications of test results for individual patients. url: https://doi.org/10.1186/1471-2288-8-20 doi: 10.1186/1471-2288-8-20 id: cord-202376-440zapcw author: Wilder, Bryan title: Tracking disease outbreaks from sparse data with Bayesian inference date: 2020-09-12 words: 5808.0 sentences: 347.0 pages: flesch: 55.0 cache: ./cache/cord-202376-440zapcw.txt txt: ./txt/cord-202376-440zapcw.txt summary: The COVID-19 pandemic provides new motivation for a classic problem in epidemiology: estimating the empirical rate of transmission during an outbreak (formally, the time-varying reproduction number) from case counts. Our model places a Gaussian process prior over the unknown reproduction number at each time step and models observations sampled from the distribution of a specific testing program. We now depart from the standard disease model used in previous work and describe a wide-ranging set of examples for how our framework can accommodate models of the process which generates the observed data from the latent (unknown) true infections. However, is complicated by the fact that x is determined by a large number of discrete latent variables, primarily n (the time series of infections) and {t i convert , t i revert } N i=1 , the times when each individual tests positive. abstract: The COVID-19 pandemic provides new motivation for a classic problem in epidemiology: estimating the empirical rate of transmission during an outbreak (formally, the time-varying reproduction number) from case counts. While standard methods exist, they work best at coarse-grained national or state scales with abundant data, and struggle to accommodate the partial observability and sparse data common at finer scales (e.g., individual schools or towns). For example, case counts may be sparse when only a small fraction of infections are caught by a testing program. Or, whether an infected individual tests positive may depend on the kind of test and the point in time when they are tested. We propose a Bayesian framework which accommodates partial observability in a principled manner. Our model places a Gaussian process prior over the unknown reproduction number at each time step and models observations sampled from the distribution of a specific testing program. For example, our framework can accommodate a variety of kinds of tests (viral RNA, antibody, antigen, etc.) and sampling schemes (e.g., longitudinal or cross-sectional screening). Inference in this framework is complicated by the presence of tens or hundreds of thousands of discrete latent variables. To address this challenge, we propose an efficient stochastic variational inference method which relies on a novel gradient estimator for the variational objective. Experimental results for an example motivated by COVID-19 show that our method produces an accurate and well-calibrated posterior, while standard methods for estimating the reproduction number can fail badly. url: https://arxiv.org/pdf/2009.05863v1.pdf doi: nan id: cord-352111-frk319q1 author: Woodruff, Amelita title: COVID-19 Follow up Testing date: 2020-05-11 words: 633.0 sentences: 47.0 pages: flesch: 64.0 cache: ./cache/cord-352111-frk319q1.txt txt: ./txt/cord-352111-frk319q1.txt summary: • 70% of patients met CDC guidelines for release from quarantine & still tested (+); • The average time from onset of symptoms to negative testing was 19 days.  70% of patients met CDC guidelines for release from quarantine & still tested (+)  The average time from onset of symptoms to negative testing was 19 days Dear Editor, There is some uncertainty regarding the incubation period of the SARS-CoV-2 virus. The non-test-based strategy recommends that COVID-19 patients can discontinue self-isolation when they have been afebrile for 72 hours without anti-pyretic medications, have improvement in respiratory symptoms, and have at least 10 days elapse since symptoms started, recently increased from 7 days. The test-based strategy requires resolution of fever without the use of anti-pyretics, improvement of respiratory symptoms, and two consecutive negative COVID-19 nasopharyngeal swabs collected ≥24 hours apart. In our patient population, the average time from the onset of symptoms to negative testing is 19 days. abstract: • Positive cases of SARS-CoV-2 were seen in the Mayo Clinic FL COVID Virtual Clinic. • 70% of patients met CDC guidelines for release from quarantine & still tested (+); • The average time from onset of symptoms to negative testing was 19 days. url: https://www.sciencedirect.com/science/article/pii/S0163445320302899?v=s5 doi: 10.1016/j.jinf.2020.05.012 id: cord-318570-wj7r6953 author: Xiao, Yinzong title: Point-of-Care Tests for Hepatitis B: An Overview date: 2020-10-02 words: 8331.0 sentences: 350.0 pages: flesch: 40.0 cache: ./cache/cord-318570-wj7r6953.txt txt: ./txt/cord-318570-wj7r6953.txt summary: If active infection is confirmed, subsequent blood tests are performed to determine the stage of disease and need for treatment, including a hepatitis B virus (HBV) polymerase chain reaction (PCR)-based quantitative DNA level or viral load, a hepatitis B eAg and eAb assay and liver function tests to determine whether an elevated aminotransferase (ALT) indicative of liver inflammation or other signs of impaired liver function are present. POCs usually require small amounts of body fluids (for example, a finger-prick blood sample or oral swab), short turn-around time, and are generally easy to use with minimal required training and therefore can be provided to people in a variety of community and outreach settings by a broad range of trained workers [22] and are scalable to rapidly reach large populations as has been seen with the highly successful Egyptian national hepatitis C screening program [23] . abstract: Despite the heavy disease burden posed by hepatitis B, around 90% of people living with hepatitis B are not diagnosed globally. Many of the affected populations still have limited or no access to essential blood tests for hepatitis B. Compared to conventional blood tests which heavily rely on centralised laboratory facilities, point-of-care testing for hepatitis B has the potential to broaden testing access in low-resource settings and to engage hard-to-reach populations. Few hepatitis B point-of-care tests have been ratified for clinical use by international and regional regulatory bodies, and countries have been slow to adopt point-of-care testing into hepatitis B programs. This review presents currently available point-of-care tests for hepatitis B and their roles in the care cascade, reviewing evidence for testing performance, utility, acceptability, costs and cost-effectiveness when integrated into hepatitis B diagnosis and monitoring programs. We further discuss challenges and future directions in aspects of technology, implementation, and regulation when adopting point-of-care testing in hepatitis B programs. url: https://doi.org/10.3390/cells9102233 doi: 10.3390/cells9102233 id: cord-006229-7yoilsho author: nan title: Abstracts of the 82(nd) Annual Meeting of the German Society for Experimental and Clinical Pharmacology and Toxicology (DGPT) and the 18(th) Annual Meeting of the Network Clinical Pharmacology Germany (VKliPha) in cooperation with the Arbeitsgemeinschaft für Angewandte Humanpharmakologie e.V. (AGAH) date: 2016-02-06 words: 133493.0 sentences: 6804.0 pages: flesch: 42.0 cache: ./cache/cord-006229-7yoilsho.txt txt: ./txt/cord-006229-7yoilsho.txt summary: It directly activates Protein Kinase A (PKA) or the Exchange protein directly activated by cAMP (Epac) which is a guanine exchange factor (GEF) for the small monomeric GTPase Rap. As Human umbilical vein endothelial cells (HUVEC) express both cAMP effectors (Epac1 and PKA), we investigated the role of cAMP-signaling using a spheroid based sprouting assay as an in vitro model for angiogenesis. After activation, S1P receptors regulate important processes in the progression of renal diseases, such as mesangial cell migration Methods and Results: Here we demonstrate that dexamethasone treatment lowered S1P 1 mRNA and protein expression levels in rat mesangial cells measured by TaqMan® and Western blot analyses. The aim of this study was to investigate the relevance of IGFBP5 in cardiogenesis and cardiac remodeling and its role as a potential target for ameliorating stress-induced cardiac remodeling Methods and Results: We investigated the expression of Igfbp5 in murine cardiac tissue at different developmental stages by qPCR normalized to Tpt1 (Tumor Protein, Translationally-Controlled 1). abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7100641/ doi: 10.1007/s00210-016-1213-y id: cord-010092-uftc8inx author: nan title: Abstract of 29th Regional Congress of the ISBT date: 2019-06-07 words: 233304.0 sentences: 13171.0 pages: flesch: 54.0 cache: ./cache/cord-010092-uftc8inx.txt txt: ./txt/cord-010092-uftc8inx.txt summary: Prospective testing of blood donations in endemic areas of the U.S. revealed 0.38% of donors were positive for Babesia DNA or antibodies (Moritz, NEJM, 2016) Aims: -To report results of ongoing Babesia clinical trial -To explain significance of Babesia as a TT infection Methods: In cobas â Babesia for use on the cobas â 6800/8800 Systems, is a qualitative polymerase chain reaction nucleic acid amplification test, developed to detect in whole blood (WB) donor samples the 4 Babesia species that cause human disease: B. In sensitivity analyses, there were two discrepant results for HIV testing, three for HCV, and five for anti-HBc. Summary/Conclusions: Elecsys â infectious disease parameters on the cobas e 801 analyser demonstrate high specificity/sensitivity for screening first-time blood donor samples, with similar clinical performance to other commercially available assays. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7169345/ doi: 10.1111/vox.12792 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-019347-tj3ye1mx author: nan title: ABSTRACT BOOK date: 2010-02-19 words: 107926.0 sentences: 6940.0 pages: flesch: 53.0 cache: ./cache/cord-019347-tj3ye1mx.txt txt: ./txt/cord-019347-tj3ye1mx.txt summary: Method:Case Report:A 15y/o w/f athlete presented with a two month history of recurrent hives and angioedema which she associated with ingestion of Halloween candy .One week before evaluation she had hives with Coconut as well.Her history was othewise unremarkable except for recurrent UTI''S, annual sinusitis, pneumonia in 1998 as well as migraines.She denied sexual activity.Her physical exam was normal.Results:An evaluation for autoimmune disease revealed normal ESR, ANA, DSDNA, mono and hepatitis serology as well as lyme titers however her CH50 was low17u/ml(normal 26-58U/ml)and evaluation of complement revealed c4 14mg/dl(normal 16-47mg//dl)and c2 <1.3mg/dl(normal 1.6-3.5mg/dl)with normal c3, c5-c9.Her father had nor-malc4 but c2 was 1.4mg/dl (normal 1.6-3.5mg/dl)Her sister had c2 of 1.5mg/dl and normal c4 and her mother had normal c2 and c4.Her workup included positive prick skin test to ragweed, ash and grass and she was started on Rhinocort and Clarinex seasonally.She has been followed for one year with resolution of hives and is asymptomatic.Her diagnosis had been confirmed by a pediatric rheumatologist.Conclusion;We present an atypical case of C2 complement deficiency in an currently asymptomatic individual. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7129269/ doi: 10.1016/s1081-1206(10)61294-x id: cord-019490-m1cuuehi author: nan title: Abstracts cont. date: 2015-12-28 words: 93588.0 sentences: 5683.0 pages: flesch: 50.0 cache: ./cache/cord-019490-m1cuuehi.txt txt: ./txt/cord-019490-m1cuuehi.txt summary: Tigecycline Evaluation Surveillance Trial (TEST) -Global in vitro antibacterial activity against selected species of glucose non-fermenting organisms Objective: Despite the introduction of new antimicrobials to treat resistant gram-positive bacteria, Staphylococcus aureus continues to be a therapeutic challenge for the clinician. Two prospective studies from our centre identified common causes of CAP in India to be Mycoplasma pneumoniae [MP] and Legionella pneumophila [LP] by serology in 11% each, and SPN in 10% by culture of respiratory secretions/blood/ Conclusion: Although SPN is the most common isolate, the rising numbers of gram negative organisms (38%) and atypical pathogens associated with increasing mortality stress the need for review of initial antibiotic choice for adults with higher PORT classes. Conclusion: The spectrum of isolates among our patients were shifting towards gram positive bacteria with high resistance to different groups of antimicrobial agents limiting few choices for alternative therapies for infection control. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7129916/ doi: 10.1111/j.1469-0691.2005.clm_1134_02.x id: cord-022650-phsr10jp author: nan title: Abstracts TPS date: 2018-08-14 words: 119675.0 sentences: 7010.0 pages: flesch: 55.0 cache: ./cache/cord-022650-phsr10jp.txt txt: ./txt/cord-022650-phsr10jp.txt summary: 0685 | Skin prick test reactivity to aeroallergens in adult allergy clinic in a tertiary hospital: a 12-year retrospective study Results: Five different human sera were screened for specific IgE level against 29 different allergen sources using test methods of three different suppliers. Conclusion: This multicenter prospective study confirmed that stepwise single-dose OFC to egg will help to clarify the severity of egg allergy, and will contribute to improved food allergy manageMethod: The study design was a retrospective cohort study extracting data from the electronic chart of children older than 4 years who visited our out-patient clinic for egg or milk allergy and who underwent an oral food challenge test (OFC) twice within 24 months between November 2013 and December 2017. Results: In the base case analysis, using Italy clinical practice patients with moderate-to severe allergic rhino-conjunctivitis (SS ranging from 6 to 15 points) and a mean age at entry of 21 years, both SCIT and SLIT were associated with increased cost but superior efficacy compared to pharmacotherapy alone. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7159469/ doi: 10.1111/all.13539 id: cord-022653-qa1uph35 author: nan title: Poster Discussion Session PDS date: 2017-08-30 words: 58292.0 sentences: 3300.0 pages: flesch: 53.0 cache: ./cache/cord-022653-qa1uph35.txt txt: ./txt/cord-022653-qa1uph35.txt summary: 0206 | G protein coupled receptor kinase 2 (GRK2) regulates endothelial permeability induced by Bradykinin 0208 | Pharmacokinetics (PK) and pharmacodynamics (PD) of c1 esterase inhibitor of chronic urticaria challenges most commonly identified were the following: time of onset of disease; frequency/duration of and provoking factors for wheals; diurnal variation; occurrence in relation to weekends, holidays, and foreign travel; shape, size, and distribution of wheals; associated angioedema; associated subjective symptoms of lesions; family and personal history regarding urticaria, atopy; previous or current allergies, infections, internal diseases, or other possible causes; psychosomatic and psychiatric diseases; surgical implantations and events during surgery; gastric/ intestinal problems; induction by physical agents or exercise; use of drugs; food allergies; relationship to the menstrual cycle; smoking habits; type of work, hobbies; stress; quality of life and emotional impact; previous therapy and response to therapy, and previous diagnostic procedures/results. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7159476/ doi: 10.1111/all.13251 id: cord-022659-chwk2bs4 author: nan title: Abstracts: Poster session date: 2004-10-08 words: 49153.0 sentences: 2598.0 pages: flesch: 49.0 cache: ./cache/cord-022659-chwk2bs4.txt txt: ./txt/cord-022659-chwk2bs4.txt summary: We investigated the usefulness of informant-based data in Alzheimer''s disease (AD) by comparing caregivers'' subjective evaluations of 83 probable A D patients'' performance on an abbreviated version of the Memory Self-Report Questionnaire to objective evaluations derived from an extensive battery of neuropsychological tests and to clinicians'' evaluations. Compared with 89 subjects (mean age 75.2 yr; 34 men, 55 women) with dementia of the Alzheimer type (DAT), there were no significant group differences for comparable Clinical Dementia Rating stages of dementia for measures of language, Activities of Daily Living, or general cognition. The mean age at onset did not differ significantly between handedness groups (F [ l,lOO] = .82), but the mean duration of symptoms ( Alterations in the optical properties of brain can be used to detect pathological changes in patients with Alzheimer''s disease (AD). abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7159508/ doi: 10.1002/ana.410320224 id: cord-023095-4dannjjm author: nan title: Research Abstract Program of the 2011 ACVIM Forum Denver, Colorado, June 15–18, 2011 date: 2011-05-03 words: 134226.0 sentences: 6834.0 pages: flesch: 51.0 cache: ./cache/cord-023095-4dannjjm.txt txt: ./txt/cord-023095-4dannjjm.txt summary: The purpose of this study was to determine the short-term effects of ivabradine on heart rate (HR), blood pressure, left ventricular (LV) systolic and diastolic function, left atrial (LA) performance, and clinical tolerance in healthy cats after repeated oral doses. The goal of this study was to investigate the relationship between heart rate and ECG time intervals to body mass in apparently healthy horses and ponies and to calculate normal ranges for different weight groups. This study aimed to investigate the prevalence of hypercoagulability in PLN dogs based on thromboelastography (TEG), and to determine whether hypercoagulability in these patients could be predicted by clinical assessments that identify systemic hypertension (systolic blood pressure 4 160 mmHg), hypoalbuminemia (serum albumin o 2.7 mg/dl), antithrombin activity (o 70%), and degree of proteinuria (urine protein:creatinine ratio [UPC] ! abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7166756/ doi: 10.1111/j.1939-1676.2011.0726.x id: cord-023346-8sqbqjm1 author: nan title: MONDAY: POSTERS date: 2005-06-08 words: 130043.0 sentences: 7330.0 pages: flesch: 54.0 cache: ./cache/cord-023346-8sqbqjm1.txt txt: ./txt/cord-023346-8sqbqjm1.txt summary: • enhancement of automation/computerisation; • process control to provide an ''error-free pathway''; • (national) surveillance and trend analysis of results, preferably based on national working standards; • significantly increased sensitivity, especially from development of antigen/antibody ''combi'' assays (e.g. for HIV, and recently, for HCV); • awareness of HBsAg vaccine-escape mutants and design of assays to cope with this; • extension of range of agents and markers tested for (varies in different countries); • increasing range of assays available for testing donors with a relevant history of exposure to malaria or Chagas'' disease infection (for retrieval of otherwise wasted blood); • European Union''s in vitro diagnostics directive: this has caused some problems and reduced flexibility. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7169255/ doi: 10.1111/j.1423-0410.2005.00652.x id: cord-023354-f2ciho6o author: nan title: TUESDAY PLENARY SESSION 3 TUESDAY: POSTERS date: 2005-06-08 words: 130046.0 sentences: 7333.0 pages: flesch: 54.0 cache: ./cache/cord-023354-f2ciho6o.txt txt: ./txt/cord-023354-f2ciho6o.txt summary: • enhancement of automation/computerisation; • process control to provide an ''error-free pathway''; • (national) surveillance and trend analysis of results, preferably based on national working standards; • significantly increased sensitivity, especially from development of antigen/antibody ''combi'' assays (e.g. for HIV, and recently, for HCV); • awareness of HBsAg vaccine-escape mutants and design of assays to cope with this; • extension of range of agents and markers tested for (varies in different countries); • increasing range of assays available for testing donors with a relevant history of exposure to malaria or Chagas'' disease infection (for retrieval of otherwise wasted blood); • European Union''s in vitro diagnostics directive: this has caused some problems and reduced flexibility. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7169300/ doi: 10.1111/j.1423-0410.2005.00654.x id: cord-023364-ut56gczm author: nan title: EDUCATION DAY MONDAY: PLENARY SESSION 1 MONDAY: PARALLEL SESSIONS date: 2005-06-08 words: 130049.0 sentences: 7334.0 pages: flesch: 54.0 cache: ./cache/cord-023364-ut56gczm.txt txt: ./txt/cord-023364-ut56gczm.txt summary: • enhancement of automation/computerisation; • process control to provide an ''error-free pathway''; • (national) surveillance and trend analysis of results, preferably based on national working standards; • significantly increased sensitivity, especially from development of antigen/antibody ''combi'' assays (e.g. for HIV, and recently, for HCV); • awareness of HBsAg vaccine-escape mutants and design of assays to cope with this; • extension of range of agents and markers tested for (varies in different countries); • increasing range of assays available for testing donors with a relevant history of exposure to malaria or Chagas'' disease infection (for retrieval of otherwise wasted blood); • European Union''s in vitro diagnostics directive: this has caused some problems and reduced flexibility. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7169338/ doi: 10.1111/j.1423-0410.2005.00651.x id: cord-263893-zb6h3q4k author: nan title: What to expect from COVID-19 serology in a period of deconfinement? date: 2020-06-01 words: 710.0 sentences: 37.0 pages: flesch: 51.0 cache: ./cache/cord-263893-zb6h3q4k.txt txt: ./txt/cord-263893-zb6h3q4k.txt summary: The level of immunity of the French population to Sars-CoV-2 thus seems very low, far from the theoretical threshold of 60% which would allow us to expect a collective level of protection. It should be noted, however, that even if a test with a specificity of 98% is used, the positive predictive value of seropositivity will only be 50% in all regions of the country spared by the epidemic, where seroprevalence is estimated an average of 2% [3] . • that only those tests that will be recommended by the CNRs and validated by the Ministry of Health and Solidarity be used, whether they are unit tests or Elisa tests; • that the sero-epidemiological population surveys be coordinated by the Regional Health Authority (ARS) and that each person recruited be informed personally and confidentially of his or her serological status; abstract: nan url: https://www.sciencedirect.com/science/article/pii/S0001407920303411 doi: 10.1016/j.banm.2020.05.100 id: cord-337462-9mvk86q6 author: nan title: Humanity tested date: 2020-04-08 words: 1263.0 sentences: 59.0 pages: flesch: 50.0 cache: ./cache/cord-337462-9mvk86q6.txt txt: ./txt/cord-337462-9mvk86q6.txt summary: The world needs mass at-home serological testing for antibodies elicited by SARS-CoV-2, and rapid and frequent point-of-care testing for the presence of the virus'' RNA in selected populations. Singapore, Hong Kong and Taiwan have shown the world that, to contain the propagation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), governments need to quickly implement aggressive testing (by detecting the viral RNA through polymerase chain reaction (PCR)), the isolation of those infected and the tracing and quarantining of their contacts, while educating their citizens about the need for physical distancing and basic public health measures (in particular, frequent hand-washing and staying at home if feeling unwell). Medical-device companies and government and research laboratories around the world have rushed to adapt and scale up nucleic acid tests (mostly employing PCR, but also CRISPR-based detection and loop-mediated isothermal amplification) to detect the virus'' RNA, and government agencies are scrambling to assess them via emergency routes (such as the Emergency Use Authorization program 3 by the United States Food and Drug Administration (FDA)). abstract: The world needs mass at-home serological testing for antibodies elicited by SARS-CoV-2, and rapid and frequent point-of-care testing for the presence of the virus’ RNA in selected populations. url: https://doi.org/10.1038/s41551-020-0553-6 doi: 10.1038/s41551-020-0553-6 id: cord-018271-ybfxtc7x author: van Doorne, Hans title: Microbiology date: 2015-02-09 words: 13173.0 sentences: 794.0 pages: flesch: 44.0 cache: ./cache/cord-018271-ybfxtc7x.txt txt: ./txt/cord-018271-ybfxtc7x.txt summary: Microbial contamination of pharmaceutical preparations may cause health hazard to the patient (e.g. infection, pyrogenic or allergic reaction), altered therapeutic activity of the product, or other decrease in quality (turbidity, loss of consistency, altered pH). Microbiological quality control of pharmaceutical preparations and monitoring of production areas depend on the detection and quantification of micro-organisms. Survival and growth of micro-organisms in pharmaceutical preparations is governed by extrinsic factors (particularly temperature) and intrinsic factors (product composition and physico-chemical characteristics). Suppliers of materials may minimise the risks of contamination of TSE by ensuring [12] : • The source animals and their geographical origin • Nature of animal material used in manufacture and any procedures in place to avoid cross-contamination with higher risk materials • Production process(es) including the quality control and quality assurance system in place to ensure product consistency and traceability Manufacturers of pharmaceutical preparations select their raw materials so they are TSE free (see also Sect. However, since vaccine preparation involves the use of materials of biological origin, such as Chinese Hamster Ovary cells, vaccines are susceptible to contamination by micro-organisms, including viruses [16] [17] [18] . abstract: Microbial contamination of pharmaceutical preparations may cause health hazard to the patient (e.g. infection, pyrogenic or allergic reaction), altered therapeutic activity of the product, or other decrease in quality (turbidity, loss of consistency, altered pH). This chapter provides a general introduction on pharmaceutical microbiology by focusing on the essential properties of micro-organisms. First of all the basic characteristics of life and the types of biological contaminants and potentially infectious agents of pharmaceutical products will be discussed: viz. prions, viruses, mollicutes, bacteria, fungi, and endotoxins. In the next section factors affecting survival and growth of micro-organisms are discussed. In addition to well-known factors such as time, temperature, and chemical and physical characteristics of the environment, attention will be paid to biofilm formation. Primary microbiological contamination is prevented by implementing an adequate microbiological quality control and quality assurance program and by following cGMPs during production. Microbiological quality control of pharmaceutical preparations and monitoring of production areas depend on the detection and quantification of micro-organisms. The classical, growth based, methods and some of the commercially available alternative methods are discussed. Understanding essential microbiological concepts is necessary in designing both microbiologically stable pharmaceutical products and ensuring an effective quality control and monitoring program within the manufacturing or preparation facility. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123110/ doi: 10.1007/978-3-319-15814-3_19 ==== 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