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V.; Viana, Henrique V.; Rodrigues, Carlos R.; Cabral, Lúcio Mendes; Silva, Thaís D. 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A.; Crook, Derrick W.; Walker, A. Sarah; Matthews, Philippa C. title: Metagenomic Nanopore Sequencing of Influenza Virus Direct from Clinical Respiratory Samples date: 2019-12-23 journal: J Clin Microbiol DOI: 10.1128/jcm.00963-19 sha: doc_id: 346906 cord_uid: 1wmp43ti file: cache/cord-323973-wszo9s3d.json key: cord-323973-wszo9s3d authors: Zhu, Hanliang; Zhang, Haoqing; Ni, Sheng; Korabečná, Marie; Yobas, Levent; Neuzil, Pavel title: The vision of point-of-care PCR tests for the COVID-19 pandemic and beyond date: 2020-07-20 journal: Trends Analyt Chem DOI: 10.1016/j.trac.2020.115984 sha: doc_id: 323973 cord_uid: wszo9s3d file: cache/cord-335375-n6q70o35.json key: cord-335375-n6q70o35 authors: Chan, Paul K. S.; Lim, Pak-Leong; Liu, Esther Y. M.; Cheung, Jo L. K.; Leung, Danny T. M.; Sung, Joseph J. Y. title: Antibody Avidity Maturation during Severe Acute Respiratory Syndrome–Associated Coronavirus Infection date: 2005-07-01 journal: J Infect Dis DOI: 10.1086/430615 sha: doc_id: 335375 cord_uid: n6q70o35 file: cache/cord-345992-3ij1vbqp.json key: cord-345992-3ij1vbqp authors: Drosten, Christian; Doerr, Hans Wilhelm; Lim, Wilina; Stöhr, Klaus; Niedrig, Matthias title: SARS Molecular Detection External Quality Assurance date: 2004-12-17 journal: Emerg Infect Dis DOI: 10.3201/eid1012.040416 sha: doc_id: 345992 cord_uid: 3ij1vbqp file: cache/cord-314753-xflhxb13.json key: cord-314753-xflhxb13 authors: Manso, Carmen F.; Bibby, David F.; Mbisa, Jean L. title: Efficient and unbiased metagenomic recovery of RNA virus genomes from human plasma samples date: 2017-06-23 journal: Sci Rep DOI: 10.1038/s41598-017-02239-5 sha: doc_id: 314753 cord_uid: xflhxb13 file: cache/cord-017248-a37t31u1.json key: cord-017248-a37t31u1 authors: nan title: Alphabetic Listing of Diseases and Conditions date: 2010-05-17 journal: Handbook of Autopsy Practice DOI: 10.1007/978-1-59745-127-7_17 sha: doc_id: 17248 cord_uid: a37t31u1 file: cache/cord-254963-cnvxlv6h.json key: cord-254963-cnvxlv6h authors: Paskey, Adrian C.; Frey, Kenneth G.; Schroth, Gary; Gross, Stephen; Hamilton, Theron; Bishop-Lilly, Kimberly A. title: Enrichment post-library preparation enhances the sensitivity of high-throughput sequencing-based detection and characterization of viruses from complex samples date: 2019-02-26 journal: BMC Genomics DOI: 10.1186/s12864-019-5543-2 sha: doc_id: 254963 cord_uid: cnvxlv6h file: cache/cord-355351-seqwx9x1.json key: cord-355351-seqwx9x1 authors: Battey, CJ; Ralph, Peter L; Kern, Andrew D title: Predicting geographic location from genetic variation with deep neural networks date: 2020-06-08 journal: eLife DOI: 10.7554/elife.54507 sha: doc_id: 355351 cord_uid: seqwx9x1 file: cache/cord-023442-4vzwc2d2.json key: cord-023442-4vzwc2d2 authors: nan title: Proceedings of SCANNING 94/SEEMS 94 Charleston, South Carolina, USA date: 2006-12-05 journal: Scanning DOI: 10.1002/sca.4950160315 sha: doc_id: 23442 cord_uid: 4vzwc2d2 file: cache/cord-353394-lq1f53qv.json key: cord-353394-lq1f53qv authors: Han, Tae-Hee; Park, Sang-Hun; Chung, Ju-Young; Jeong, Hyo-Won; Jung, Jihun; Lee, Jae-In; Hwang, Young-Ok; Kim, Il-Young; Lee, Jip-Ho; Jung, Kweon title: Detection of Pathogenic Viruses in the Ambient Air in Seoul, Korea date: 2018-05-14 journal: Food Environ Virol DOI: 10.1007/s12560-018-9348-2 sha: doc_id: 353394 cord_uid: lq1f53qv file: cache/cord-354372-vfvnjmv1.json key: cord-354372-vfvnjmv1 authors: Carpenito, L.; D'Ercole, M.; Porta, F.; Di Blasi, E.; Doi, P.; Fagara, G. Redolfi; Rey, R.; Bulfamante, G. title: The autopsy at the time of SARS-CoV-2: Protocol and lessons date: 2020-07-04 journal: Ann Diagn Pathol DOI: 10.1016/j.anndiagpath.2020.151562 sha: doc_id: 354372 cord_uid: vfvnjmv1 file: cache/cord-281916-v6u5mr2i.json key: cord-281916-v6u5mr2i authors: Bonnin, Paul; Miszczak, Fabien; Kin, Nathalie; Resa, Cecile; Dina, Julia; Gouarin, Stephanie; Viron, Florent; Morello, Remy; Vabret, Astrid title: Study and interest of cellular load in respiratory samples for the optimization of molecular virological diagnosis in clinical practice date: 2016-08-09 journal: BMC Infect Dis DOI: 10.1186/s12879-016-1730-9 sha: doc_id: 281916 cord_uid: v6u5mr2i file: cache/cord-300399-21xozruq.json key: cord-300399-21xozruq authors: Jayamohan, Harikrishnan; Lambert, Christopher J.; Sant, Himanshu J.; Jafek, Alexander; Patel, Dhruv; Feng, Haidong; Beeman, Michael; Mahmood, Tawsif; Nze, Ugochukwu; Gale, Bruce K. title: SARS-CoV-2 pandemic: a review of molecular diagnostic tools including sample collection and commercial response with associated advantages and limitations date: 2020-10-18 journal: Anal Bioanal Chem DOI: 10.1007/s00216-020-02958-1 sha: doc_id: 300399 cord_uid: 21xozruq file: cache/cord-313887-8sabsrgy.json key: cord-313887-8sabsrgy authors: Quandt, Sara A.; LaMonto, Natalie J.; Mora, Dana C.; Talton, Jennifer W.; Laurienti, Paul J.; Arcury, Thomas A. title: COVID-19 Pandemic among Latinx Farmworker and Nonfarmworker Families in North Carolina: Knowledge, Risk Perceptions, and Preventive Behaviors date: 2020-08-10 journal: Int J Environ Res Public Health DOI: 10.3390/ijerph17165786 sha: doc_id: 313887 cord_uid: 8sabsrgy file: cache/cord-335372-tncjfdtp.json key: cord-335372-tncjfdtp authors: HACKNEY, RAYMOND W.; CRAWFORD, JAMES J.; TULIS, JERRY J. title: USING A BIOLOGICAL INDICATOR TO DETECT POTENTIAL SOURCES OF CROSS-CONTAMINATION IN THE DENTAL OPERATORY date: 1998-11-30 journal: The Journal of the American Dental Association DOI: 10.14219/jada.archive.1998.0103 sha: doc_id: 335372 cord_uid: tncjfdtp file: cache/cord-342538-5bwsm290.json key: cord-342538-5bwsm290 authors: Izquierdo Lara, R. W.; Elsinga, G.; Heijnen, L.; Oude Munnink, B. B.; Schapendonk, C. M. E.; Nieuwenhuijse, D.; Kon, M.; Lu, L.; Aarestrup, F. M.; Lycett, S.; Medema, G.; Koopmans, M. P. G.; de Graaf, M. title: Monitoring SARS-CoV-2 circulation and diversity through community wastewater sequencing date: 2020-09-22 journal: nan DOI: 10.1101/2020.09.21.20198838 sha: doc_id: 342538 cord_uid: 5bwsm290 file: cache/cord-313670-tbah33ro.json key: cord-313670-tbah33ro authors: Cannovo, Nunzia; Cingolani, Mariano; Guarino, Rosa; Fedeli, Piergiorgio title: Regulation of Biobanks in Italy date: 2020-09-02 journal: Front Pediatr DOI: 10.3389/fped.2020.00415 sha: doc_id: 313670 cord_uid: tbah33ro file: cache/cord-348464-1c08mb2k.json key: cord-348464-1c08mb2k authors: Winter, Taylor; Riordan, Benjamin C.; Pakpour, Amir H.; Griffiths, Mark D.; Mason, Andre; Poulgrain, John W.; Scarf, Damian title: Evaluation of the English Version of the Fear of COVID-19 Scale and Its Relationship with Behavior Change and Political Beliefs date: 2020-06-15 journal: Int J Ment Health Addict DOI: 10.1007/s11469-020-00342-9 sha: doc_id: 348464 cord_uid: 1c08mb2k file: cache/cord-345302-wbkfjz8r.json key: cord-345302-wbkfjz8r authors: Devaney, Ryan; Trudgett, James; Trudgett, Alan; Meharg, Caroline; Smyth, Victoria title: A metagenomic comparison of endemic viruses from broiler chickens with runting-stunting syndrome and from normal birds date: 2016-10-04 journal: Avian Pathol DOI: 10.1080/03079457.2016.1193123 sha: doc_id: 345302 cord_uid: wbkfjz8r file: cache/cord-294062-3esrg1jw.json key: cord-294062-3esrg1jw authors: Tam, Clarence C.; Offeddu, Vittoria; Anderson, Kathryn B.; Weg, Alden L.; Macareo, Louis R.; Ellison, Damon W.; Rangsin, Ram; Fernandez, Stefan; Gibbons, Robert V.; Yoon, In-Kyu; Simasathien, Sriluck title: Association between semi-quantitative microbial load and respiratory symptoms among Thai military recruits: a prospective cohort study date: 2018-09-14 journal: BMC Infect Dis DOI: 10.1186/s12879-018-3358-4 sha: doc_id: 294062 cord_uid: 3esrg1jw file: cache/cord-355743-vjiecd4k.json key: cord-355743-vjiecd4k authors: Ghosh, Sabyasachi; Rajwade, Ajit; Krishna, Srikar; Gopalkrishnan, Nikhil; Schaus, Thomas E.; Chakravarthy, Anirudh; Varahan, Sriram; Appu, Vidhya; Ramakrishnan, Raunak; Ch, Shashank; Jindal, Mohit; Bhupathi, Vadhir; Gupta, Aditya; Jain, Abhinav; Agarwal, Rishi; Pathak, Shreya; Rehan, Mohammed Ali; Consul, Sarthak; Gupta, Yash; Gupta, Nimay; Agarwal, Pratyush; Goyal, Ritika; Sagar, Vinay; Ramakrishnan, Uma; Krishna, Sandeep; Yin, Peng; Palakodeti, Dasaradhi; Gopalkrishnan, Manoj title: Tapestry: A Single-Round Smart Pooling Technique for COVID-19 Testing date: 2020-04-29 journal: nan DOI: 10.1101/2020.04.23.20077727 sha: doc_id: 355743 cord_uid: vjiecd4k file: cache/cord-315054-kji2kfek.json key: cord-315054-kji2kfek authors: Chakraborty, Nabarun; Schmitt, Connie W.; Honnold, Cary L.; Moyler, Candace; Butler, Stephen; Nachabe, Hisham; Gautam, Aarti; Hammamieh, Rasha title: Protocol Improvement for RNA Extraction From Compromised Frozen Specimens Generated in Austere Conditions: A Path Forward to Transcriptomics-Pathology Systems Integration date: 2020-07-22 journal: Front Mol Biosci DOI: 10.3389/fmolb.2020.00142 sha: doc_id: 315054 cord_uid: kji2kfek file: cache/cord-336103-ufvq0ngl.json key: cord-336103-ufvq0ngl authors: Sharma, R.; Goyal, S.; Bist, P. title: Optimal sample pooling: an efficient tool against SARS-CoV-2 date: 2020-07-04 journal: nan DOI: 10.1101/2020.07.03.20145953 sha: doc_id: 336103 cord_uid: ufvq0ngl file: cache/cord-102613-hly07ne3.json key: cord-102613-hly07ne3 authors: Danko, David; Bezdan, Daniela; Afshinnekoo, Ebrahim; Ahsanuddin, Sofia; Bhattacharya, Chandrima; Butler, Daniel J; Chng, Kern Rei; Donnellan, Daisy; Hecht, Jochen; Kuchin, Katerina; Karasikov, Mikhail; Lyons, Abigail; Mak, Lauren; Meleshko, Dmitry; Mustafa, Harun; Mutai, Beth; Neches, Russell Y; Ng, Amanda; Nikolayeva, Olga; Nikolayeva, Tatyana; Png, Eileen; Ryon, Krista; Sanchez, Jorge L; Shaaban, Heba; Sierra, Maria A; Thomas, Dominique; Young, Ben; Abudayyeh, Omar O.; Alicea, Josue; Bhattacharyya, Malay; Blekhman, Ran; Castro-Nallar, Eduardo; Cañas, Ana M; Chatziefthimiou, Aspassia D; Crawford, Robert W; De Filippis, Francesca; Deng, Youping; Desnues, Christelle; Dias-Neto, Emmanuel; Dybwad, Marius; Elhaik, Eran; Ercolini, Danilo; Frolova, Alina; Gankin, Dennis; Gootenberg, Jonathan S.; Graf, Alexandra B; Green, David C; Hajirasouliha, Iman; Hernandez, Mark; Iraola, Gregorio; Jang, Soojin; Kahles, Andre; Kelly, Frank J; Knights, Kaymisha; Kyrpides, Nikos C; Łabaj, Paweł P; Lee, Patrick K H; Leung, Marcus H Y; Ljungdahl, Per; Mason-Buck, Gabriella; McGrath, Ken; Meydan, Cem; Mongodin, Emmanuel F; Moraes, Milton Ozorio; Nagarajan, Niranjan; Nieto-Caballero, Marina; Noushmehr, Houtan; Oliveira, Manuela; Ossowski, Stephan; Osuolale, Olayinka O; Özcan, Orhan; Paez-Espino, David; Rascovan, Nicolas; Richard, Hugues; Rätsch, Gunnar; Schriml, Lynn M; Semmler, Torsten; Sezerman, Osman U; Shi, Leming; Shi, Tieliu; Song, Le Huu; Suzuki, Haruo; Tighe, Scott W; Tong, Xinzhao; Udekwu, Klas I; Ugalde, Juan A; Valentine, Brandon; Vassilev, Dimitar I; Vayndorf, Elena; Velavan, Thirumalaisamy P; Wu, Jun; Zambrano, María M; Zhu, Jifeng; Zhu, Sibo; Mason, Christopher E title: Global Genetic Cartography of Urban Metagenomes and Anti-Microbial Resistance date: 2020-05-04 journal: bioRxiv DOI: 10.1101/724526 sha: doc_id: 102613 cord_uid: hly07ne3 file: cache/cord-307874-0obomty2.json key: cord-307874-0obomty2 authors: Pardon, Bart; Buczinski, Sébastien title: Bovine Respiratory Disease Diagnosis: What Progress Has Been Made in Infectious Diagnosis? date: 2020-05-23 journal: Vet Clin North Am Food Anim Pract DOI: 10.1016/j.cvfa.2020.03.005 sha: doc_id: 307874 cord_uid: 0obomty2 file: cache/cord-324944-ixh3ykrc.json key: cord-324944-ixh3ykrc authors: Mitsakakis, Konstantinos; D'Acremont, Valérie; Hin, Sebastian; von Stetten, Felix; Zengerle, Roland title: Diagnostic tools for tackling febrile illness and enhancing patient management date: 2018-12-05 journal: Microelectron Eng DOI: 10.1016/j.mee.2018.10.001 sha: doc_id: 324944 cord_uid: ixh3ykrc file: cache/cord-317213-vhprfb1o.json key: cord-317213-vhprfb1o authors: Tram, Dai Thien Nhan; Wang, Hao; Sugiarto, Sigit; Li, Tao; Ang, Wee Han; Lee, Chengkuo; Pastorin, Giorgia title: Advances in nanomaterials and their applications in point of care (POC) devices for the diagnosis of infectious diseases date: 2016-09-26 journal: Biotechnol Adv DOI: 10.1016/j.biotechadv.2016.09.003 sha: doc_id: 317213 cord_uid: vhprfb1o file: cache/cord-326133-d46wbfrx.json key: cord-326133-d46wbfrx authors: Nakayasu, Ernesto S.; Nicora, Carrie D.; Sims, Amy C.; Burnum-Johnson, Kristin E.; Kim, Young-Mo; Kyle, Jennifer E.; Matzke, Melissa M.; Shukla, Anil K.; Chu, Rosalie K.; Schepmoes, Athena A.; Jacobs, Jon M.; Baric, Ralph S.; Webb-Robertson, Bobbie-Jo; Smith, Richard D.; Metz, Thomas O. title: MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses date: 2016-05-10 journal: mSystems DOI: 10.1128/msystems.00043-16 sha: doc_id: 326133 cord_uid: d46wbfrx file: cache/cord-329162-6w8qcv1c.json key: cord-329162-6w8qcv1c authors: Ayginin, Andrey A.; Pimkina, Ekaterina V.; Matsvay, Alina D.; Speranskaya, Anna S.; Safonova, Marina V.; Blinova, Ekaterina A.; Artyushin, Ilya V.; Dedkov, Vladimir G.; Shipulin, German A.; Khafizov, Kamil title: The Study of Viral RNA Diversity in Bird Samples Using De Novo Designed Multiplex Genus-Specific Primer Panels date: 2018-08-12 journal: Adv Virol DOI: 10.1155/2018/3248285 sha: doc_id: 329162 cord_uid: 6w8qcv1c file: cache/cord-310061-nro623aa.json key: cord-310061-nro623aa authors: Valitutto, Marc T.; Aung, Ohnmar; Tun, Kyaw Yan Naing; Vodzak, Megan E.; Zimmerman, Dawn; Yu, Jennifer H.; Win, Ye Tun; Maw, Min Thein; Thein, Wai Zin; Win, Htay Htay; Dhanota, Jasjeet; Ontiveros, Victoria; Smith, Brett; Tremeau-Brevard, Alexandre; Goldstein, Tracey; Johnson, Christine K.; Murray, Suzan; Mazet, Jonna title: Detection of novel coronaviruses in bats in Myanmar date: 2020-04-09 journal: PLoS One DOI: 10.1371/journal.pone.0230802 sha: doc_id: 310061 cord_uid: nro623aa file: cache/cord-333413-8buawes0.json key: cord-333413-8buawes0 authors: Liebing, J.; Völker, I.; Curland, N.; Wohlsein, P.; Baumgärtner, W.; Braune, S.; Runge, M.; Moss, A.; Rautenschlein, S.; Jung, A.; Ryll, M.; Raue, K.; Strube, C.; Schulz, J.; Heffels-Redmann, U.; Fischer, L.; Gethöffer, F.; Voigt, U.; Lierz, M.; Siebert, U. title: Health status of free-ranging ring-necked pheasant chicks (Phasianus colchicus) in North-Western Germany date: 2020-06-16 journal: PLoS One DOI: 10.1371/journal.pone.0234044 sha: doc_id: 333413 cord_uid: 8buawes0 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-031907-ilhr3iu5.json key: cord-031907-ilhr3iu5 authors: nan title: ISEV2020 Abstract Book date: 2020-07-15 journal: nan DOI: 10.1080/20013078.2020.1784511 sha: doc_id: 31907 cord_uid: ilhr3iu5 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-sample-cord parallel: Warning: No more processes: Decreasing number of running jobs to 84. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. parallel: Warning: No more processes: Decreasing number of running jobs to 84. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 45996 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 47753 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 47046 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 47743 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 46264 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 49003 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 48150 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 48713 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 48045 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 49088 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 49702 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 49961 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 49829 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 49561 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes parallel: Warning: No more processes: Decreasing number of running jobs to 84. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 49870 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/cordwrd2carrel.sh: fork: retry: No child processes === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 50393 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 48747 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 51926 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/txt2adr.sh: fork: retry: No child processes parallel: Warning: No more processes: Decreasing number of running jobs to 83. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable === 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: 50151 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 50556 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 50137 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 51304 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 51285 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 51613 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 49808 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 51101 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 51253 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 51576 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 51914 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 51332 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 53684 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 53698 Aborted $FILE2BIB "$FILE" > "$OUTPUT" /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /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/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: Resource temporarily unavailable === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 55084 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 54539 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 56407 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 55537 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-011444-6jh3lvm3 author: Loureiro, Natália I. V. title: Solving an ethical issue involved in experimentation with animals in a brazilian teaching laboratory date: 2006-11-03 pages: extension: .txt txt: ./txt/cord-011444-6jh3lvm3.txt cache: ./cache/cord-011444-6jh3lvm3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-011444-6jh3lvm3.txt' === file2bib.sh === /data-disk/reader-compute/reader-cord/bin/file2bib.sh: fork: retry: No child processes OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 55576 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 55351 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-030725-876arxiu author: nan title: September 2020 New in Review date: 2020-08-20 pages: extension: .txt txt: ./txt/cord-030725-876arxiu.txt cache: ./cache/cord-030725-876arxiu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-030725-876arxiu.txt' === file2bib.sh === id: cord-002560-pue5q5wp author: Moreno, Paloma S. title: Characterisation of the canine faecal virome in healthy dogs and dogs with acute diarrhoea using shotgun metagenomics date: 2017-06-01 pages: extension: .txt txt: ./txt/cord-002560-pue5q5wp.txt cache: ./cache/cord-002560-pue5q5wp.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-002560-pue5q5wp.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: 56083 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-030409-bwxkxvsl author: Mamontov, Eugene title: Effect of Hydration on the Molecular Dynamics of Hydroxychloroquine Sulfate date: 2020-08-10 pages: extension: .txt txt: ./txt/cord-030409-bwxkxvsl.txt cache: ./cache/cord-030409-bwxkxvsl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-030409-bwxkxvsl.txt' === file2bib.sh === id: cord-313107-6cfenpxm author: Singh, Anirudh K. title: Evaluation of pooled sample analysis strategy in expediting case detection in areas with emerging outbreaks of COVID-19: A pilot study date: 2020-09-22 pages: extension: .txt txt: ./txt/cord-313107-6cfenpxm.txt cache: ./cache/cord-313107-6cfenpxm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-313107-6cfenpxm.txt' === file2bib.sh === id: cord-344627-w2efsshj author: Han, Tae-Hee title: Human Bocavirus 2 in Children, South Korea date: 2009-10-17 pages: extension: .txt txt: ./txt/cord-344627-w2efsshj.txt cache: ./cache/cord-344627-w2efsshj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-344627-w2efsshj.txt' === file2bib.sh === id: cord-002178-ggtxuulg author: Mauk, Michael G. title: Integrated Microfluidic Nucleic Acid Isolation, Isothermal Amplification, and Amplicon Quantification date: 2015-10-20 pages: extension: .txt txt: ./txt/cord-002178-ggtxuulg.txt cache: ./cache/cord-002178-ggtxuulg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-002178-ggtxuulg.txt' === file2bib.sh === id: cord-001207-yjaiybwf author: Sachsenröder, Jana title: The General Composition of the Faecal Virome of Pigs Depends on Age, but Not on Feeding with a Probiotic Bacterium date: 2014-02-19 pages: extension: .txt txt: ./txt/cord-001207-yjaiybwf.txt cache: ./cache/cord-001207-yjaiybwf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-001207-yjaiybwf.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: 55078 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-335375-n6q70o35 author: Chan, Paul K. S. title: Antibody Avidity Maturation during Severe Acute Respiratory Syndrome–Associated Coronavirus Infection date: 2005-07-01 pages: extension: .txt txt: ./txt/cord-335375-n6q70o35.txt cache: ./cache/cord-335375-n6q70o35.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-335375-n6q70o35.txt' === file2bib.sh === id: cord-336103-ufvq0ngl author: Sharma, R. title: Optimal sample pooling: an efficient tool against SARS-CoV-2 date: 2020-07-04 pages: extension: .txt txt: ./txt/cord-336103-ufvq0ngl.txt cache: ./cache/cord-336103-ufvq0ngl.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-336103-ufvq0ngl.txt' === file2bib.sh === id: cord-313670-tbah33ro author: Cannovo, Nunzia title: Regulation of Biobanks in Italy date: 2020-09-02 pages: extension: .txt txt: ./txt/cord-313670-tbah33ro.txt cache: ./cache/cord-313670-tbah33ro.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-313670-tbah33ro.txt' === file2bib.sh === id: cord-308687-wrzzb9cy author: Brunner, Jesse L. title: Pooled samples and eDNA-based detection can facilitate the “clean trade” of aquatic animals date: 2020-06-24 pages: extension: .txt txt: ./txt/cord-308687-wrzzb9cy.txt cache: ./cache/cord-308687-wrzzb9cy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-308687-wrzzb9cy.txt' === file2bib.sh === id: cord-298295-epxd03pt author: Eckermann, M. title: 3d Virtual Patho-Histology of Lung Tissue from Covid-19 Patients based on Phase Contrast X-ray Tomography date: 2020-06-23 pages: extension: .txt txt: ./txt/cord-298295-epxd03pt.txt cache: ./cache/cord-298295-epxd03pt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-298295-epxd03pt.txt' === file2bib.sh === id: cord-281916-v6u5mr2i author: Bonnin, Paul title: Study and interest of cellular load in respiratory samples for the optimization of molecular virological diagnosis in clinical practice date: 2016-08-09 pages: extension: .txt txt: ./txt/cord-281916-v6u5mr2i.txt cache: ./cache/cord-281916-v6u5mr2i.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-281916-v6u5mr2i.txt' === file2bib.sh === id: cord-348464-1c08mb2k author: Winter, Taylor title: Evaluation of the English Version of the Fear of COVID-19 Scale and Its Relationship with Behavior Change and Political Beliefs date: 2020-06-15 pages: extension: .txt txt: ./txt/cord-348464-1c08mb2k.txt cache: ./cache/cord-348464-1c08mb2k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-348464-1c08mb2k.txt' === file2bib.sh === id: cord-103735-nil1vv6h author: Alfano, Niccolo title: Non-invasive surveys of mammalian viruses using environmental DNA date: 2020-03-29 pages: extension: .txt txt: ./txt/cord-103735-nil1vv6h.txt cache: ./cache/cord-103735-nil1vv6h.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-103735-nil1vv6h.txt' === file2bib.sh === id: cord-301823-fbeb1nw1 author: Sridhar, Sushmita title: A blueprint for the implementation of a validated approach for the detection of SARS-Cov2 in clinical samples in academic facilities date: 2020-10-21 pages: extension: .txt txt: ./txt/cord-301823-fbeb1nw1.txt cache: ./cache/cord-301823-fbeb1nw1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-301823-fbeb1nw1.txt' === file2bib.sh === id: cord-346906-1wmp43ti author: Lewandowski, Kuiama title: Metagenomic Nanopore Sequencing of Influenza Virus Direct from Clinical Respiratory Samples date: 2019-12-23 pages: extension: .txt txt: ./txt/cord-346906-1wmp43ti.txt cache: ./cache/cord-346906-1wmp43ti.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-346906-1wmp43ti.txt' === file2bib.sh === id: cord-102547-nxut8ov1 author: Grädel, C. title: Whole genome sequencing of human enteroviruses from clinical samples by nanopore direct RNA sequencing date: 2020-06-09 pages: extension: .txt txt: ./txt/cord-102547-nxut8ov1.txt cache: ./cache/cord-102547-nxut8ov1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-102547-nxut8ov1.txt' === file2bib.sh === id: cord-342538-5bwsm290 author: Izquierdo Lara, R. W. title: Monitoring SARS-CoV-2 circulation and diversity through community wastewater sequencing date: 2020-09-22 pages: extension: .txt txt: ./txt/cord-342538-5bwsm290.txt cache: ./cache/cord-342538-5bwsm290.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-342538-5bwsm290.txt' === file2bib.sh === id: cord-355743-vjiecd4k author: Ghosh, Sabyasachi title: Tapestry: A Single-Round Smart Pooling Technique for COVID-19 Testing date: 2020-04-29 pages: extension: .txt txt: ./txt/cord-355743-vjiecd4k.txt cache: ./cache/cord-355743-vjiecd4k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-355743-vjiecd4k.txt' === file2bib.sh === id: cord-314753-xflhxb13 author: Manso, Carmen F. title: Efficient and unbiased metagenomic recovery of RNA virus genomes from human plasma samples date: 2017-06-23 pages: extension: .txt txt: ./txt/cord-314753-xflhxb13.txt cache: ./cache/cord-314753-xflhxb13.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-314753-xflhxb13.txt' === file2bib.sh === id: cord-329162-6w8qcv1c author: Ayginin, Andrey A. title: The Study of Viral RNA Diversity in Bird Samples Using De Novo Designed Multiplex Genus-Specific Primer Panels date: 2018-08-12 pages: extension: .txt txt: ./txt/cord-329162-6w8qcv1c.txt cache: ./cache/cord-329162-6w8qcv1c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-329162-6w8qcv1c.txt' === file2bib.sh === id: cord-326133-d46wbfrx author: Nakayasu, Ernesto S. title: MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses date: 2016-05-10 pages: extension: .txt txt: ./txt/cord-326133-d46wbfrx.txt cache: ./cache/cord-326133-d46wbfrx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-326133-d46wbfrx.txt' === file2bib.sh === id: cord-333413-8buawes0 author: Liebing, J. title: Health status of free-ranging ring-necked pheasant chicks (Phasianus colchicus) in North-Western Germany date: 2020-06-16 pages: extension: .txt txt: ./txt/cord-333413-8buawes0.txt cache: ./cache/cord-333413-8buawes0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-333413-8buawes0.txt' === file2bib.sh === id: cord-018761-vm86d4mj author: Bradt, David A. title: Technical Annexes date: 2017-11-08 pages: extension: .txt txt: ./txt/cord-018761-vm86d4mj.txt cache: ./cache/cord-018761-vm86d4mj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-018761-vm86d4mj.txt' === file2bib.sh === id: cord-355351-seqwx9x1 author: Battey, CJ title: Predicting geographic location from genetic variation with deep neural networks date: 2020-06-08 pages: extension: .txt txt: ./txt/cord-355351-seqwx9x1.txt cache: ./cache/cord-355351-seqwx9x1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-355351-seqwx9x1.txt' === file2bib.sh === id: cord-307874-0obomty2 author: Pardon, Bart title: Bovine Respiratory Disease Diagnosis: What Progress Has Been Made in Infectious Diagnosis? date: 2020-05-23 pages: extension: .txt txt: ./txt/cord-307874-0obomty2.txt cache: ./cache/cord-307874-0obomty2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-307874-0obomty2.txt' === file2bib.sh === id: cord-323973-wszo9s3d author: Zhu, Hanliang title: The vision of point-of-care PCR tests for the COVID-19 pandemic and beyond date: 2020-07-20 pages: extension: .txt txt: ./txt/cord-323973-wszo9s3d.txt cache: ./cache/cord-323973-wszo9s3d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-323973-wszo9s3d.txt' === file2bib.sh === id: cord-314503-u1y1bznk author: Jaluria, Pratik title: A perspective on microarrays: current applications, pitfalls, and potential uses date: 2007-01-25 pages: extension: .txt txt: ./txt/cord-314503-u1y1bznk.txt cache: ./cache/cord-314503-u1y1bznk.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-314503-u1y1bznk.txt' === file2bib.sh === id: cord-345302-wbkfjz8r author: Devaney, Ryan title: A metagenomic comparison of endemic viruses from broiler chickens with runting-stunting syndrome and from normal birds date: 2016-10-04 pages: extension: .txt txt: ./txt/cord-345302-wbkfjz8r.txt cache: ./cache/cord-345302-wbkfjz8r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-345302-wbkfjz8r.txt' === file2bib.sh === id: cord-102613-hly07ne3 author: Danko, David title: Global Genetic Cartography of Urban Metagenomes and Anti-Microbial Resistance date: 2020-05-04 pages: extension: .txt txt: ./txt/cord-102613-hly07ne3.txt cache: ./cache/cord-102613-hly07ne3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-102613-hly07ne3.txt' === file2bib.sh === id: cord-313887-8sabsrgy author: Quandt, Sara A. title: COVID-19 Pandemic among Latinx Farmworker and Nonfarmworker Families in North Carolina: Knowledge, Risk Perceptions, and Preventive Behaviors date: 2020-08-10 pages: extension: .txt txt: ./txt/cord-313887-8sabsrgy.txt cache: ./cache/cord-313887-8sabsrgy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-313887-8sabsrgy.txt' === file2bib.sh === id: cord-301991-n87le8ix author: Saxena, Abhishek title: Diatoms recovery from wastewater: Overview from an ecological and economic perspective date: 2020-10-16 pages: extension: .txt txt: ./txt/cord-301991-n87le8ix.txt cache: ./cache/cord-301991-n87le8ix.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-301991-n87le8ix.txt' === file2bib.sh === id: cord-004133-32w6g7qk author: Walker, Faye M. title: Advances in Directly Amplifying Nucleic Acids from Complex Samples date: 2019-09-30 pages: extension: .txt txt: ./txt/cord-004133-32w6g7qk.txt cache: ./cache/cord-004133-32w6g7qk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-004133-32w6g7qk.txt' === file2bib.sh === id: cord-017543-60q9iecq author: Tian, Wei-Chang title: Microfluidic Applications in Biodefense date: 2008-08-23 pages: extension: .txt txt: ./txt/cord-017543-60q9iecq.txt cache: ./cache/cord-017543-60q9iecq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-017543-60q9iecq.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-344131-e7phs0jd author: Ford, Richard B. title: Section 4 Diagnostic and Therapeutic Procedures date: 2012-12-31 pages: extension: .txt txt: ./txt/cord-344131-e7phs0jd.txt cache: ./cache/cord-344131-e7phs0jd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-344131-e7phs0jd.txt' === file2bib.sh === id: cord-022147-istz1iql author: nan title: Procedures to Investigate Waterborne Illness date: 2016-07-13 pages: extension: .txt txt: ./txt/cord-022147-istz1iql.txt cache: ./cache/cord-022147-istz1iql.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 6 resourceName b'cord-022147-istz1iql.txt' === file2bib.sh === id: cord-023442-4vzwc2d2 author: nan title: Proceedings of SCANNING 94/SEEMS 94 Charleston, South Carolina, USA date: 2006-12-05 pages: extension: .txt txt: ./txt/cord-023442-4vzwc2d2.txt cache: ./cache/cord-023442-4vzwc2d2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.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-023442-4vzwc2d2.txt' === file2bib.sh === id: cord-017248-a37t31u1 author: nan title: Alphabetic Listing of Diseases and Conditions date: 2010-05-17 pages: extension: .txt txt: ./txt/cord-017248-a37t31u1.txt cache: ./cache/cord-017248-a37t31u1.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-017248-a37t31u1.txt' === file2bib.sh === /data-disk/reader-compute/reader-cord/bin/file2bib.sh: fork: retry: No child processes 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 11 resourceName b'cord-023095-4dannjjm.txt' === file2bib.sh === /data-disk/reader-compute/reader-cord/bin/file2bib.sh: fork: retry: No child processes id: cord-031907-ilhr3iu5 author: nan title: ISEV2020 Abstract Book date: 2020-07-15 pages: extension: .txt txt: ./txt/cord-031907-ilhr3iu5.txt cache: ./cache/cord-031907-ilhr3iu5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 27 resourceName b'cord-031907-ilhr3iu5.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 16 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 12 resourceName b'cord-010119-t1x9gknd.txt' Que is empty; done keyword-sample-cord === reduce.pl bib === id = cord-001207-yjaiybwf author = Sachsenröder, Jana title = The General Composition of the Faecal Virome of Pigs Depends on Age, but Not on Feeding with a Probiotic Bacterium date = 2014-02-19 pages = extension = .txt mime = text/plain words = 5919 sentences = 302 flesch = 49 summary = faecium) NCIMB 10415 on the pig faecal virome composition was analysed in a pig feeding trial with sows and their piglets, which received either the probiotic bacterium or not. RESULTS: From 8 pooled faecal samples derived from the feeding trial, DNA and RNA virus particles were prepared and subjected to process-controlled Next Generation Sequencing resulting in 390,650 sequence reads. However, it is not known so far, whether probiotic bacteria can also influence the general composition of the faecal virome, e.g. by changing the composition of the bacterial community, which represents the host population for bacteriophages, or by direct interactions with specific viruses. Faecal samples from sows and their piglets experimentally fed with or without the probiotic bacterium were analyzed using a process-controlled deep sequencing method. As the detection rate of the bacteriophages is -besides technical factors -also dependent on the amount of viruses initially present in the analyzed sample, improved deep sequencing methods enabling quantitative analyses should be developed in future for comparative virome investigations. cache = ./cache/cord-001207-yjaiybwf.txt txt = ./txt/cord-001207-yjaiybwf.txt === reduce.pl bib === id = cord-002178-ggtxuulg author = Mauk, Michael G. title = Integrated Microfluidic Nucleic Acid Isolation, Isothermal Amplification, and Amplicon Quantification date = 2015-10-20 pages = extension = .txt mime = text/plain words = 5753 sentences = 257 flesch = 39 summary = A portable, miniaturized POC NAAT with performance comparable to conventional PCR (polymerase-chain reaction)-based tests in clinical laboratories can be realized with a disposable, palm-sized, plastic microfluidic chip in which: (1) nucleic acids (NAs) are extracted from relatively large (~mL) volume sample lysates using an embedded porous silica glass fiber or cellulose binding phase ("membrane") to capture sample NAs in a flow-through, filtration mode; (2) NAs captured on the membrane are isothermally (~65 °C) amplified; (3) amplicon production is monitored by real-time fluorescence detection, such as with a smartphone CCD camera serving as a low-cost detector; and (4) paraffin-encapsulated, lyophilized reagents for temperature-activated release are pre-stored in the chip. cache = ./cache/cord-002178-ggtxuulg.txt txt = ./txt/cord-002178-ggtxuulg.txt === reduce.pl bib === === reduce.pl bib === id = cord-011444-6jh3lvm3 author = Loureiro, Natália I. V. title = Solving an ethical issue involved in experimentation with animals in a brazilian teaching laboratory date = 2006-11-03 pages = extension = .txt mime = text/plain words = 2829 sentences = 130 flesch = 44 summary = These were i) avoid the use of laboratory animals that would be sacrificed; ii) the inclusion of other topics of metabolism such as glycolysis, citric acid cycle, fatty acid and amino acid synthesis and catabolism, and ketogenesis in the experimental discussion; iii) the experiment should have low cost and be performed after the relevant theory material is studied; and finally iv) it also should be easy and fast, due to the limited time of the practical class. In this article, we will present the protocol and approach used in this practice class, also including the evaluation by student teaching assistants and undergraduate students from nine different courses ("Biological Science," "Pharmacy," "Medicine," "Veterinary Medicine," "Nutrition," "Nursing," "Odontology," "Chemistry," and "Industrial Chemistry"). After the preparation of the protocol and arranging all necessary laboratory material including the guarurine, it was possible to evaluate this new practical class with the group of student teaching assistants from the Biochemistry discipline (n ϭ 6). cache = ./cache/cord-011444-6jh3lvm3.txt txt = ./txt/cord-011444-6jh3lvm3.txt === reduce.pl bib === === reduce.pl bib === id = cord-002560-pue5q5wp author = Moreno, Paloma S. title = Characterisation of the canine faecal virome in healthy dogs and dogs with acute diarrhoea using shotgun metagenomics date = 2017-06-01 pages = extension = .txt mime = text/plain words = 5137 sentences = 265 flesch = 50 summary = Recently, due to the advent of molecular enrichment protocols, high throughput sequencing and new metagenomic analytical methods we are now able to explore, identify and characterise viruses from different biological and environmental samples with a greater capacity [2, [5] [6] [7] [8] [9] [10] [11] In studies of human faeces, the virome has been shown to include viruses that infect eukaryotic organisms and viruses that infect prokaryotes (bacteriophages) [2, 5, [12] [13] [14] [15] [16] [17] [18] . Another eukaryotic viral family found in one healthy dog sample was Parvoviridae, genetic analysis of the 3 contigs/singletons showed a coverage of approximately 3.5% of the complete genome of canine parvovirus reference sequence (NC_001539), or 9.3% of the polyprotetin Ns1-Ns2. Nucleic acids from a single faecal sample from a dog with acute diarrhoea (DD1), which had 18 contigs/singletons of canine astrovirus (after tBLASTx analysis) was used to determine the complete genome sequence. cache = ./cache/cord-002560-pue5q5wp.txt txt = ./txt/cord-002560-pue5q5wp.txt === reduce.pl bib === id = cord-030409-bwxkxvsl author = Mamontov, Eugene title = Effect of Hydration on the Molecular Dynamics of Hydroxychloroquine Sulfate date = 2020-08-10 pages = extension = .txt mime = text/plain words = 6127 sentences = 275 flesch = 49 summary = When hydration, even at a low level, results in a disordered structure, as opposed to the highly ordered structure of dry hydroxychloroquine sulfate, the activation barriers for the rotation of methyl groups in the drug molecules become randomized and, on average, significantly reduced. The free base HCQ and more ordered hydrated HCQS also show the methyl rotation peak at the same position, in agreement with their similar activation energies (for the broad dynamic component) presented in Figure 7 . This suggests that the effect of hydration on the activation energy for the methyl group rotation may be due to the disorder introduced by the water molecules in the main hydrated and less ordered hydrated HCQS samples. While the upper panels of Figures 10 and 11 show the measured spectra, the lower panels present a comparison of the difference spectra between the main hydrated and dry HCQS samples to the spectra of H 2 O ice-Ih (5 K) and liquid water (295 K) as well as the structural H 2 O in WO 3 ·H 2 O data. cache = ./cache/cord-030409-bwxkxvsl.txt txt = ./txt/cord-030409-bwxkxvsl.txt === reduce.pl bib === id = cord-030725-876arxiu author = nan title = September 2020 New in Review date = 2020-08-20 pages = extension = .txt mime = text/plain words = 2743 sentences = 170 flesch = 47 summary = Researchers assessed nutritional risks among older patients diagnosed with COVID-19 along with their associated clinical outcomes. The NRS 2002 was designed to predict clinical effects of nutritional treatment in hospital settings with two levels: level 1 and level 2 contained factors of BMI status, weight loss history, nutritional intake, and disease severity. Association of work requirements with Supplemental Nutrition Assistance Program participation by race/ ethnicity and disability status, 2013-2017. Dietary patterns studied included the Alternative Healthy Eating Index, Dietary Approaches to Stop Hypertension diet score, and Mediterranean-style, adherence to which was determined via the food frequency questionnaire. Association between lifestyle factors, vitamin and garlic supplementation, and gastric cancer outcomes: A secondary analysis of a randomized clinical trial. A secondary analysis of a randomized controlled trial was performed to examine this issue using a sample of 3,365 participants. Demographic variables taken included age, sex, race/ethnicity, participation in the Supplemental Nutrition Assistance Program, family income level, education of parents, and health insurance status. cache = ./cache/cord-030725-876arxiu.txt txt = ./txt/cord-030725-876arxiu.txt === reduce.pl bib === === reduce.pl bib === id = cord-018761-vm86d4mj author = Bradt, David A. title = Technical Annexes date = 2017-11-08 pages = extension = .txt mime = text/plain words = 10430 sentences = 805 flesch = 53 summary = cache = ./cache/cord-018761-vm86d4mj.txt txt = ./txt/cord-018761-vm86d4mj.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-308687-wrzzb9cy author = Brunner, Jesse L. title = Pooled samples and eDNA-based detection can facilitate the “clean trade” of aquatic animals date = 2020-06-24 pages = extension = .txt mime = text/plain words = 6488 sentences = 322 flesch = 46 summary = swabs) and eDNA samples collected from finite populations and discuss key assumptions and considerations for their use with a focus on detecting Batrachochytrium salamandrivorans, an emerging pathogen that threatens global salamander diversity. www.nature.com/scientificreports www.nature.com/scientificreports/ context of screening U.S. service members for syphilis, pooling samples to reduce the number of tests required to detect rare infections is common in numerous contexts 22 , including surveys for disease freedom. In this paper I therefore develop formulae for imperfect tests of pooled samples in closed populations and eDNA, discuss the key assumptions and considerations in their application, and illustrate how eDNA may be especially useful for detecting infections in the live animal trade. Pooling and batch-processing samples collected from individual animals (e.g., swabs) can reduce several fold the number of diagnostic tests (e.g., DNA extractions and PCR reactions) required to detect rare infections. cache = ./cache/cord-308687-wrzzb9cy.txt txt = ./txt/cord-308687-wrzzb9cy.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-313107-6cfenpxm author = Singh, Anirudh K. title = Evaluation of pooled sample analysis strategy in expediting case detection in areas with emerging outbreaks of COVID-19: A pilot study date = 2020-09-22 pages = extension = .txt mime = text/plain words = 2889 sentences = 124 flesch = 50 summary = In this context, a pooled sample testing strategy was evaluated in the setting of emerging disease outbreak in 3 central Indian districts to assess if the cost of the test and turn-around time could be reduced without compromising its diagnostic characteristics and thus lead to early containment of the outbreak. At the reported point prevalence of 4.8% in this study, the negative predictive value of qRT-PCR on pooled samples was around 96% suggesting that the adoption of this strategy as an effective screening tool for COVID-19 needs to be carefully evaluated. We hypothesized that testing of pooled respiratory samples, collected from potentially infected individuals, could lead to faster laboratory confirmation and quicker containment of the emerging infection in these districts and, thus, undertook this study to evaluate the diagnostic concordance between the strategies of pooled vs. cache = ./cache/cord-313107-6cfenpxm.txt txt = ./txt/cord-313107-6cfenpxm.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-004133-32w6g7qk author = Walker, Faye M. title = Advances in Directly Amplifying Nucleic Acids from Complex Samples date = 2019-09-30 pages = extension = .txt mime = text/plain words = 13585 sentences = 664 flesch = 42 summary = Studies were included if they involved direct amplification and detection of genetic material from one of six representative sample types: blood, dried blood spot, serum and plasma, saliva and sputum, swabs, urine, and stool. However, it is important to note that the sensitivity does not necessarily suffer in much more concentrated samples-in Liu et al.'s highly robust two-step amplification process with direct hairpin assembly and HCR-based detection of SNP DNA sequences in 50% (v/v) serum, they achieved a very low LOD of 100 pg [119] . However, it is important to note that the sensitivity does not necessarily suffer in much more concentrated samples-in Liu et al.'s highly robust two-step amplification process with direct hairpin assembly and HCR-based detection of SNP DNA sequences in 50% (v/v) serum, they achieved a very low LOD of 100 pg [119] . cache = ./cache/cord-004133-32w6g7qk.txt txt = ./txt/cord-004133-32w6g7qk.txt === reduce.pl bib === id = cord-017543-60q9iecq author = Tian, Wei-Chang title = Microfluidic Applications in Biodefense date = 2008-08-23 pages = extension = .txt mime = text/plain words = 16557 sentences = 831 flesch = 37 summary = Sections cover microscale sample preparation methods; immunomagnetic separations and immunoassays; proteomics; polymerase chain reaction (PCR), quantitative PCR (qPCR) and other nucleic acid amplification methods; DNA microarrays, microelectrophoresis, and finally integrated Lab-on-a-Chip systems. The intent of JBAIDS Block III, Next Generation Diagnostics (NGD), is to establish a new system incorporating the capabilities of Block I and Block II capabilities (Table 10 .1) and adding immunoassay capabilities and the ability to identify up to 50 agents including toxins in 15 minutes using automated, miniaturized sample preparation integrated with analysis for nucleic acids and proteins, in a hand held or smaller format. They will need to be completely automated or simple to use; incorporate advanced technologies including sample preparation starting from primary samples (aerosols, blood, etc.), molecular detection, automation, microfluidics, and bioinformatics; reduce reagent consumption and space requirements; and provide cost and performance advantages compared to present systems. cache = ./cache/cord-017543-60q9iecq.txt txt = ./txt/cord-017543-60q9iecq.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-301823-fbeb1nw1 author = Sridhar, Sushmita title = A blueprint for the implementation of a validated approach for the detection of SARS-Cov2 in clinical samples in academic facilities date = 2020-10-21 pages = extension = .txt mime = text/plain words = 6118 sentences = 309 flesch = 51 summary = Here we describe our experience in establishing a COVID-19 diagnostics laboratory in an academic containment level 2 (CL2) research facility (UK) in which we validated and established a real-time PCR workflow to detect SARS-CoV2 in nose and throat swabs from HCWs. We developed an assay and workflow over eight working days (set-up to validation to screening) that can produce a quantitative diagnostic result ~4 hours after swabbing. Establishing and validating the workflow in our setting Establishing a workflow for SARS-Cov2 qRT-PCR Upon the decision to rapidly establish the qRT-PCR assay we identified several challenges, and these included: a) establishment and validation of a method suitable for diagnostic reporting, b) safe extraction of nucleic acid from a highly transmissible virus, c) accessing reagents required for performing extractions and amplifications, d) establishing a "clean" diagnostic workflow to minimise the risk of contamination, and e) creating a system in which HCWs could be swabbed and the data reported confidentially within a specified timeframe. cache = ./cache/cord-301823-fbeb1nw1.txt txt = ./txt/cord-301823-fbeb1nw1.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-022147-istz1iql author = nan title = Procedures to Investigate Waterborne Illness date = 2016-07-13 pages = extension = .txt mime = text/plain words = 38204 sentences = 1874 flesch = 50 summary = • Identifying illness associated with an exposure and verifying that the causative agent is waterborne • Detecting all cases, the causative agent, and the place of exposure • Determining the water source, mode of contamination, processes, or practices by which proliferation and/or survival of the etiological agent occurred • Implementing emergency measures to control the spread of the outbreak • Gathering information on the epidemiology of waterborne diseases and the etiology of the causative agents that can be used for education, training, and program planning, thereby impacting on the prevention of waterborne illness • Determining if the outbreak under investigation is part of a larger outbreak by immediately reporting to state/provincial/national epidemiologists In the instance of a bottled water outbreak, halting of distribution and sale of product and recall of product, some of which may already be in consumers' homes, are necessary to prevent further illness. cache = ./cache/cord-022147-istz1iql.txt txt = ./txt/cord-022147-istz1iql.txt === reduce.pl bib === id = cord-103735-nil1vv6h author = Alfano, Niccolo title = Non-invasive surveys of mammalian viruses using environmental DNA date = 2020-03-29 pages = extension = .txt mime = text/plain words = 5829 sentences = 373 flesch = 53 summary = Using a curated set of RNA oligonucleotides based on the ViroChip microarray assay [7] as baits in a hybridization capture system, multiple mammalian RNA and DNA viruses were detected from both eDNA and iDNA samples. Highlights Environmental DNA (water and blood-sucking leeches) provided a non-invasive method of screening wildlife for viruses A comprehensive viral RNA oligonucleotide bait set was developed to capture known and unknown mammalian virus diversity Leech blood meal host determination and viruses identified were congruent Viruses determined from water correlated with known and observed species visiting the water sources In brief Alfano, Dayaram, et al. In filtered water and sediment samples collected from the same waterhole, only one virus per sample was generally identified and in one location (WM20 and SM20) contigs from different viral families were isolated based on sample type. We provide evidence that environmental and invertebrate-derived DNA samples including waterhole water, sediment and wild haematophagous terrestrial leeches can be used to survey known and unknown viruses. cache = ./cache/cord-103735-nil1vv6h.txt txt = ./txt/cord-103735-nil1vv6h.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-344131-e7phs0jd author = Ford, Richard B. title = Section 4 Diagnostic and Therapeutic Procedures date = 2012-12-31 pages = extension = .txt mime = text/plain words = 40123 sentences = 2277 flesch = 51 summary = Before actually collecting and submitting a sample to a laboratory for bacterial culture, it is appropriate (whenever feasible to do so) to prepare, stain, and examine, under direct microscopy, exudates or fluid from the suspect material or tissue. Fine-needle aspiration, the use of needle and syringe to remove cells from normal and abnormal tissue, apply them to a glass slide, stain the smear, and review the results immediately is among the most useful, cost-effective procedures available in clinical practice. Do not remove the syringe from the tissue while maintaining negative pressure, because this can Enlargement of nucleus or nuclei larger than 10 nm Decreased nuclear/cytoplasmic ratio Multinucleation because of abnormal mitosis Abnormal or frequent mitosis Variations in size and shape of nuclei Increase in size and number of nucleoli Increased basophilia of cellular cytoplasm; increased RNA content Anisokaryosis or pleomorphism Multinucleated giant cells box 4-4 cytologic feAtuRes of mAlignAncy 4 result in the aspiration of significant amounts of blood from the skin, thereby significantly diluting the sample with peripheral blood. cache = ./cache/cord-344131-e7phs0jd.txt txt = ./txt/cord-344131-e7phs0jd.txt === reduce.pl bib === id = cord-301991-n87le8ix author = Saxena, Abhishek title = Diatoms recovery from wastewater: Overview from an ecological and economic perspective date = 2020-10-16 pages = extension = .txt mime = text/plain words = 9968 sentences = 533 flesch = 40 summary = Because diatoms produce organic matter to a large extent that permits natural inbuilt capacity to withstand toxicity levels in water bodies, extended survival rate, short regeneration time than microalgae, fishes, and other micro invertebrates thus making them one of the best candidate for water quality monitoring, and excellent bioindicators of aquatic biological integrity [12, 13] . Isolation and identification of benthic diatoms are problematic in comparison with planktonic species due to difficulties in sample treatment, sampling, and microscopic observation though benthic diatoms play the main role as bioindicators in the aquatic ecosystem because they attached to the substratum with secreted mucilage from their cell wall [44, 45] . An outline of isolation of pure diatom species getting affected by the surrounding contaminants is challenging since they get heavily occupied with different interfering organisms, which pose a significant threat in obtaining axenic culture, as presented in Fig. 3 . cache = ./cache/cord-301991-n87le8ix.txt txt = ./txt/cord-301991-n87le8ix.txt === reduce.pl bib === id = cord-102547-nxut8ov1 author = Grädel, C. title = Whole genome sequencing of human enteroviruses from clinical samples by nanopore direct RNA sequencing date = 2020-06-09 pages = extension = .txt mime = text/plain words = 6505 sentences = 349 flesch = 53 summary = DRS of total RNA extracted from three different enterovirus-positive stool samples produced long RNA fragments, covering between 59% to 99.6 % of the best reference genomes. Taxonomic classification of viral reads (Oxford Nanopore) and contigs (Illumina MiSeq) using MEGAN based on BLASTN matches against NCBI's nucleotide (nt) database at the species and genotype levels. In order to confirm the genotype identification and to obtain a highly accurate whole genome sequence of the enterovirus genome, we subsequently subjected the sample E590 also to cDNA sequencing using Illumina MiSeq. In this case, the cDNA was produced using genotype-specific primers given that low number of reads was obtained by DRS and MiSeq . Illumina sequencing of the cDNA from sample E026 produced using oligo-dT primers and random hexamers showed similar distributions on the domain level: The majority of contigs belonged to bacterial species (98.6% and 98.9%, respectively for oligo-dT and random hexamer approaches), with a minority of reads mapping to eukaryotes (0.49%, 0.50%) and viruses (0.87%, 0.56%). cache = ./cache/cord-102547-nxut8ov1.txt txt = ./txt/cord-102547-nxut8ov1.txt === reduce.pl bib === id = cord-344627-w2efsshj author = Han, Tae-Hee title = Human Bocavirus 2 in Children, South Korea date = 2009-10-17 pages = extension = .txt mime = text/plain words = 1433 sentences = 82 flesch = 48 summary = We looked for HBoV-2 in clinical samples from children with various diseases, including acute LRTIs, Kawasaki disease, Henoch-Schönlein purpura, and hepatitis. Of the 212 samples tested, the following viruses were detected: human respiratory syncytial virus ( HBoV-1 was not detected in the study population. Recent studies have detected HBoV-1 in serum samples of children with Kawasaki disease and of an immunocompromised child with hepatitis (7, 8) . However, neither HBoV-1 nor HBoV-2 was detected in the 172 serum samples from 61 patients with hepatitis, 12 with Kawasaki disease, 18 with Henoch-Schönlein purpura, and 81 healthy children. We demonstrated HBoV-2 DNA in the respiratory tract secretions of children with acute LRTIs. In most positive samples, the virus was found in addition to other respiratory viruses. Human bocavirus infection in young children in the United States: molecular epidemiological profile and clinical characteristics of a newly emerging respiratory virus cache = ./cache/cord-344627-w2efsshj.txt txt = ./txt/cord-344627-w2efsshj.txt === reduce.pl bib === id = cord-314503-u1y1bznk author = Jaluria, Pratik title = A perspective on microarrays: current applications, pitfalls, and potential uses date = 2007-01-25 pages = extension = .txt mime = text/plain words = 7764 sentences = 349 flesch = 38 summary = Therefore, this text aims to outline key features in microarray technology, paying particular attention to current applications as outlined in recent publications, experimental design, statistical methods, and potential uses. Several organizations such as the Microarray Gene Expression Data (MGED) Society and the European Bioinformatics Institute (EBI) have established guidelines to aid researchers in the design and implementation of microarray experiments [8, 9, 16] . As mentioned earlier, verification is critical in order to assign distinct expression patterns to specific genes with certainty (i.e. statistical significance) because of the inherent variability present in microarray data. To verify the results generated from microarray experiments, a combinatorial approach is usually needed; checking the statistical significance associated with the expression levels of specific genes, reviewing the literature, and conducting additional experiments such as RT-PCR or Northern blotting. A large number of microarray-related studies in the past have aimed to either characterize diseased cells in comparison to healthy cells or highlight the genes involved in a particular biological pathway [4, 8] . cache = ./cache/cord-314503-u1y1bznk.txt txt = ./txt/cord-314503-u1y1bznk.txt === reduce.pl bib === id = cord-298295-epxd03pt author = Eckermann, M. title = 3d Virtual Patho-Histology of Lung Tissue from Covid-19 Patients based on Phase Contrast X-ray Tomography date = 2020-06-23 pages = extension = .txt mime = text/plain words = 6497 sentences = 369 flesch = 51 summary = We present a new approach of three-dimensional (3d) virtual histology and patho-histology based on multi-scale phase contrast x-ray tomography, and use this to investigate the parenchymal-architecture of unstained lung tissue from patients who succumbed to Covid-19. Based on this first proof-of-concept study, we can propose multi-scale phase contrast x-ray tomography as a novel tool to unravel the patho-physiology of Covid-19, extending conventional histology by a third dimension and allowing for a full quantification of tissue remodeling.By combining parallel and cone beam geometry, autopsy samples with a cross section of 4mm are scanned and reconstructed at a resolution and image quality which allows for the segmentation of individual cells. The 3d virtual pathohistology approach for Covid-19 presented here was realized by implementing a novel multi-scale phase contrast x-ray tomography concept, with dedicated xray optics and instrumentation to image the tissue structure on multiple length scales, while at the same time covering large reconstruction volumes. cache = ./cache/cord-298295-epxd03pt.txt txt = ./txt/cord-298295-epxd03pt.txt === reduce.pl bib === id = cord-346906-1wmp43ti author = Lewandowski, Kuiama title = Metagenomic Nanopore Sequencing of Influenza Virus Direct from Clinical Respiratory Samples date = 2019-12-23 pages = extension = .txt mime = text/plain words = 6766 sentences = 328 flesch = 43 summary = We determine its sensitivity compared to that of existing diagnostic methods and its accuracy compared to short-read (Illumina) sequencing, using clinical samples from hospital patients during an influenza season and samples from a controlled laboratory infection in ferrets. During the study, respiratory samples submitted to the clinical diagnostic laboratory were routinely tested by a PCR-based test using the GeneXpert assay (Cepheid) to detect influenza A and B viruses and respiratory syncytial virus (RSV). Comparing this final method with our original protocol, using triplicate extractions from the pooled set of influenza A virus-positive samples demonstrated no significant loss in performance in the more rapid protocol (Fig. S3) , and we adopted this approach as our routine protocol, giving a wet-lab processing time of ϳ8 h. Future application of this method will involve real-time laboratory testing of respiratory samples, running the platform head to head with existing clinical diagnostics to further assess sensitivity and specificity, and using influenza virus sequence data to investigate transmission events. cache = ./cache/cord-346906-1wmp43ti.txt txt = ./txt/cord-346906-1wmp43ti.txt === reduce.pl bib === id = cord-314753-xflhxb13 author = Manso, Carmen F. title = Efficient and unbiased metagenomic recovery of RNA virus genomes from human plasma samples date = 2017-06-23 pages = extension = .txt mime = text/plain words = 6333 sentences = 296 flesch = 48 summary = The percentage of reads mapping to RNA virus genomes in the rRNA-depleted BBV Panel samples was between 40 and 150-fold higher than in corresponding untreated controls. The depth plots in Fig. 3 again show unbiased and even coverages across both genomes, and the percentages of reads mapping to viral targets was again much higher in the rRNA-depleted sample than in the untreated comparator (61-fold and 85-fold for HCV and HPgV respectively). By depleting host-derived nucleic acids and making modifications to an existing library preparation protocol to account for ultra-low RNA input quantities, we have been able to reconstruct effectively full-length genomes of HCV, HEV and HIV from plasma samples with viral loads of 10 4 IU/ml (copies/ml for HIV) and substantial fractions of complete genomes at 10 3 IU/ml. Additionally, our system was able to recover viral sequences from a panel of diverse RNA viruses diluted in human plasma, with a broad correlation between the genomic coverage and depth metrics and approximate concentration. cache = ./cache/cord-314753-xflhxb13.txt txt = ./txt/cord-314753-xflhxb13.txt === reduce.pl bib === id = cord-323973-wszo9s3d author = Zhu, Hanliang title = The vision of point-of-care PCR tests for the COVID-19 pandemic and beyond date = 2020-07-20 pages = extension = .txt mime = text/plain words = 9784 sentences = 493 flesch = 50 summary = [9] The analysis of larger volumes of biological fluids with a low viral load is likely to reduce the risk of false-negative results, but microfluidic point-of-care (POC) devices are typically unable to handle mL-scale volumes in a short time due to the requirement of slow flow rates. [15] The PCR test on samples prepared from blood and urine specimens is capable of detecting the virus in the early stages of the disease, resulting in early diagnosis and subsequent isolation of infected patients to block transmission. The total reaction time depends on a series of parameters, such as the chip size, the PCR master mix volume determining the value of C, the thermal conductivity of the substrate (G), and the temperature cycling rate. A number of fully integrated systems have so far been developed, starting with the non-portable GenExpert from Cepheid, which was first utilized for anthrax detection by the United States Postal Service, [64] and then with different primers to perform HIV and tuberculosis diagnostics in South Africa. cache = ./cache/cord-323973-wszo9s3d.txt txt = ./txt/cord-323973-wszo9s3d.txt === reduce.pl bib === id = cord-017248-a37t31u1 author = nan title = Alphabetic Listing of Diseases and Conditions date = 2010-05-17 pages = extension = .txt mime = text/plain words = 48753 sentences = 4281 flesch = 41 summary = Possible Associated Conditions: Disseminated intravascular coagulation;* eclampsia;* glucose-6-phosphatase deficiency (G6PD); hemolytic uremic syndrome;* malignant hypertension; lymphoma* and other malignancies; paroxysmal nocturnal hemo-globinuria; sickle cell disease;*thalassemia;* thrombotic thrombocytopenic purpura.* (See also below under "NOTE.") NOTE: Hemolysis also may be caused by conditions such as poisoning with chemicals or drugs, heat injury, snake bite,* or infections or may develop as a transfusion reaction* or be secondary to adenocarcinoma, heart valve prostheses (see below), liver disease (see below), renal disease, or congenital erythropoietic porphyria. Unusual under-lying or associated conditions include chronic aortic stenosis or regurgitation; coronary artery anomalies; coronary artery dissection; coronary embolism; coronary ostial stenosis (due to calcification of aortic sinotubular junction or, rarely, to syphilitic aortitis); coronary vasculitis (for instance, in polyarteritis nodosa* or acute hypersensitivity arteritis); hyperthyroidism,* gastrointestinal hemorrhage; * hypothyroidism, * idiopathic arterial calcification of infancy; intramural coronary amyloidosis; pheochromocytoma, polycythemia vera; * pseudoxanthoma elasticum,* radiationinduced coronary stenosis; severe pulmonary hypertension (with right ventricular ischemia); sickle cell disease;* and others. cache = ./cache/cord-017248-a37t31u1.txt txt = ./txt/cord-017248-a37t31u1.txt === reduce.pl bib === === reduce.pl bib === id = cord-335375-n6q70o35 author = Chan, Paul K. S. title = Antibody Avidity Maturation during Severe Acute Respiratory Syndrome–Associated Coronavirus Infection date = 2005-07-01 pages = extension = .txt mime = text/plain words = 2186 sentences = 109 flesch = 55 summary = Samples collected р50 days after fever onset were also tested for anti-SARS-CoV IgM antibody, so that IgM antibody detection and IgG antibody avidity measurement could be compared with respect to demonstrating a recent infection. Changes in severe acute respiratory syndrome-associated coronavirus-specific IgG antibody avidity in paired serum samples ples were measured by an in-house indirect immunofluorescence assay that has been described elsewhere [12] . Of the 45 samples collected р50 days after fever onset, only 18 (40.0%) were positive for anti-SARS-CoV IgM antibody, as determined by the ELISARS assay. Of the 26 paired samples, only 6 (23.1%) showed a significant (у4-fold) increase in anti-SARS-CoV IgG antibody titer (as determined by an in-house indirect immunofluorescence assay) from the first to the second sample, a result that could be regarded as evidence of recent infection. Our data show that anti-SARS-CoV IgG antibody avidity is low during primary infection and increases with time in a unidirectional manner. cache = ./cache/cord-335375-n6q70o35.txt txt = ./txt/cord-335375-n6q70o35.txt === reduce.pl bib === === reduce.pl bib === id = cord-355351-seqwx9x1 author = Battey, CJ title = Predicting geographic location from genetic variation with deep neural networks date = 2020-06-08 pages = extension = .txt mime = text/plain words = 8728 sentences = 397 flesch = 44 summary = At least in the context of windowed analyses, differences in predictions among windows appears to primarily reflect variation in ancestry rather than uncertainty in the inference itself, so we suggest the intervals returned by Locator's kernel density estimation are best interpreted as representing areas from which a given proportion of the genome is likely to have originated. To test whether outlier geographic predictions reflect error in the model fitting procedure versus true variation in ancestry in a given region of the genome, we ran principal component analyses on windows for which a Maya individual (sample HGDP00871) has predicted locations in Europe and Africa. Test error was estimated as the distance in kilometers from the true sampling location to the geographic centroid of the cloud of per-window predictions, and is shown in Figure 8 plotted against local recombination rates from the HapMap genetic map (International HapMap Consortium, 2003) . cache = ./cache/cord-355351-seqwx9x1.txt txt = ./txt/cord-355351-seqwx9x1.txt === reduce.pl bib === id = cord-023442-4vzwc2d2 author = nan title = Proceedings of SCANNING 94/SEEMS 94 Charleston, South Carolina, USA date = 2006-12-05 pages = extension = .txt mime = text/plain words = 55552 sentences = 2821 flesch = 48 summary = IV-4 Scanning Vol. 16, Supplement IV (1994) Simulation of image formation and detection systems in the SEM is a vital link in performing image analysis to obtain precise measurements, to provide the necessary connection between image parameters and structural dimensions, and to reflect important microscope beam and detector parameters. By knowing the transfer function, noise, and distortion figure in digital form, it is relatively easy to obtain more accurate comparison of the measured and calculated signal (Fig. 1 The calculation of image contrast in the scanning electron microscope (SEM) can be done using Monte Carlo techniques if the electron trajectories can be calculated through the composition profiles in the specimen. Specimens providing IV-18 Scanning Vol. 16, Supplement IV (1994) FIG highly redundant structures and relatively smooth fractures, such as cell suspensions or o/w emulsions, were investigated using freeze fracture/replication and ambient temperature transmission electron microscopy (AT-TEM). cache = ./cache/cord-023442-4vzwc2d2.txt txt = ./txt/cord-023442-4vzwc2d2.txt === reduce.pl bib === === reduce.pl bib === id = cord-281916-v6u5mr2i author = Bonnin, Paul title = Study and interest of cellular load in respiratory samples for the optimization of molecular virological diagnosis in clinical practice date = 2016-08-09 pages = extension = .txt mime = text/plain words = 4124 sentences = 229 flesch = 46 summary = METHODS: Our study included 800 upper respiratory tract specimens of which 400 negative and 400 positive for viral detection in multiplex PCR. If a rich cell collection appears to be an important prerequisite for the quality of respiratory viral diagnosis, there is currently no information on a possible cellularity threshold that would validate the result of the viral molecular detection. These 800 aliquots were selected in the laboratory samples bank according to their results in virological diagnosis: 400 Positive and 400 Negative for molecular detection of respiratory panel using the RespiFinder ® Smart_22_Fast technique (Pathofinder, Maastricht, Netherlands). The main objectives of this work have been to study the cellularity of these clinical respiratory specimens, to propose a possible definition of what is commonly called "cellular richness," and to measure the impact of this marker on the molecular viral diagnosis. (2014) performed a molecular cell quantification using real time PCR in order to validate viral detection on nasal swabs. cache = ./cache/cord-281916-v6u5mr2i.txt txt = ./txt/cord-281916-v6u5mr2i.txt === reduce.pl bib === id = cord-313887-8sabsrgy author = Quandt, Sara A. title = COVID-19 Pandemic among Latinx Farmworker and Nonfarmworker Families in North Carolina: Knowledge, Risk Perceptions, and Preventive Behaviors date = 2020-08-10 pages = extension = .txt mime = text/plain words = 7451 sentences = 353 flesch = 50 summary = Taken together, the rapidly changing messages, coupled with public concern, and limited availability of up-to-date information in formats for those with limited English proficiency created a situation in the USA in which Latinx workers such as farmworkers were likely to lack consistent and accurate information and, as a result, practice ineffective behaviors to protect themselves and prevent spreading disease to their social network. This study was designed to describe the knowledge, perceived risk and susceptibility, and preventive behaviors reported by Latinx immigrant farmworker and nonfarmworker families in North Carolina during the first months of the COVID-19 pandemic. In total, these results indicate that, despite relatively high knowledge, strong perceptions of risk from COVID-19, and claims of avoiding situations where contracting or spreading infection might be likely, many of the farmworker families included here do not practice safe physical distancing measures as recommended; and their use of masks appears to be confined to work settings. cache = ./cache/cord-313887-8sabsrgy.txt txt = ./txt/cord-313887-8sabsrgy.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-313670-tbah33ro author = Cannovo, Nunzia title = Regulation of Biobanks in Italy date = 2020-09-02 pages = extension = .txt mime = text/plain words = 3400 sentences = 152 flesch = 43 summary = In Italy, a biobank is "a non-profit organization that must be officially recognized by the appropriate healthcare authority in the member states and must guarantee the treatment, distribution and conservation of biological material according to standards of quality and professionalism," but must not conserve material already regulated by specific laws, as is the case for organs for transplants, blood for transfusions, as well as embryos and gametes for medically assisted reproduction. It can be said that a biobank is "a structured collection of human biological material accessible on the basis of certain criteria" (3, 4) , "in accordance with a code of good practice and correct behavior and with further indications provided by ethics committees and universities" (5) and "in which the information contained in the biological material can be traced to a specific person" (2), "for diagnostic, treatment and research purposes" (6) . cache = ./cache/cord-313670-tbah33ro.txt txt = ./txt/cord-313670-tbah33ro.txt === reduce.pl bib === id = cord-342538-5bwsm290 author = Izquierdo Lara, R. W. title = Monitoring SARS-CoV-2 circulation and diversity through community wastewater sequencing date = 2020-09-22 pages = extension = .txt mime = text/plain words = 5031 sentences = 281 flesch = 56 summary = Here we have explored the possibility of using next-generation sequencing (NGS) of sewage samples to evaluate the diversity of SARS-CoV-2 at the community level from routine wastewater testing, and compared these results with the virus diversity in patients from the Netherlands and Belgium. Low frequency variant (LFV) analysis showed that some known LFVs can be associated with particular clusters within a clade, different to those of their consensus sequences, suggesting the presence of at least 2 clades within a single sewage sample. Moreover, we detected a total of 51 novel mutations present in sewage consensus sequences that were not previously reported (supplementary Table S2 ), of which 48 were supported by coverage above the set thresholds to be considered as high quality (coverage >30x for Nanopore; and coverage >5X and Phred score >30 for Illumina). cache = ./cache/cord-342538-5bwsm290.txt txt = ./txt/cord-342538-5bwsm290.txt === reduce.pl bib === id = cord-348464-1c08mb2k author = Winter, Taylor title = Evaluation of the English Version of the Fear of COVID-19 Scale and Its Relationship with Behavior Change and Political Beliefs date = 2020-06-15 pages = extension = .txt mime = text/plain words = 3455 sentences = 185 flesch = 54 summary = Consistent with the earlier validation studies, the FCV-19S displayed a moderately strong relationship with the perceived infectability and germ aversion subscales of the perceived vulnerability to disease scale (PVDS). With respect to the motivating role of fear, there was a significant relationship between FCV-19S scores and adherence to the lockdown rules that were implemented in New Zealand. Finally, consistent with recent reports on the politicization of the COVID-19 pandemic, an exploratory question found that participants who rated themselves as more conservative tended to report lower FCV-19S scores. The current study demonstrates that the English version of the COVID-19S is a sound unidimensional scale with robust psychometric properties that can be used with confidence Also shown is the association between FCV-19S and adherence to each rule among English-speaking populations. Validation and psychometric evaluation of the Italian version of the fear of COVID-19 scale cache = ./cache/cord-348464-1c08mb2k.txt txt = ./txt/cord-348464-1c08mb2k.txt === reduce.pl bib === id = cord-345302-wbkfjz8r author = Devaney, Ryan title = A metagenomic comparison of endemic viruses from broiler chickens with runting-stunting syndrome and from normal birds date = 2016-10-04 pages = extension = .txt mime = text/plain words = 7869 sentences = 352 flesch = 41 summary = This paper attempts to characterize the viral pathogens associated with 2–3-week-old RSS-affected and unaffected broiler chickens using next-generation sequencing and comparative metagenomics. Of specific interest is the enteric viral population associated with RSS of which many RNA and DNA viruses have been implicated and co-infections of multiple viruses such as rotavirus, chicken astrovirus (CAstV), avian nephritis virus (ANV), and reoviruses have been detected in birds affected with RSS or with poor performance (Reynolds et al., 1986; Guy, 1998; Kang et al., 2012) . Other enteric pathogens associated with avian malabsorption diseases include reoviruses, parvoviruses, and members of the family Caliciviridae; many of which have also been observed in broiler chickens Smyth et al., 2007; Pantin-Jackwood et al., 2008 , Wolf et al., 2011 . cache = ./cache/cord-345302-wbkfjz8r.txt txt = ./txt/cord-345302-wbkfjz8r.txt === reduce.pl bib === id = cord-355743-vjiecd4k author = Ghosh, Sabyasachi title = Tapestry: A Single-Round Smart Pooling Technique for COVID-19 Testing date = 2020-04-29 pages = extension = .txt mime = text/plain words = 4826 sentences = 279 flesch = 63 summary = The decoding algorithm takes as input cycle threshold values from qPCR tests on the pools, and returns a result for each sample, along with an estimate of viral load if positive. Once pooled tests are run, the cycle threshold values can be entered into the app which solves for and displays the list of positive and negative samples along with an estimate of viral loads. 16 × 40 pooling matrix: Table 2 shows the emulated cycle threshold (Ct) values for the 16 RT-qPCR tests corresponding to five different trials (0, 1, 2, 3 or 4 positive samples out of a total of 40 samples). 24 × 60 pooling matrix: Table 3 shows the cycle threshold (Ct) values obtained for the 24 RT-qPCR tests corresponding to a trial with 2 positive samples out of a total of 60 samples. cache = ./cache/cord-355743-vjiecd4k.txt txt = ./txt/cord-355743-vjiecd4k.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-336103-ufvq0ngl author = Sharma, R. title = Optimal sample pooling: an efficient tool against SARS-CoV-2 date = 2020-07-04 pages = extension = .txt mime = text/plain words = 1563 sentences = 125 flesch = 64 summary = 2, 3 To identify such cases, the World Health Organization has stressed on multiple occasions the significant role of sample testing. While the current guidelines from ICMR state that up to 5 samples can be pooled, 20 multiple studies have confirmed that the pooling size of up to 8 does not harm the specificity and the sensitivity of the test. The determination of sample pool size for each lab using its prevalence rate would yield desired efficiency and be easy to implement. Strategizing to have a common sample pool size across the nation would not yield optimum results as the variance of prevalence rates is extremely high. Hence, sample pool size should be decided individually for a testing facility using the prevalence rates recorded by the same lab. This prevalence rate can then be looked up on the decision matrix table to arrive at the optimal sample pool size. Pooled Sample Testing for SARS-CoV-2 cache = ./cache/cord-336103-ufvq0ngl.txt txt = ./txt/cord-336103-ufvq0ngl.txt === reduce.pl bib === id = cord-102613-hly07ne3 author = Danko, David title = Global Genetic Cartography of Urban Metagenomes and Anti-Microbial Resistance date = 2020-05-04 pages = extension = .txt mime = text/plain words = 6548 sentences = 360 flesch = 55 summary = We identified covariates which influenced the taxonomic composition 204 of our samples: city, population density, average temperature in June, region, elevation above sea-level, 205 surface type, surface material, elevation above or below ground and proximity to the coast. To quantify how the principle covariates, climate, continent, and surface material impacted the taxo-213 nomic composition of samples, we performed a Principal Component Analysis (PCA) on our taxonomic 214 data normalized by proportion and identified principal components (PCs) which were strongly associated 215 with a metadata covariate in a positive or negative direction (PCs were centered so an average direction 216 indicates an association). In general, negative controls had 798 lower k-mer complexity, fewer reads, and lower post PCR Qubit scores than case samples and no major Previous studies have reported that microbial species whose relative abundance is negatively cor-803 related with DNA concentration may be contaminants. cache = ./cache/cord-102613-hly07ne3.txt txt = ./txt/cord-102613-hly07ne3.txt === reduce.pl bib === id = cord-307874-0obomty2 author = Pardon, Bart title = Bovine Respiratory Disease Diagnosis: What Progress Has Been Made in Infectious Diagnosis? date = 2020-05-23 pages = extension = .txt mime = text/plain words = 7061 sentences = 388 flesch = 43 summary = Evidence-based guidelines for precise interpretation of microbiologic tests results are lacking; however, approaches that have been practically useful for the management of bovine respiratory disease outbreaks are presented. However, naturally resistant to fluoroquinolones 71 Escherichia coli, Gallibacterium anatis, Enterobacter hormaechei, staphylococci, streptococci, fungi Secondary Single reports on cattle-specific strains isolated in pure culture in an outbreak of pneumonia in calves 52, [72] [73] [74] Multiple other bacterial species can be detected in the bovine respiratory tract. 10, 35, 54 However, with current knowledge on the interpretation of DNS results at the individual or group level, samples of the lower respiratory tract are likely a better option to evaluate potential involvement of opportunistic pathogens. In the example where the pathogen is causing the disease in 100% of affected calves, the risk of not finding an infected animal after sampling n cases is (1-Se)n , where Se is the test sensitivity. cache = ./cache/cord-307874-0obomty2.txt txt = ./txt/cord-307874-0obomty2.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 === === reduce.pl bib === id = cord-329162-6w8qcv1c author = Ayginin, Andrey A. title = The Study of Viral RNA Diversity in Bird Samples Using De Novo Designed Multiplex Genus-Specific Primer Panels date = 2018-08-12 pages = extension = .txt mime = text/plain words = 4838 sentences = 222 flesch = 49 summary = The existing approaches for the design of oligonucleotides for targeted enrichment are usually involved in the development of primers for the PCR-based detection of particular viral species or genera, but not for families or higher taxonomic orders. We have subsequently designed a genus-specific oligonucleotide panel for targeted enrichment of viral nucleic acids in biological material and demonstrated the possibility of its application for virus detection in bird samples. We have applied this approach to design genus-specific primer pairs for targeted enrichment of cDNA from zoonotic RNA viruses and have evaluated it using several samples from birds. The control samples cDNA was obtained by reverse transcription reaction performed on 5 L of the extracted RNA using the Reverta-L RT kit (AmpliSens; total volume of the reaction mixture is 20 L); after that 5 L of the reaction mixture containing cDNAs was further used for evaluation of the ability of the primer pair to amplify the targeted region of viruses, both in single and in multiplex PCR format. cache = ./cache/cord-329162-6w8qcv1c.txt txt = ./txt/cord-329162-6w8qcv1c.txt === reduce.pl bib === id = cord-326133-d46wbfrx author = Nakayasu, Ernesto S. title = MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses date = 2016-05-10 pages = extension = .txt mime = text/plain words = 6104 sentences = 271 flesch = 39 summary = We then applied this methodology and integrated proteomic, lipidomic, and metabolomic analyses in the study of Middle East respiratory syndrome coronavirus (MERS-CoV) infections in a lung epithelial cell line, which showed the impact of viral infection on different host metabolic pathways. We then evaluated if these protein losses affected the ability to obtain useful proteomic data, since a method that can simultaneously extract multiple omics sources from the same sample would be extremely useful for systems biology experiments and subsequent integrated data analysis, as well as in cases where limited sample amounts are available (e.g., a survey of data from the National Cancer Institute showed that obtaining an adequate number of samples to conduct a study is a major difficulty facing researchers [21] ). cache = ./cache/cord-326133-d46wbfrx.txt txt = ./txt/cord-326133-d46wbfrx.txt === reduce.pl bib === === reduce.pl bib === id = cord-333413-8buawes0 author = Liebing, J. title = Health status of free-ranging ring-necked pheasant chicks (Phasianus colchicus) in North-Western Germany date = 2020-06-16 pages = extension = .txt mime = text/plain words = 5556 sentences = 306 flesch = 51 summary = Being a typical ground-breeding bird of the agricultural landscape in Germany, the pheasant has experienced a strong and persistent population decline with a hitherto unexplained cause. In the present study, 62 free-ranging pheasant chicks were caught within a two-year period in three federal states of Germany; Lower Saxony, North Rhine-Westphalia and Schleswig-Holstein. Pheasant chick deaths may often have been triggered by poor nutritional status, probably in association with inflammatory changes in various tissues and organs as well as bacterial and parasitic pathogens. In 2014 and 2015, the Institute for Terrestrial and Aquatic Wildlife Research (ITAW), University of Veterinary Medicine Hannover, Foundation, Hannover and the Wildlife Research Institute, State Office for Nature, Environment and Consumer Protection of North Rhine-Westphalia caught free-living Ring-necked Pheasant chicks from Lower Saxony (Cuxhaven, Grafschaft Bentheim, Emsland, Osnabrück, Vechta), North Rhine-Westphalia (Coesfeld, Warendorf) and Schleswig-Holstein (Dithmarschen) to assess the health state by means of pathological, microbiological, virological, parasitological and toxicological investigations. cache = ./cache/cord-333413-8buawes0.txt txt = ./txt/cord-333413-8buawes0.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 === reduce.pl bib === id = cord-031907-ilhr3iu5 author = nan title = ISEV2020 Abstract Book date = 2020-07-15 pages = extension = .txt mime = text/plain words = 200999 sentences = 11528 flesch = 44 summary = L.M., and the National Institutes of Health (R35GM119623) to T.R.G. The addition of a size exclusion chromatography step to various urinary extracellular vesicle concentrating methods reveals differences in the small RNA profile Introduction: Urinary extracellular vesicles (EVs) and their RNA cargo are a novel source of biomarkers for various diseases, however non-vesicular RNA (e.g. associated with proteins) is also present within urine. We then evaluated efficiency of heart targeting for eAAV9 or eAAV6 and standard AAV9 or AAV6 encoding for EGFP, mCherry or firefly luciferase in different human cell lines in vitro, in black mouse and in passive immunity nude mouse model in vivo using flow cytometry, confocal microscopy, Langendorff perfusion system and Methods: HLHS patients (n = 3) after Glenn procedure and swine (n = 3) after PAB were given RV injections of allogeneic/xenogeneic MSCs. Donor-specific, HLA-I+, exosomes were isolated from plasma. cache = ./cache/cord-031907-ilhr3iu5.txt txt = ./txt/cord-031907-ilhr3iu5.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 ===== Reducing email addresses cord-329162-6w8qcv1c Creating transaction Updating adr table ===== Reducing keywords cord-001207-yjaiybwf cord-002178-ggtxuulg cord-015482-ovuofl9q cord-011444-6jh3lvm3 cord-003640-psnec2qp cord-002560-pue5q5wp cord-030409-bwxkxvsl cord-290722-neqj85xf cord-030725-876arxiu cord-009295-4c0zwhdh cord-275360-uphdzj5l cord-018761-vm86d4mj cord-003523-byxuruk1 cord-032379-pelz3ygf cord-263831-7aj9ozpn cord-024503-f4ibgn9i cord-102471-dtukacm7 cord-103180-5hkoeca7 cord-308687-wrzzb9cy cord-254596-wsmnlnlk cord-258014-lzzi4rnz cord-298697-v1qdizwx cord-321549-r7bmtloy cord-305282-x2zzzw43 cord-307261-0a3iztns cord-313107-6cfenpxm cord-280846-bbv6f5gf cord-305755-6jup93v4 cord-303647-c4umbcvn cord-291540-raksomda cord-004133-32w6g7qk cord-288202-r3r2bc7v cord-017543-60q9iecq cord-345144-zvu22n8f cord-024553-jat7pttf cord-319685-dw0qsl4s cord-011485-15wtv6bt cord-301823-fbeb1nw1 cord-022879-j6cecioe cord-130198-pyg81vwb cord-022147-istz1iql cord-103735-nil1vv6h cord-273495-hruq0hdw cord-326380-9ecsp66y cord-301991-n87le8ix cord-344131-e7phs0jd cord-102547-nxut8ov1 cord-314503-u1y1bznk cord-344627-w2efsshj cord-298295-epxd03pt cord-346906-1wmp43ti cord-323973-wszo9s3d cord-314753-xflhxb13 cord-017248-a37t31u1 cord-345992-3ij1vbqp cord-335375-n6q70o35 cord-254963-cnvxlv6h cord-023442-4vzwc2d2 cord-355351-seqwx9x1 cord-354372-vfvnjmv1 cord-353394-lq1f53qv cord-281916-v6u5mr2i cord-300399-21xozruq cord-313887-8sabsrgy cord-335372-tncjfdtp cord-313670-tbah33ro cord-348464-1c08mb2k cord-345302-wbkfjz8r cord-294062-3esrg1jw cord-315054-kji2kfek cord-355743-vjiecd4k cord-336103-ufvq0ngl cord-102613-hly07ne3 cord-307874-0obomty2 cord-342538-5bwsm290 cord-324944-ixh3ykrc cord-317213-vhprfb1o cord-326133-d46wbfrx cord-329162-6w8qcv1c cord-310061-nro623aa cord-333413-8buawes0 cord-023095-4dannjjm cord-010092-uftc8inx cord-010119-t1x9gknd cord-031907-ilhr3iu5 Creating transaction Updating wrd table ===== Reducing urls cord-003640-psnec2qp cord-030409-bwxkxvsl cord-002560-pue5q5wp cord-030725-876arxiu cord-290722-neqj85xf cord-275360-uphdzj5l cord-032379-pelz3ygf cord-263831-7aj9ozpn cord-102471-dtukacm7 cord-308687-wrzzb9cy cord-258014-lzzi4rnz cord-254596-wsmnlnlk cord-298697-v1qdizwx cord-321549-r7bmtloy cord-313107-6cfenpxm cord-280846-bbv6f5gf cord-305755-6jup93v4 cord-291540-raksomda cord-004133-32w6g7qk cord-288202-r3r2bc7v cord-301823-fbeb1nw1 cord-022147-istz1iql cord-103735-nil1vv6h cord-102547-nxut8ov1 cord-298295-epxd03pt cord-346906-1wmp43ti cord-314753-xflhxb13 cord-355351-seqwx9x1 cord-335372-tncjfdtp cord-348464-1c08mb2k cord-355743-vjiecd4k cord-324944-ixh3ykrc cord-317213-vhprfb1o cord-342538-5bwsm290 cord-326133-d46wbfrx cord-336103-ufvq0ngl cord-010092-uftc8inx cord-031907-ilhr3iu5 cord-010119-t1x9gknd cord-310061-nro623aa Creating transaction Updating url table ===== Reducing named entities cord-002178-ggtxuulg cord-001207-yjaiybwf cord-003640-psnec2qp cord-011444-6jh3lvm3 cord-015482-ovuofl9q cord-002560-pue5q5wp cord-030409-bwxkxvsl cord-030725-876arxiu cord-275360-uphdzj5l cord-032379-pelz3ygf cord-009295-4c0zwhdh cord-290722-neqj85xf cord-003523-byxuruk1 cord-018761-vm86d4mj cord-263831-7aj9ozpn cord-102471-dtukacm7 cord-103180-5hkoeca7 cord-308687-wrzzb9cy cord-254596-wsmnlnlk cord-258014-lzzi4rnz cord-321549-r7bmtloy cord-298697-v1qdizwx cord-305282-x2zzzw43 cord-307261-0a3iztns cord-313107-6cfenpxm cord-280846-bbv6f5gf cord-291540-raksomda cord-305755-6jup93v4 cord-303647-c4umbcvn cord-004133-32w6g7qk cord-017543-60q9iecq cord-288202-r3r2bc7v cord-345144-zvu22n8f cord-319685-dw0qsl4s cord-024553-jat7pttf cord-024503-f4ibgn9i cord-011485-15wtv6bt cord-301823-fbeb1nw1 cord-130198-pyg81vwb cord-022879-j6cecioe cord-022147-istz1iql cord-103735-nil1vv6h cord-326380-9ecsp66y cord-273495-hruq0hdw cord-102547-nxut8ov1 cord-301991-n87le8ix cord-314503-u1y1bznk cord-344627-w2efsshj cord-346906-1wmp43ti cord-323973-wszo9s3d cord-298295-epxd03pt cord-344131-e7phs0jd cord-314753-xflhxb13 cord-017248-a37t31u1 cord-345992-3ij1vbqp cord-254963-cnvxlv6h cord-335375-n6q70o35 cord-355351-seqwx9x1 cord-023442-4vzwc2d2 cord-353394-lq1f53qv cord-300399-21xozruq cord-281916-v6u5mr2i cord-354372-vfvnjmv1 cord-313887-8sabsrgy cord-335372-tncjfdtp cord-342538-5bwsm290 cord-348464-1c08mb2k cord-313670-tbah33ro cord-294062-3esrg1jw cord-345302-wbkfjz8r cord-355743-vjiecd4k cord-315054-kji2kfek cord-336103-ufvq0ngl cord-102613-hly07ne3 cord-307874-0obomty2 cord-324944-ixh3ykrc cord-317213-vhprfb1o cord-326133-d46wbfrx cord-329162-6w8qcv1c cord-310061-nro623aa cord-333413-8buawes0 cord-023095-4dannjjm cord-031907-ilhr3iu5 cord-010119-t1x9gknd cord-010092-uftc8inx Creating transaction Updating ent table ===== Reducing parts of speech cord-001207-yjaiybwf cord-002178-ggtxuulg cord-011444-6jh3lvm3 cord-015482-ovuofl9q cord-003640-psnec2qp cord-002560-pue5q5wp cord-030409-bwxkxvsl cord-030725-876arxiu cord-290722-neqj85xf cord-009295-4c0zwhdh cord-275360-uphdzj5l cord-003523-byxuruk1 cord-018761-vm86d4mj cord-032379-pelz3ygf cord-024503-f4ibgn9i cord-102471-dtukacm7 cord-263831-7aj9ozpn cord-103180-5hkoeca7 cord-308687-wrzzb9cy cord-254596-wsmnlnlk cord-258014-lzzi4rnz cord-321549-r7bmtloy cord-298697-v1qdizwx cord-305282-x2zzzw43 cord-307261-0a3iztns cord-313107-6cfenpxm cord-280846-bbv6f5gf cord-305755-6jup93v4 cord-291540-raksomda cord-303647-c4umbcvn cord-288202-r3r2bc7v cord-004133-32w6g7qk cord-017543-60q9iecq cord-345144-zvu22n8f cord-024553-jat7pttf cord-319685-dw0qsl4s cord-011485-15wtv6bt cord-301823-fbeb1nw1 cord-130198-pyg81vwb cord-022879-j6cecioe cord-022147-istz1iql cord-103735-nil1vv6h cord-273495-hruq0hdw cord-326380-9ecsp66y cord-301991-n87le8ix cord-102547-nxut8ov1 cord-314503-u1y1bznk cord-344627-w2efsshj cord-298295-epxd03pt cord-344131-e7phs0jd cord-346906-1wmp43ti cord-323973-wszo9s3d cord-314753-xflhxb13 cord-345992-3ij1vbqp cord-254963-cnvxlv6h cord-335375-n6q70o35 cord-353394-lq1f53qv cord-355351-seqwx9x1 cord-354372-vfvnjmv1 cord-313887-8sabsrgy cord-017248-a37t31u1 cord-300399-21xozruq cord-281916-v6u5mr2i cord-342538-5bwsm290 cord-023442-4vzwc2d2 cord-335372-tncjfdtp cord-348464-1c08mb2k cord-313670-tbah33ro cord-345302-wbkfjz8r cord-294062-3esrg1jw cord-355743-vjiecd4k cord-315054-kji2kfek cord-336103-ufvq0ngl cord-102613-hly07ne3 cord-307874-0obomty2 cord-324944-ixh3ykrc cord-317213-vhprfb1o cord-326133-d46wbfrx cord-329162-6w8qcv1c cord-310061-nro623aa cord-333413-8buawes0 cord-023095-4dannjjm cord-031907-ilhr3iu5 cord-010119-t1x9gknd cord-010092-uftc8inx Creating transaction Updating pos table Building ./etc/reader.txt cord-010119-t1x9gknd cord-010092-uftc8inx cord-023095-4dannjjm cord-031907-ilhr3iu5 cord-010119-t1x9gknd cord-010092-uftc8inx number of items: 85 sum of words: 1,226,353 average size in words: 27,252 average readability score: 48 nouns: blood; samples; results; cells; sample; patients; study; evs; cell; methods; time; data; analysis; transfusion; donors; detection; disease; plasma; dogs; group; method; number; testing; system; test; platelet; use; patient; virus; treatment; water; conclusion; donor; ev; sequencing; risk; studies; dna; expression; cases; ml; protein; control; units; levels; days; infection; type; antibody; assay verbs: using; showed; include; performed; based; compared; identified; detected; increased; associated; determine; found; collected; followed; test; provided; reported; obtained; require; evaluate; developed; see; reduced; derived; make; observed; containing; demonstrated; treated; suggesting; resulting; isolated; indicates; described; assess; allowing; measured; aimed; confirmed; given; taken; received; related; known; considered; caused; investigated; improved; remaining; needed adjectives: clinical; positive; high; different; human; viral; non; specific; anti; significant; negative; low; higher; available; single; small; first; new; total; respiratory; red; possible; large; diagnostic; present; whole; molecular; bacterial; extracellular; lower; several; many; similar; acute; multiple; common; normal; important; potential; healthy; additional; free; current; novel; standard; patient; pre; nucleic; rapid; severe adverbs: also; however; well; significantly; respectively; therefore; previously; even; highly; often; prior; especially; still; directly; currently; recently; clinically; usually; particularly; approximately; furthermore; commonly; generally; first; potentially; additionally; relatively; less; statistically; together; fully; finally; rather; typically; frequently; least; moreover; specifically; now; widely; immediately; much; mainly; successfully; subsequently; alone; hence; easily; always; yet pronouns: we; it; our; their; they; its; them; i; her; us; he; his; you; she; one; themselves; your; itself; my; yourself; ourselves; me; him; s; ours; o139; igg4; himself; ™; u; thier; srbcs; sevs; rbcs/100; o103; nsp(+)-evs; mrnas; mine; microev; magpixv; iu/; herself; grch37; exrna; em; egfp; clustalx; ccrcc; casp3-/mice; casp3-/-mice proper nouns: PCR; RNA; Summary; RBC; EV; C; SARS; Study; AE; Background; Design; HIV; mg; Case; Blood; Studies; Conclusions; Fig; ABO; CoV-2; University; RT; A; RHD; DNA; Hb; T; D; EVs; MSC; USA; B; Health; HCV; L; Transfusion; MS; Table; COVID-19; Rh; HLA; •; M; S; National; PLT; HBV; II; Center; miRNA keywords: sample; pcr; dna; rna; sars; study; patient; hiv; blood; result; dog; covid-19; cell; virus; test; system; respiratory; method; detection; analysis; amplification; university; tissue; pool; poc; illumina; hcv; group; elisa; disease; cat; case; water; viral; usa; type; transfusion; tem; table; surface; summary; specie; rhd; red; rbc; procedure; plt; platelet; note; non one topic; one dimension: blood file(s): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3929612/ titles(s): The General Composition of the Faecal Virome of Pigs Depends on Age, but Not on Feeding with a Probiotic Bacterium three topics; one dimension: samples; blood; evs file(s): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121759/, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7169716/, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7480431/ titles(s): Alphabetic Listing of Diseases and Conditions | Abstract Presentations from the AABB Annual Meeting San Diego, CA ctober 7‐10, 2017 | ISEV2020 Abstract Book five topics; three dimensions: blood transfusion donors; samples dogs sample; evs ev cells; may sample samples; species diatoms diatom file(s): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7169716/, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7153435/, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7480431/, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7169609/, https://www.sciencedirect.com/science/article/pii/S2214714420305833 titles(s): Abstract Presentations from the AABB Annual Meeting San Diego, CA ctober 7‐10, 2017 | Procedures to Investigate Waterborne Illness | ISEV2020 Abstract Book | Proceedings of SCANNING 94/SEEMS 94 Charleston, South Carolina, USA | Diatoms recovery from wastewater: Overview from an ecological and economic perspective Type: cord title: keyword-sample-cord date: 2021-05-25 time: 16:19 username: emorgan patron: Eric Morgan email: emorgan@nd.edu input: keywords:sample ==== make-pages.sh htm files ==== make-pages.sh complex files ==== make-pages.sh named enities ==== making bibliographics id: cord-103735-nil1vv6h author: Alfano, Niccolo title: Non-invasive surveys of mammalian viruses using environmental DNA date: 2020-03-29 words: 5829.0 sentences: 373.0 pages: flesch: 53.0 cache: ./cache/cord-103735-nil1vv6h.txt txt: ./txt/cord-103735-nil1vv6h.txt summary: Using a curated set of RNA oligonucleotides based on the ViroChip microarray assay [7] as baits in a hybridization capture system, multiple mammalian RNA and DNA viruses were detected from both eDNA and iDNA samples. Highlights Environmental DNA (water and blood-sucking leeches) provided a non-invasive method of screening wildlife for viruses A comprehensive viral RNA oligonucleotide bait set was developed to capture known and unknown mammalian virus diversity Leech blood meal host determination and viruses identified were congruent Viruses determined from water correlated with known and observed species visiting the water sources In brief Alfano, Dayaram, et al. In filtered water and sediment samples collected from the same waterhole, only one virus per sample was generally identified and in one location (WM20 and SM20) contigs from different viral families were isolated based on sample type. We provide evidence that environmental and invertebrate-derived DNA samples including waterhole water, sediment and wild haematophagous terrestrial leeches can be used to survey known and unknown viruses. abstract: Environmental DNA (eDNA) and its subdiscipline, invertebrate-derived DNA (iDNA) have been used to survey biodiversity non-invasively [1,2]. Water is ubiquitous in most ecosystems, and, among invertebrates, terrestrial haematophagous leeches are abundant and can be easily collected in many tropical rainforests [3,4]. Such non-invasive nucleic acid sources can mitigate difficulties of obtaining wildlife samples, particularly in remote areas or for rare species. Recently, eDNA/iDNA sources have been applied to monitoring specific wildlife pathogens [5,6]. However, previous studies have focused on known pathogens, whereas most wildlife pathogens are uncharacterized and unknown. Non-invasive approaches to monitoring known and novel pathogens may be of particular benefit in ecosystems prone to viral emergence, many of which occur in areas where invasive sampling is challenging, such as tropical rainforests. Here, we show that both eDNA from natural waterholes, and iDNA from terrestrial haematophagous leeches, can be used to detect unknown viruses circulating in mammalian hosts (Figure 1). Using a curated set of RNA oligonucleotides based on the ViroChip microarray assay [7] as baits in a hybridization capture system, multiple mammalian RNA and DNA viruses were detected from both eDNA and iDNA samples. Congruence was found between host DNA assignment and viruses identified in leeches, and between animals observed visiting the waterholes and the viruses detected. Our results demonstrate that eDNA/iDNA samples may represent an effective non-invasive resource for studying wildlife viral diversity. Several of the detected viruses were novel, highlighting the potential of eDNA/iDNA for epidemiological analysis of emerging viruses prior to their emergence. Highlights Environmental DNA (water and blood-sucking leeches) provided a non-invasive method of screening wildlife for viruses A comprehensive viral RNA oligonucleotide bait set was developed to capture known and unknown mammalian virus diversity Leech blood meal host determination and viruses identified were congruent Viruses determined from water correlated with known and observed species visiting the water sources In brief Alfano, Dayaram, et al. demonstrate that environmental DNA from southeast Asian leech bloodmeals and waterholes from Africa and Mongolia can be used as to detect viruses circulating in wildlife. These nucleic acid sources may represent an effective non-invasive resource for studying wildlife viral diversity and emerging viruses pre-emergence. url: https://doi.org/10.1101/2020.03.26.009993 doi: 10.1101/2020.03.26.009993 id: cord-329162-6w8qcv1c author: Ayginin, Andrey A. title: The Study of Viral RNA Diversity in Bird Samples Using De Novo Designed Multiplex Genus-Specific Primer Panels date: 2018-08-12 words: 4838.0 sentences: 222.0 pages: flesch: 49.0 cache: ./cache/cord-329162-6w8qcv1c.txt txt: ./txt/cord-329162-6w8qcv1c.txt summary: The existing approaches for the design of oligonucleotides for targeted enrichment are usually involved in the development of primers for the PCR-based detection of particular viral species or genera, but not for families or higher taxonomic orders. We have subsequently designed a genus-specific oligonucleotide panel for targeted enrichment of viral nucleic acids in biological material and demonstrated the possibility of its application for virus detection in bird samples. We have applied this approach to design genus-specific primer pairs for targeted enrichment of cDNA from zoonotic RNA viruses and have evaluated it using several samples from birds. The control samples cDNA was obtained by reverse transcription reaction performed on 5 L of the extracted RNA using the Reverta-L RT kit (AmpliSens; total volume of the reaction mixture is 20 L); after that 5 L of the reaction mixture containing cDNAs was further used for evaluation of the ability of the primer pair to amplify the targeted region of viruses, both in single and in multiplex PCR format. abstract: Advances in the next generation sequencing (NGS) technologies have significantly increased our ability to detect new viral pathogens and systematically determine the spectrum of viruses prevalent in various biological samples. In addition, this approach has also helped in establishing the associations of viromes with many diseases. However, unlike the metagenomic studies using 16S rRNA for the detection of bacteria, it is impossible to create universal oligonucleotides to target all known and novel viruses, owing to their genomic diversity and variability. On the other hand, sequencing the entire genome is still expensive and has relatively low sensitivity for such applications. The existing approaches for the design of oligonucleotides for targeted enrichment are usually involved in the development of primers for the PCR-based detection of particular viral species or genera, but not for families or higher taxonomic orders. In this study, we have developed a computational pipeline for designing the oligonucleotides capable of covering a significant number of known viruses within various taxonomic orders, as well as their novel variants. We have subsequently designed a genus-specific oligonucleotide panel for targeted enrichment of viral nucleic acids in biological material and demonstrated the possibility of its application for virus detection in bird samples. We have tested our panel using a number of collected samples and have observed superior efficiency in the detection and identification of viral pathogens. Since a reliable, bioinformatics-based analytical method for the rapid identification of the sequences was crucial, an NGS-based data analysis module was developed in this study, and its functionality in the detection of novel viruses and analysis of virome diversity was demonstrated. url: https://doi.org/10.1155/2018/3248285 doi: 10.1155/2018/3248285 id: cord-009295-4c0zwhdh author: Bal, A. title: Molecular characterization of SARS-CoV-2 in the first COVID-19 cluster in France reveals an amino acid deletion in nsp2 (Asp268del) date: 2020-03-28 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7142683/ doi: 10.1016/j.cmi.2020.03.020 id: cord-355351-seqwx9x1 author: Battey, CJ title: Predicting geographic location from genetic variation with deep neural networks date: 2020-06-08 words: 8728.0 sentences: 397.0 pages: flesch: 44.0 cache: ./cache/cord-355351-seqwx9x1.txt txt: ./txt/cord-355351-seqwx9x1.txt summary: At least in the context of windowed analyses, differences in predictions among windows appears to primarily reflect variation in ancestry rather than uncertainty in the inference itself, so we suggest the intervals returned by Locator''s kernel density estimation are best interpreted as representing areas from which a given proportion of the genome is likely to have originated. To test whether outlier geographic predictions reflect error in the model fitting procedure versus true variation in ancestry in a given region of the genome, we ran principal component analyses on windows for which a Maya individual (sample HGDP00871) has predicted locations in Europe and Africa. Test error was estimated as the distance in kilometers from the true sampling location to the geographic centroid of the cloud of per-window predictions, and is shown in Figure 8 plotted against local recombination rates from the HapMap genetic map (International HapMap Consortium, 2003) . abstract: Most organisms are more closely related to nearby than distant members of their species, creating spatial autocorrelations in genetic data. This allows us to predict the location of origin of a genetic sample by comparing it to a set of samples of known geographic origin. Here, we describe a deep learning method, which we call Locator, to accomplish this task faster and more accurately than existing approaches. In simulations, Locator infers sample location to within 4.1 generations of dispersal and runs at least an order of magnitude faster than a recent model-based approach. We leverage Locator’s computational efficiency to predict locations separately in windows across the genome, which allows us to both quantify uncertainty and describe the mosaic ancestry and patterns of geographic mixing that characterize many populations. Applied to whole-genome sequence data from Plasmodium parasites, Anopheles mosquitoes, and global human populations, this approach yields median test errors of 16.9km, 5.7km, and 85km, respectively. url: https://www.ncbi.nlm.nih.gov/pubmed/32511092/ doi: 10.7554/elife.54507 id: cord-281916-v6u5mr2i author: Bonnin, Paul title: Study and interest of cellular load in respiratory samples for the optimization of molecular virological diagnosis in clinical practice date: 2016-08-09 words: 4124.0 sentences: 229.0 pages: flesch: 46.0 cache: ./cache/cord-281916-v6u5mr2i.txt txt: ./txt/cord-281916-v6u5mr2i.txt summary: METHODS: Our study included 800 upper respiratory tract specimens of which 400 negative and 400 positive for viral detection in multiplex PCR. If a rich cell collection appears to be an important prerequisite for the quality of respiratory viral diagnosis, there is currently no information on a possible cellularity threshold that would validate the result of the viral molecular detection. These 800 aliquots were selected in the laboratory samples bank according to their results in virological diagnosis: 400 Positive and 400 Negative for molecular detection of respiratory panel using the RespiFinder ® Smart_22_Fast technique (Pathofinder, Maastricht, Netherlands). The main objectives of this work have been to study the cellularity of these clinical respiratory specimens, to propose a possible definition of what is commonly called "cellular richness," and to measure the impact of this marker on the molecular viral diagnosis. (2014) performed a molecular cell quantification using real time PCR in order to validate viral detection on nasal swabs. abstract: BACKGROUND: Respiratory viral diagnosis of upper respiratory tract infections has largely developed through multiplex molecular techniques. Although the sensitivity of different types of upper respiratory tract samples seems to be correlated to the number of sampled cells, this link remains largely unexplored. METHODS: Our study included 800 upper respiratory tract specimens of which 400 negative and 400 positive for viral detection in multiplex PCR. All samples were selected and matched for age in these 2 groups. For the positive group, samples were selected for the detected viral species. RESULTS: Among the factors influencing the cellularity were the type of sample (p < 0.0001); patient age (p < 0.001); viral positive or negative nature of the sample (p = 0.002); and, for the positive samples, the number of viral targets detected (0.004 < p < 0.049) and viral species. CONCLUSION: The cellular load of upper respiratory samples is multifactorial and occurs for many in the sensitivity of molecular detection. However it was not possible to determine a minimum cellularity threshold allowing molecular viral detection. The differences according to the type of virus remain to be studied on a larger scale. url: https://doi.org/10.1186/s12879-016-1730-9 doi: 10.1186/s12879-016-1730-9 id: cord-018761-vm86d4mj author: Bradt, David A. title: Technical Annexes date: 2017-11-08 words: 10430.0 sentences: 805.0 pages: flesch: 53.0 cache: ./cache/cord-018761-vm86d4mj.txt txt: ./txt/cord-018761-vm86d4mj.txt summary: abstract: This chapter provides guidance on technical issues in the health sector. The annexes contain selective compilations of frequently used reference information. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123725/ doi: 10.1007/978-3-319-69871-7_8 id: cord-308687-wrzzb9cy author: Brunner, Jesse L. title: Pooled samples and eDNA-based detection can facilitate the “clean trade” of aquatic animals date: 2020-06-24 words: 6488.0 sentences: 322.0 pages: flesch: 46.0 cache: ./cache/cord-308687-wrzzb9cy.txt txt: ./txt/cord-308687-wrzzb9cy.txt summary: swabs) and eDNA samples collected from finite populations and discuss key assumptions and considerations for their use with a focus on detecting Batrachochytrium salamandrivorans, an emerging pathogen that threatens global salamander diversity. www.nature.com/scientificreports www.nature.com/scientificreports/ context of screening U.S. service members for syphilis, pooling samples to reduce the number of tests required to detect rare infections is common in numerous contexts 22 , including surveys for disease freedom. In this paper I therefore develop formulae for imperfect tests of pooled samples in closed populations and eDNA, discuss the key assumptions and considerations in their application, and illustrate how eDNA may be especially useful for detecting infections in the live animal trade. Pooling and batch-processing samples collected from individual animals (e.g., swabs) can reduce several fold the number of diagnostic tests (e.g., DNA extractions and PCR reactions) required to detect rare infections. abstract: The regional and international trade of live animals facilitates the movement, spillover, and emergence of zoonotic and epizootic pathogens around the world. Detecting pathogens in trade is critical for preventing their continued movement and introduction, but screening a sufficient fraction to ensure rare infections are detected is simply infeasible for many taxa and settings because of the vast numbers of animals involved—hundreds of millions of live animals are imported into the U.S.A. alone every year. Batch processing pools of individual samples or using environmental DNA (eDNA)—the genetic material shed into an organism’s environment—collected from whole consignments of animals may substantially reduce the time and cost associated with pathogen surveillance. Both approaches, however, lack a framework with which to determine sampling requirements and interpret results. Here I present formulae for pooled individual samples (e.g,. swabs) and eDNA samples collected from finite populations and discuss key assumptions and considerations for their use with a focus on detecting Batrachochytrium salamandrivorans, an emerging pathogen that threatens global salamander diversity. While empirical validation is key, these formulae illustrate the potential for eDNA-based detection in particular to reduce sample sizes and help bring clean trade into reach for a greater number of taxa, places, and contexts. url: https://www.ncbi.nlm.nih.gov/pubmed/32581260/ doi: 10.1038/s41598-020-66280-7 id: cord-313670-tbah33ro author: Cannovo, Nunzia title: Regulation of Biobanks in Italy date: 2020-09-02 words: 3400.0 sentences: 152.0 pages: flesch: 43.0 cache: ./cache/cord-313670-tbah33ro.txt txt: ./txt/cord-313670-tbah33ro.txt summary: In Italy, a biobank is "a non-profit organization that must be officially recognized by the appropriate healthcare authority in the member states and must guarantee the treatment, distribution and conservation of biological material according to standards of quality and professionalism," but must not conserve material already regulated by specific laws, as is the case for organs for transplants, blood for transfusions, as well as embryos and gametes for medically assisted reproduction. It can be said that a biobank is "a structured collection of human biological material accessible on the basis of certain criteria" (3, 4) , "in accordance with a code of good practice and correct behavior and with further indications provided by ethics committees and universities" (5) and "in which the information contained in the biological material can be traced to a specific person" (2), "for diagnostic, treatment and research purposes" (6) . abstract: In Italy, a biobank is “a non-profit organization that must be officially recognized by the appropriate healthcare authority in the member states and must guarantee the treatment, distribution and conservation of biological material according to standards of quality and professionalism,” but must not conserve material already regulated by specific laws, as is the case for organs for transplants, blood for transfusions, as well as embryos and gametes for medically assisted reproduction. The concept of biobank includes not only biological samples, but also the related database of clinical and personal information, from which the subject's lifestyle can be deduced. Unfortunately, at the moment, Italian law does not offer specific itineraries for achieving this legal status. url: https://www.ncbi.nlm.nih.gov/pubmed/32984196/ doi: 10.3389/fped.2020.00415 id: cord-354372-vfvnjmv1 author: Carpenito, L. title: The autopsy at the time of SARS-CoV-2: Protocol and lessons date: 2020-07-04 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: A new viral disease named COVID-19 has recently turned into a pandemic. Compared to a common viral pneumonia it may evolve in an atypical way, causing the rapid death of the patient. For over two centuries, autopsy has been recognized as a fundamental diagnostic technique, particularly for new or little-known diseases. To date, it is often considered obsolete giving the inadequacy to provide samples of a quality appropriate to the sophisticated diagnostic techniques available today. This is probably one of the reasons why during this pandemic autopsies were often requested only in few cases, late and discouraged, if not prohibited, by more than one nation. This is in contrast with our firm conviction: to understand the unknown we must look at it directly and with our own eyes. This has led us to implement an autopsy procedure that allows the beginning of the autopsy shortly after death (within 1–2 h) and its rapid execution, also including sampling for ultrastructural and molecular investigations. In our experience, the tissue sample collected for diagnosis and research were of quality similar to biopsy or surgical resections. This procedure was performed ensuring staff and environmental safety. We want to propose our experience, our main qualitative results and a few general considerations, hoping that they can be an incentive to use autopsy with a new procedure adjusted to match the diagnostic challenges of the third millennium. url: https://www.ncbi.nlm.nih.gov/pubmed/32653819/ doi: 10.1016/j.anndiagpath.2020.151562 id: cord-315054-kji2kfek author: Chakraborty, Nabarun title: Protocol Improvement for RNA Extraction From Compromised Frozen Specimens Generated in Austere Conditions: A Path Forward to Transcriptomics-Pathology Systems Integration date: 2020-07-22 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: At the heart of the phenome-to-genome approach is high throughput assays, which are liable to produce false results. This risk can be mitigated by minimizing the sample bias, specifically, recycling the same tissue specimen for both phenotypic and genotypic investigations. Therefore, our aim is to suggest a methodology of obtaining robust results from frozen specimens of compromised quality, particularly if the sample is produced in conditions with limited resources. For example, generating samples at the International Space Station (ISS) is challenging because the time and laboratory footprint allotted to a project can get expensive. In an effort to be economical with available resources, snap-frozen euthanized mice are the straightforward solution; however, this method increases the risk of temperature abuse during the thawing process at the beginning of the tissue collection. We found that prolonged immersion of snap frozen mouse carcass in 10% neutral buffered formalin at 4°C yielded minimal microscopic signs of ice crystallization and delivered tissues with histomorphology that is optimal for hematoxylin and eosin (H&E) staining and fixation on glass slides. We further optimized a method to sequester the tissue specimen from the H&E slides using an incubator shaker. Using this method, we were able to recover an optimal amount of RNA that could be used for downstream transcriptomics assays. Overall, we demonstrated a protocol that enables us to maximize scientific values from tissues collected in austere condition. Furthermore, our protocol can suggest an improvement in the spatial resolution of transcriptomic assays. url: https://doi.org/10.3389/fmolb.2020.00142 doi: 10.3389/fmolb.2020.00142 id: cord-335375-n6q70o35 author: Chan, Paul K. S. title: Antibody Avidity Maturation during Severe Acute Respiratory Syndrome–Associated Coronavirus Infection date: 2005-07-01 words: 2186.0 sentences: 109.0 pages: flesch: 55.0 cache: ./cache/cord-335375-n6q70o35.txt txt: ./txt/cord-335375-n6q70o35.txt summary: Samples collected р50 days after fever onset were also tested for anti-SARS-CoV IgM antibody, so that IgM antibody detection and IgG antibody avidity measurement could be compared with respect to demonstrating a recent infection. Changes in severe acute respiratory syndrome-associated coronavirus-specific IgG antibody avidity in paired serum samples ples were measured by an in-house indirect immunofluorescence assay that has been described elsewhere [12] . Of the 45 samples collected р50 days after fever onset, only 18 (40.0%) were positive for anti-SARS-CoV IgM antibody, as determined by the ELISARS assay. Of the 26 paired samples, only 6 (23.1%) showed a significant (у4-fold) increase in anti-SARS-CoV IgG antibody titer (as determined by an in-house indirect immunofluorescence assay) from the first to the second sample, a result that could be regarded as evidence of recent infection. Our data show that anti-SARS-CoV IgG antibody avidity is low during primary infection and increases with time in a unidirectional manner. abstract: The maturation of virus-specific immunoglobulin G avidity during severe acute respiratory syndrome–associated coronavirus infection was examined. The avidity indices were low (mean ± SD, 30.8% ± 11.6%) among serum samples collected ⩽50 days after fever onset, intermediate (mean ± SD, 52.1% ± 14.1%) among samples collected between days 51 and 90, and high (mean ± SD, 78.1% ± 8.0%) among samples collected after day 90. Avidity indices of 40% and 55% could be considered as cutoff values for determination of recent (⩽50 days) and past (>65 days) infection, respectively. Measurement of antibody avidity can be used to differentiate primary infection from reexposure and to assess humoral responses to candidate vaccines url: https://www.ncbi.nlm.nih.gov/pubmed/15942907/ doi: 10.1086/430615 id: cord-298697-v1qdizwx author: Chang, Jia Jin Marc title: Takeaways from Mobile DNA Barcoding with BentoLab and MinION date: 2020-09-24 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Since the release of the MinION sequencer in 2014, it has been applied to great effect in the remotest and harshest of environments, and even in space. One of the most common applications of MinION is for nanopore-based DNA barcoding in situ for species identification and discovery, yet the existing sample capability is limited (n ≤ 10). Here, we assembled a portable sequencing setup comprising the BentoLab and MinION and developed a workflow capable of processing 32 samples simultaneously. We demonstrated this enhanced capability out at sea, where we collected samples and barcoded them onboard a dive vessel moored off Sisters’ Islands Marine Park, Singapore. In under 9 h, we generated 105 MinION barcodes, of which 19 belonged to fresh metazoans processed immediately after collection. Our setup is thus viable and would greatly fortify existing portable DNA barcoding capabilities. We also tested the performance of the newly released R10.3 nanopore flow cell for DNA barcoding, and showed that the barcodes generated were ~99.9% accurate when compared to Illumina references. A total of 80% of the R10.3 nanopore barcodes also had zero base ambiguities, compared to 50–60% for R9.4.1, suggesting an improved homopolymer resolution and making the use of R10.3 highly recommended. url: https://www.ncbi.nlm.nih.gov/pubmed/32987804/ doi: 10.3390/genes11101121 id: cord-015482-ovuofl9q author: Chen, Xinguang title: Probability Sampling by Connecting Space with Households Using GIS/GPS Technologies date: 2018-01-23 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Sampling methods for survey studies are challenged by the replacement of landline telephones with mobile phones, the lack of timely census data, and the growing need for studies to address new health challenges. GIS/GPS-assisted methods provide a promising alternative, but these methods need further improvement. We established a stratified 3-stage GIS/GPS-assisted sampling method in which residential areas of a target population are divided into mutually exclusive cells – geographic units (geounits) as the primary sampling frame (PSF). Geounits with residential households were randomly selected from the PSF with a semi-automatic algorithm implemented in R. Novel methods were used to sample households and participants. Simulations and application studies indicated adequate feasibility, efficiency and validity of the method in sampling rural-to-urban migrants from a large city with complex residential arrangements. With this method, researchers can determine sample size and number of geounits, households and participants to be sampled; optimally allocate geounits; determine area size of sampled geounits and estimate sample weights; and complete sampling for field data collection in a short period. Our method adds an integrative approach for GIS/GPS-assisted random sampling with a de facto population assumption. Additional evaluation studies are needed to assess the utility of this method in different settings. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7107540/ doi: 10.1093/jssam/smx032 id: cord-258014-lzzi4rnz author: Chorna, Nataliya title: A Protocol for the Multi-Omic Integration of Cervical Microbiota and Urine Metabolomics to Understand Human Papillomavirus (HPV)-Driven Dysbiosis date: 2020-04-08 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The multi-omic integration of microbiota data with metabolomics has gained popularity. This protocol is based on a human multi-omics study, integrating cervicovaginal microbiota, HPV status and neoplasia, with urinary metabolites. Indeed, to understand the biology of the infections and to develop adequate interventions for cervical cancer prevention, studies are needed to characterize in detail the cervical microbiota and understand the systemic metabolome. This article is a detailed protocol for the multi-omic integration of cervical microbiota and urine metabolome to shed light on the systemic effects of cervical dysbioses associated with Human Papillomavirus (HPV) infections. This methods article suggests detailed sample collection and laboratory processes of metabolomics, DNA extraction for microbiota, HPV typing, and the bioinformatic analyses of the data, both to characterize the metabolome, the microbiota, and joint multi-omic analyses, useful for the development of new point-of-care diagnostic tests based on these approaches. url: https://doi.org/10.3390/biomedicines8040081 doi: 10.3390/biomedicines8040081 id: cord-345144-zvu22n8f author: Compagnone, D. title: Chapter 29 Rapid detection of organophosphates, Ochratoxin A, and Fusarium sp. in durum wheat via screen printed based electrochemical sensors date: 2007-12-31 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Publisher Summary Most of the inhibition bioassays or biosensors for organophosphate and carbamate pesticides are based on the amperometric detection of the enzymatic product of the reaction. Applications of amperometric biosensing strategies for pesticide detection in real or spiked food samples have been recently reported. Most of the applications have been developed for vegetable matrices. Different formats of biosensors have been used: disposable screenprinted choline oxidase biosensors using acetylcholinesterase (AChE) in solution were utilized to detect pesticides. Screen-printed sensor developed using photolithographic conducting copper track, graphite–epoxy composite, and either AChE or butirrylcholinesterase was also used in the analysis of spiked (paraoxon and carbofuran) samples of tap water and fruit juices at sub-nanomolar concentration. Additionally, the developed device, which consists of the hand-held potentiostat, the multiplexer for eight-channel control and a dedicated software, can be used to detect organophosphates pesticides, such as dichlorvos and pirimiphos methyl at contamination level below the maximum residue limit settled by the European Union and also amplified DNA of F. culmorum. url: https://www.sciencedirect.com/science/article/pii/S0166526X06490292 doi: 10.1016/s0166-526x(06)49029-2 id: cord-102613-hly07ne3 author: Danko, David title: Global Genetic Cartography of Urban Metagenomes and Anti-Microbial Resistance date: 2020-05-04 words: 6548.0 sentences: 360.0 pages: flesch: 55.0 cache: ./cache/cord-102613-hly07ne3.txt txt: ./txt/cord-102613-hly07ne3.txt summary: We identified covariates which influenced the taxonomic composition 204 of our samples: city, population density, average temperature in June, region, elevation above sea-level, 205 surface type, surface material, elevation above or below ground and proximity to the coast. To quantify how the principle covariates, climate, continent, and surface material impacted the taxo-213 nomic composition of samples, we performed a Principal Component Analysis (PCA) on our taxonomic 214 data normalized by proportion and identified principal components (PCs) which were strongly associated 215 with a metadata covariate in a positive or negative direction (PCs were centered so an average direction 216 indicates an association). In general, negative controls had 798 lower k-mer complexity, fewer reads, and lower post PCR Qubit scores than case samples and no major Previous studies have reported that microbial species whose relative abundance is negatively cor-803 related with DNA concentration may be contaminants. abstract: Although studies have shown that urban environments and mass-transit systems have distinct genetic profiles, there are no systematic worldwide studies of these dense, human microbial ecosystems. To address this gap in knowledge, we created a global metagenomic and antimicrobial resistance (AMR) atlas of urban mass transit systems from 60 cities, spanning 4,728 samples and 4,424 taxonomically-defined microorganisms collected for three years. This atlas provides an annotated, geospatial profile of microbial strains, functional characteristics, antimicrobial resistance markers, and novel genetic elements, including 10,928 novel predicted viral species, 1302 novel bacteria, and 2 novel archaea. Urban microbiomes often resemble human commensal microbiomes from the skin and airways, but also contain a consistent “core” of 31 species which are predominantly not human commensal species. Samples show distinct microbial signatures which may be used to accurately predict properties of their city of origin including population, proximity to the coast, and taxonomic profile. These data also show that AMR density across cities varies by several orders of magnitude, including many AMRs present on plasmids with cosmopolitan distributions. Together, these results constitute a high-resolution, global metagenomic atlas, which enables the discovery of new genetic components of the built human environment, highlights potential forensic applications, and provides an essential first draft of the global AMR burden of the world’s cities. url: https://doi.org/10.1101/724526 doi: 10.1101/724526 id: cord-345302-wbkfjz8r author: Devaney, Ryan title: A metagenomic comparison of endemic viruses from broiler chickens with runting-stunting syndrome and from normal birds date: 2016-10-04 words: 7869.0 sentences: 352.0 pages: flesch: 41.0 cache: ./cache/cord-345302-wbkfjz8r.txt txt: ./txt/cord-345302-wbkfjz8r.txt summary: This paper attempts to characterize the viral pathogens associated with 2–3-week-old RSS-affected and unaffected broiler chickens using next-generation sequencing and comparative metagenomics. Of specific interest is the enteric viral population associated with RSS of which many RNA and DNA viruses have been implicated and co-infections of multiple viruses such as rotavirus, chicken astrovirus (CAstV), avian nephritis virus (ANV), and reoviruses have been detected in birds affected with RSS or with poor performance (Reynolds et al., 1986; Guy, 1998; Kang et al., 2012) . Other enteric pathogens associated with avian malabsorption diseases include reoviruses, parvoviruses, and members of the family Caliciviridae; many of which have also been observed in broiler chickens Smyth et al., 2007; Pantin-Jackwood et al., 2008 , Wolf et al., 2011 . abstract: Runting-stunting syndrome (RSS) in broiler chickens is an enteric disease that causes significant economic losses to poultry producers worldwide due to elevated feed conversion ratios, decreased body weight during growth, and excessive culling. Of specific interest are the viral agents associated with RSS which have been difficult to fully characterize to date. Past research into the aetiology of RSS has implicated a wide variety of RNA and DNA viruses however, to date, no individual virus has been identified as the main agent of RSS and the current opinion is that it may be caused by a community of viruses, collectively known as the virome. This paper attempts to characterize the viral pathogens associated with 2–3-week-old RSS-affected and unaffected broiler chickens using next-generation sequencing and comparative metagenomics. Analysis of the viromes identified a total of 20 DNA and RNA viral families, along with 2 unidentified categories, comprised of 31 distinct viral genera and 7 unclassified genera. The most abundant viral families identified in this study were the Astroviridae, Caliciviridae, Picornaviridae, Parvoviridae, Coronaviridae, Siphoviridae, and Myoviridae. This study has identified historically significant viruses associated with the disease such as chicken astrovirus, avian nephritis virus, chicken parvovirus, and chicken calicivirus along with relatively novel viruses such as chicken megrivirus and sicinivirus 1 and will help expand the knowledge related to enteric disease in broiler chickens, provide insights into the viral constituents of a healthy avian gut, and identify a variety of enteric viruses and viral communities appropriate for further study. url: https://www.ncbi.nlm.nih.gov/pubmed/27215546/ doi: 10.1080/03079457.2016.1193123 id: cord-345992-3ij1vbqp author: Drosten, Christian title: SARS Molecular Detection External Quality Assurance date: 2004-12-17 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Inactivated severe acute respiratory syndrome–associated coronavirus samples were used for an external quality assurance study within the World Health Organization SARS Reference and Verification Network and other reference institutions. Of 58 participants, 51 correctly detected virus in all samples >9,400 RNA copies per milliliter and none in negative samples. Commercial test kits significantly improved the outcome. url: https://www.ncbi.nlm.nih.gov/pubmed/15663861/ doi: 10.3201/eid1012.040416 id: cord-298295-epxd03pt author: Eckermann, M. title: 3d Virtual Patho-Histology of Lung Tissue from Covid-19 Patients based on Phase Contrast X-ray Tomography date: 2020-06-23 words: 6497.0 sentences: 369.0 pages: flesch: 51.0 cache: ./cache/cord-298295-epxd03pt.txt txt: ./txt/cord-298295-epxd03pt.txt summary: We present a new approach of three-dimensional (3d) virtual histology and patho-histology based on multi-scale phase contrast x-ray tomography, and use this to investigate the parenchymal-architecture of unstained lung tissue from patients who succumbed to Covid-19. Based on this first proof-of-concept study, we can propose multi-scale phase contrast x-ray tomography as a novel tool to unravel the patho-physiology of Covid-19, extending conventional histology by a third dimension and allowing for a full quantification of tissue remodeling.By combining parallel and cone beam geometry, autopsy samples with a cross section of 4mm are scanned and reconstructed at a resolution and image quality which allows for the segmentation of individual cells. The 3d virtual pathohistology approach for Covid-19 presented here was realized by implementing a novel multi-scale phase contrast x-ray tomography concept, with dedicated xray optics and instrumentation to image the tissue structure on multiple length scales, while at the same time covering large reconstruction volumes. abstract: We present a new approach of three-dimensional (3d) virtual histology and patho-histology based on multi-scale phase contrast x-ray tomography, and use this to investigate the parenchymal-architecture of unstained lung tissue from patients who succumbed to Covid-19. Based on this first proof-of-concept study, we can propose multi-scale phase contrast x-ray tomography as a novel tool to unravel the patho-physiology of Covid-19, extending conventional histology by a third dimension and allowing for a full quantification of tissue remodeling.By combining parallel and cone beam geometry, autopsy samples with a cross section of 4mm are scanned and reconstructed at a resolution and image quality which allows for the segmentation of individual cells. Using the zoom capability of the cone beam geometry, regions-of-interest are reconstructed with a minimum voxel size of 160nm. We exemplify the capability of this approach by 3d visualisation of the diffuse alveolar damage with its prominent hyaline membrane formation, by mapping the 3d distribution and density of lymphocytes infiltrating the tissue, and by providing histograms of characteristic distances from tissue interior to the closest air compartment. url: http://medrxiv.org/cgi/content/short/2020.06.21.20134882v1?rss=1 doi: 10.1101/2020.06.21.20134882 id: cord-022879-j6cecioe author: Fager, Edward W. title: Determination and Analysis of Recurrent Groups date: 1957-10-01 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7163427/ doi: 10.2307/1943124 id: cord-024553-jat7pttf author: Fan, Haoyi title: Correlation-Aware Deep Generative Model for Unsupervised Anomaly Detection date: 2020-04-17 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Unsupervised anomaly detection aims to identify anomalous samples from highly complex and unstructured data, which is pervasive in both fundamental research and industrial applications. However, most existing methods neglect the complex correlation among data samples, which is important for capturing normal patterns from which the abnormal ones deviate. In this paper, we propose a method of Correlation aware unsupervised Anomaly detection via Deep Gaussian Mixture Model (CADGMM), which captures the complex correlation among data points for high-quality low-dimensional representation learning. More specifically, the relations among data samples are correlated firstly in forms of a graph structure, in which, the node denotes the sample and the edge denotes the correlation between two samples from the feature space. Then, a dual-encoder that consists of a graph encoder and a feature encoder, is employed to encode both the feature and correlation information of samples into the low-dimensional latent space jointly, followed by a decoder for data reconstruction. Finally, a separate estimation network as a Gaussian Mixture Model is utilized to estimate the density of the learned latent vector, and the anomalies can be detected by measuring the energy of the samples. Extensive experiments on real-world datasets demonstrate the effectiveness of the proposed method. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7206313/ doi: 10.1007/978-3-030-47436-2_52 id: cord-344131-e7phs0jd author: Ford, Richard B. title: Section 4 Diagnostic and Therapeutic Procedures date: 2012-12-31 words: 40123.0 sentences: 2277.0 pages: flesch: 51.0 cache: ./cache/cord-344131-e7phs0jd.txt txt: ./txt/cord-344131-e7phs0jd.txt summary: Before actually collecting and submitting a sample to a laboratory for bacterial culture, it is appropriate (whenever feasible to do so) to prepare, stain, and examine, under direct microscopy, exudates or fluid from the suspect material or tissue. Fine-needle aspiration, the use of needle and syringe to remove cells from normal and abnormal tissue, apply them to a glass slide, stain the smear, and review the results immediately is among the most useful, cost-effective procedures available in clinical practice. Do not remove the syringe from the tissue while maintaining negative pressure, because this can Enlargement of nucleus or nuclei larger than 10 nm Decreased nuclear/cytoplasmic ratio Multinucleation because of abnormal mitosis Abnormal or frequent mitosis Variations in size and shape of nuclei Increase in size and number of nucleoli Increased basophilia of cellular cytoplasm; increased RNA content Anisokaryosis or pleomorphism Multinucleated giant cells box 4-4 cytologic feAtuRes of mAlignAncy 4 result in the aspiration of significant amounts of blood from the skin, thereby significantly diluting the sample with peripheral blood. abstract: nan url: https://www.sciencedirect.com/science/article/pii/B9781437707984000049 doi: 10.1016/b978-1-4377-0798-4.00004-9 id: cord-003523-byxuruk1 author: Fritsch, Annemarie title: Influenza C virus in pre-school children with respiratory infections: retrospective analysis of data from the national influenza surveillance system in Germany, 2012 to 2014 date: 2019-03-07 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: INTRODUCTION: Recent data on influenza C virus indicate a possible higher clinical impact in specified patient populations than previously thought. AIM: We aimed to investigate influenza C virus circulation in Germany. METHODS: A total of 1,588 samples from 0 to 4 year-old children presenting as outpatients with influenza-like illness (ILI) or acute respiratory infection were analysed retrospectively. The samples represented a subset of all samples from the German national surveillance system for influenza in this age group in 2012–14. The presence of influenza C virus was investigated by real-time PCR. For positive samples, information on symptoms as well as other respiratory virus co-infections was considered. Retrieved influenza C viral sequences were phylogenetically characterised. RESULTS: Influenza C viral RNA was detected in 20 (1.3% of) samples, including 16 during the 2012/13 season. The majority (18/20) of influenza C-positive patients had ILI according to the European Union definition, one patient had pneumonia. Viruses belonged to the C/Sao Paulo and C/Kanagawa lineages. Most (11/20) samples were co-infected with other respiratory viruses. CONCLUSION: Our data are the first on influenza C virus circulation in Germany and notably from a European national surveillance system. The low detection frequency and the identified virus variants confirm earlier observations outside a surveillance system. More virus detections during the 2012/13 season indicate a variable circulation intensity in the different years studied. Influenza C virus can be considered for ILI patients. Future studies addressing its clinical impact, especially in patients with severe disease are needed. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6415498/ doi: 10.2807/1560-7917.es.2019.24.10.1800174 id: cord-103180-5hkoeca7 author: Furstenau, Tara N. title: Sample pooling methods for efficient pathogen screening: Practical implications date: 2020-07-16 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Due to the large number of negative tests, individually screening large populations for rare pathogens can be wasteful and expensive. Sample pooling methods improve the efficiency of large-scale pathogen screening campaigns by reducing the number of tests and reagents required to accurately categorize positive and negative individuals. Such methods rely on group testing theory which mainly focuses on minimizing the total number of tests; however, many other practical concerns and tradeoffs must be considered when choosing an appropriate method for a given set of circumstances. Here we use computational simulations to determine how several theoretical approaches compare in terms of (a) the number of tests, to minimize costs and save reagents, (b) the number of sequential steps, to reduce the time it takes to complete the assay, (c) the number of samples per pool, to avoid the limits of detection, (d) simplicity, to reduce the risk of human error, and (e) robustness, to poor estimates of the number of positive samples. We found that established methods often perform very well in one area but very poorly in others. Therefore, we introduce and validate a new method which performs fairly well across each of the above criteria making it a good general use approach. url: https://doi.org/10.1101/2020.07.16.206060 doi: 10.1101/2020.07.16.206060 id: cord-355743-vjiecd4k author: Ghosh, Sabyasachi title: Tapestry: A Single-Round Smart Pooling Technique for COVID-19 Testing date: 2020-04-29 words: 4826.0 sentences: 279.0 pages: flesch: 63.0 cache: ./cache/cord-355743-vjiecd4k.txt txt: ./txt/cord-355743-vjiecd4k.txt summary: The decoding algorithm takes as input cycle threshold values from qPCR tests on the pools, and returns a result for each sample, along with an estimate of viral load if positive. Once pooled tests are run, the cycle threshold values can be entered into the app which solves for and displays the list of positive and negative samples along with an estimate of viral loads. 16 × 40 pooling matrix: Table 2 shows the emulated cycle threshold (Ct) values for the 16 RT-qPCR tests corresponding to five different trials (0, 1, 2, 3 or 4 positive samples out of a total of 40 samples). 24 × 60 pooling matrix: Table 3 shows the cycle threshold (Ct) values obtained for the 24 RT-qPCR tests corresponding to a trial with 2 positive samples out of a total of 60 samples. abstract: The COVID-19 pandemic has strained testing capabilities worldwide. There is an urgent need to find economical and scalable ways to test more people. We present Tapestry, a novel quantitative nonadaptive pooling scheme to test many samples using only a few tests. The underlying molecular diagnostic test is any real-time RT-PCR diagnostic panel approved for the detection of the SARS-CoV-2 virus. In cases where most samples are negative for the virus, Tapestry accurately identifies the status of each individual sample with a single round of testing in fewer tests than simple two-round pooling. We also present a companion Android application BYOM Smart Testing which guides users through the pipetting steps required to perform the combinatorial pooling. The results of the pooled tests can be fed into the application to recover the status and estimated viral load for each individual sample. url: https://doi.org/10.1101/2020.04.23.20077727 doi: 10.1101/2020.04.23.20077727 id: cord-305755-6jup93v4 author: Gouveia, Duarte title: Proteotyping SARS-CoV-2 Virus from Nasopharyngeal Swabs: A Proof-of-Concept Focused on a 3 Min Mass Spectrometry Window date: 2020-07-22 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: [Image: see text] Rapid but yet sensitive, specific, and high-throughput detection of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in clinical samples is key to diagnose infected people and to better control the spread of the virus. Alternative methodologies to PCR and immunodiagnostics that would not require specific reagents are worthy to investigate not only for fighting the COVID-19 pandemic but also to detect other emergent pathogenic threats. Here, we propose the use of tandem mass spectrometry to detect SARS-CoV-2 marker peptides in nasopharyngeal swabs. We documented that the signal from the microbiota present in such samples is low and can be overlooked when interpreting shotgun proteomic data acquired on a restricted window of the peptidome landscape. In this proof-of-concept study, simili nasopharyngeal swabs spiked with different quantities of purified SARS-CoV-2 viral material were used to develop a nanoLC–MS/MS acquisition method, which was then successfully applied on COVID-19 clinical samples. We argue that peptides ADETQALPQR and GFYAQGSR from the nucleocapsid protein are of utmost interest as their signal is intense and their elution can be obtained within a 3 min window in the tested conditions. These results pave the way for the development of time-efficient viral diagnostic tests based on mass spectrometry. url: https://www.ncbi.nlm.nih.gov/pubmed/32697082/ doi: 10.1021/acs.jproteome.0c00535 id: cord-102547-nxut8ov1 author: Grädel, C. title: Whole genome sequencing of human enteroviruses from clinical samples by nanopore direct RNA sequencing date: 2020-06-09 words: 6505.0 sentences: 349.0 pages: flesch: 53.0 cache: ./cache/cord-102547-nxut8ov1.txt txt: ./txt/cord-102547-nxut8ov1.txt summary: DRS of total RNA extracted from three different enterovirus-positive stool samples produced long RNA fragments, covering between 59% to 99.6 % of the best reference genomes. Taxonomic classification of viral reads (Oxford Nanopore) and contigs (Illumina MiSeq) using MEGAN based on BLASTN matches against NCBI''s nucleotide (nt) database at the species and genotype levels. In order to confirm the genotype identification and to obtain a highly accurate whole genome sequence of the enterovirus genome, we subsequently subjected the sample E590 also to cDNA sequencing using Illumina MiSeq. In this case, the cDNA was produced using genotype-specific primers given that low number of reads was obtained by DRS and MiSeq . Illumina sequencing of the cDNA from sample E026 produced using oligo-dT primers and random hexamers showed similar distributions on the domain level: The majority of contigs belonged to bacterial species (98.6% and 98.9%, respectively for oligo-dT and random hexamer approaches), with a minority of reads mapping to eukaryotes (0.49%, 0.50%) and viruses (0.87%, 0.56%). abstract: Enteroviruses are small RNA viruses that affect millions of people each year by causing an important burden of disease with a broad spectrum of symptoms. In routine diagnostic laboratories, those viruses are identified by PCR based methods, often combined with partial sequencing for genotyping. In this proof-of-principle study, we assessed direct RNA sequencing (DRS) using nanopore sequencing technology for fast whole-genome sequencing of viruses directly from clinical samples. Results of the approach were complemented with those obtained by sequencing the corresponding viral cDNA via Illumina MiSeq sequencing. DRS of total RNA extracted from three different enterovirus-positive stool samples produced long RNA fragments, covering between 59% to 99.6 % of the best reference genomes. The identification of the enterovirus sequences in the sample was confirmed by the short-read cDNA sequencing. Sequence identity between DRS and Illumina MiSeq enterovirus consensus sequences ranged between 94-97%. Here we show that nanopore DRS can be used to correctly identify the genotypes of enteroviruses from patient stool samples with high viral load. url: http://medrxiv.org/cgi/content/short/2020.06.09.20126219v1?rss=1 doi: 10.1101/2020.06.09.20126219 id: cord-280846-bbv6f5gf author: Greninger, Alexander L. title: A Metagenomic Analysis of Pandemic Influenza A (2009 H1N1) Infection in Patients from North America date: 2010-10-18 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Although metagenomics has been previously employed for pathogen discovery, its cost and complexity have prevented its use as a practical front-line diagnostic for unknown infectious diseases. Here we demonstrate the utility of two metagenomics-based strategies, a pan-viral microarray (Virochip) and deep sequencing, for the identification and characterization of 2009 pandemic H1N1 influenza A virus. Using nasopharyngeal swabs collected during the earliest stages of the pandemic in Mexico, Canada, and the United States (n = 17), the Virochip was able to detect a novel virus most closely related to swine influenza viruses without a priori information. Deep sequencing yielded reads corresponding to 2009 H1N1 influenza in each sample (percentage of aligned sequences corresponding to 2009 H1N1 ranging from 0.0011% to 10.9%), with up to 97% coverage of the influenza genome in one sample. Detection of 2009 H1N1 by deep sequencing was possible even at titers near the limits of detection for specific RT-PCR, and the percentage of sequence reads was linearly correlated with virus titer. Deep sequencing also provided insights into the upper respiratory microbiota and host gene expression in response to 2009 H1N1 infection. An unbiased analysis combining sequence data from all 17 outbreak samples revealed that 90% of the 2009 H1N1 genome could be assembled de novo without the use of any reference sequence, including assembly of several near full-length genomic segments. These results indicate that a streamlined metagenomics detection strategy can potentially replace the multiple conventional diagnostic tests required to investigate an outbreak of a novel pathogen, and provide a blueprint for comprehensive diagnosis of unexplained acute illnesses or outbreaks in clinical and public health settings. url: https://doi.org/10.1371/journal.pone.0013381 doi: 10.1371/journal.pone.0013381 id: cord-326380-9ecsp66y author: Griesemer, Sara B title: Assessment of sample pooling for clinical SARS-CoV-2 testing date: 2020-05-27 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Accommodating large increases in sample workloads has presented one of the biggest challenges to clinical laboratories during the COVID-19 pandemic. Despite the implementation of new automated detection systems, and previous efficiencies such as barcoding, electronic data transfer and extensive robotics, throughput capacities have struggled to meet the demand. Sample pooling has been suggested as an additional strategy to further address this need. The greatest concern with this approach in a clinical setting is the potential for reduced sensitivity, particularly the risk of false negative results when weak positive samples are pooled. To investigate this possibility, detection rates in pooled samples were evaluated, with extensive assessment of pools containing weak positive specimens. Additionally, the frequency of occurrence of weak positive samples across ten weeks of the pandemic were reviewed. Weak positive specimens were detected in all five-sample pools but failed to be detected in four of the 24 nine-sample pools tested. Weak positive samples comprised an average 16.5% of the positive specimens tested during the pandemic thus far, slightly increasing in frequency during later weeks. Other aspects of the testing process should be considered, however, such as accessioning and reporting, which are not streamlined and may be complicated by pooling procedures. Therefore, the impact on the entire laboratory process needs to be carefully assessed prior to implementing such a strategy. url: https://doi.org/10.1101/2020.05.26.118133 doi: 10.1101/2020.05.26.118133 id: cord-254596-wsmnlnlk author: Grädel, Carole title: Whole-Genome Sequencing of Human Enteroviruses from Clinical Samples by Nanopore Direct RNA Sequencing date: 2020-07-31 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Enteroviruses are small RNA viruses that affect millions of people each year by causing an important burden of disease with a broad spectrum of symptoms. In routine diagnostic laboratories, enteroviruses are identified by PCR-based methods, often combined with partial sequencing for genotyping. In this proof-of-principle study, we assessed direct RNA sequencing (DRS) using nanopore sequencing technology for fast whole-genome sequencing of viruses directly from clinical samples. The approach was complemented by sequencing the corresponding viral cDNA via Illumina MiSeq sequencing. DRS of total RNA extracted from three different enterovirus-positive stool samples produced long RNA fragments, covering between 59% and 99.6% of the most similar reference genome sequences. The identification of the enterovirus sequences in the samples was confirmed by short-read cDNA sequencing. Sequence identity between DRS and Illumina MiSeq enterovirus consensus sequences ranged between 94% and 97%. Here, we show that nanopore DRS can be used to correctly identify enterovirus genotypes from patient stool samples with high viral load and that the approach also provides rich metatranscriptomic information on sample composition for all life domains. url: https://doi.org/10.3390/v12080841 doi: 10.3390/v12080841 id: cord-335372-tncjfdtp author: HACKNEY, RAYMOND W. title: USING A BIOLOGICAL INDICATOR TO DETECT POTENTIAL SOURCES OF CROSS-CONTAMINATION IN THE DENTAL OPERATORY date: 1998-11-30 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: ABSTRACT The authors conducted a study using surveillance monitoring methodology to identify operatory contamination and to evaluate the effectiveness of infection control procedures. Viridans streptococci were evaluated as biological indicators of oral contamination. Viridans streptococci, abundant in human saliva, were detected on operatory surfaces after dental treatments were finished and surfaces were disinfected. The findings validate current concepts of infection control as demonstrated in barrier methods. url: https://api.elsevier.com/content/article/pii/S000281771560112X doi: 10.14219/jada.archive.1998.0103 id: cord-344627-w2efsshj author: Han, Tae-Hee title: Human Bocavirus 2 in Children, South Korea date: 2009-10-17 words: 1433.0 sentences: 82.0 pages: flesch: 48.0 cache: ./cache/cord-344627-w2efsshj.txt txt: ./txt/cord-344627-w2efsshj.txt summary: We looked for HBoV-2 in clinical samples from children with various diseases, including acute LRTIs, Kawasaki disease, Henoch-Schönlein purpura, and hepatitis. Of the 212 samples tested, the following viruses were detected: human respiratory syncytial virus ( HBoV-1 was not detected in the study population. Recent studies have detected HBoV-1 in serum samples of children with Kawasaki disease and of an immunocompromised child with hepatitis (7, 8) . However, neither HBoV-1 nor HBoV-2 was detected in the 172 serum samples from 61 patients with hepatitis, 12 with Kawasaki disease, 18 with Henoch-Schönlein purpura, and 81 healthy children. We demonstrated HBoV-2 DNA in the respiratory tract secretions of children with acute LRTIs. In most positive samples, the virus was found in addition to other respiratory viruses. Human bocavirus infection in young children in the United States: molecular epidemiological profile and clinical characteristics of a newly emerging respiratory virus abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/19861084/ doi: 10.3201/eid1510.090337 id: cord-353394-lq1f53qv author: Han, Tae-Hee title: Detection of Pathogenic Viruses in the Ambient Air in Seoul, Korea date: 2018-05-14 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The possible transport of pathogenic microorganisms during Asian dust events could be an important concern for health workers; however, this is still uncertain owing to a lack of supporting evidence. The present study aimed to investigate the presence of pathogenic microorganisms in air samples collected during the Asian and non-Asian dust periods. Between March and September 2016, air samples were collected at three weather observation stations in Seoul using a high-volume air sampler. Multiplex PCR was performed using the Allplex™ respiratory and gastrointestinal panel assay kits to detect 46 microorganisms. RT-PCR was performed for klassevirus, Aichivirus, and human parechovirus (HPeV) detection. In total, 71 air samples were collected during the Asian (8 samples) and non-Asian (63 samples) dust events. During an Asian dust event, only one human rhinovirus (HRV)-positive air sample was collected on April 23. During the non-Asian dust period, HRV, HPeV, norovirus (NoV), enteroaggregative Escherichia coli (EAEC), enterotoxigenic E. coli (ETEC), and Blastocystis hominis were detected in four, two, one, one, one, and one air samples, respectively. Pathogenic viruses were mostly detected in ambient air samples during the non-Asian dust period, which suggests a possible air-borne transmission of viral pathogens; however, the role of Asian dust in epidemics caused by pathogenic viruses is unclear. url: https://www.ncbi.nlm.nih.gov/pubmed/29761411/ doi: 10.1007/s12560-018-9348-2 id: cord-307261-0a3iztns author: Hayden, Randall T. title: Comparison of two broadly multiplexed PCR systems for viral detection in clinical respiratory tract specimens from immunocompromised children date: 2012-01-30 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: The detection of viral respiratory tract infections has evolved greatly with the development of PCR based commercial systems capable of simultaneously detecting a wide variety of pathogens. OBJECTIVES: Evaluate the relative performance of two commercial broad range systems for the detection of viral agents in clinical respiratory tract specimens from immunocompromised children. STUDY DESIGN: A total of 176 patient samples were included in the analysis, representing only the first sample collected for each patient, and excluding failed reactions. Samples were de-identified and assayed in parallel using two different, broadly multiplexed PCR systems: ResPlex™ II Panel v2.0 (ResPlex), Qiagen, Hilden, Germany and FilmArray(®) Respiratory Panel (FilmArray), Idaho Technology Inc., Salt Lake City, UT. Method comparison was based upon pair-wise concordance of results according to patient age, viral target and number of targets detected. RESULTS: The two systems showed an overall concordance, by patient, of 83.8% (p = 0.0001). FilmArray detected at least one target in 68.8% of samples, while ResPlex detected at least one target in 56.8%. ResPlex failed to detect 20.7% of FilmArray positives, and FilmArray failed to detect 4% of ResPlex positives. The relative performance of each system (including which system detected a higher number of positive samples) varied when stratified by target viral pathogen. CONCLUSIONS: Broadly multiplexed PCR is an effective means of detecting large numbers of clinically relevant respiratory viral pathogens. url: https://www.sciencedirect.com/science/article/pii/S1386653211005531 doi: 10.1016/j.jcv.2011.12.020 id: cord-342538-5bwsm290 author: Izquierdo Lara, R. W. title: Monitoring SARS-CoV-2 circulation and diversity through community wastewater sequencing date: 2020-09-22 words: 5031.0 sentences: 281.0 pages: flesch: 56.0 cache: ./cache/cord-342538-5bwsm290.txt txt: ./txt/cord-342538-5bwsm290.txt summary: Here we have explored the possibility of using next-generation sequencing (NGS) of sewage samples to evaluate the diversity of SARS-CoV-2 at the community level from routine wastewater testing, and compared these results with the virus diversity in patients from the Netherlands and Belgium. Low frequency variant (LFV) analysis showed that some known LFVs can be associated with particular clusters within a clade, different to those of their consensus sequences, suggesting the presence of at least 2 clades within a single sewage sample. Moreover, we detected a total of 51 novel mutations present in sewage consensus sequences that were not previously reported (supplementary Table S2 ), of which 48 were supported by coverage above the set thresholds to be considered as high quality (coverage >30x for Nanopore; and coverage >5X and Phred score >30 for Illumina). abstract: The current SARS-CoV-2 pandemic has rapidly become a major global health problem for which public health surveillance is crucial to monitor virus spread. Given the presence of viral RNA in feces in around 40% of infected persons, wastewater-based epidemiology has been proposed as an addition to disease-based surveillance to assess the spread of the virus at the community level. Here we have explored the possibility of using next-generation sequencing (NGS) of sewage samples to evaluate the diversity of SARS-CoV-2 at the community level from routine wastewater testing, and compared these results with the virus diversity in patients from the Netherlands and Belgium. Phylogenetic analysis revealed the presence of viruses belonging to the most prevalent clades (19A, 20A and 20B) in both countries. Clades 19B and 20C were not identified, while they were present in clinical samples during the same period. Low frequency variant (LFV) analysis showed that some known LFVs can be associated with particular clusters within a clade, different to those of their consensus sequences, suggesting the presence of at least 2 clades within a single sewage sample. Additionally, combining genome consensus and LFV analyses we found a total of 57 unique mutations in the SARS-CoV-2 genome which have not been described before. In conclusion, this work illustrates how NGS analysis of wastewater can be used to approximate the diversity of SARS-CoV-2 viruses circulating in a community. url: https://doi.org/10.1101/2020.09.21.20198838 doi: 10.1101/2020.09.21.20198838 id: cord-314503-u1y1bznk author: Jaluria, Pratik title: A perspective on microarrays: current applications, pitfalls, and potential uses date: 2007-01-25 words: 7764.0 sentences: 349.0 pages: flesch: 38.0 cache: ./cache/cord-314503-u1y1bznk.txt txt: ./txt/cord-314503-u1y1bznk.txt summary: Therefore, this text aims to outline key features in microarray technology, paying particular attention to current applications as outlined in recent publications, experimental design, statistical methods, and potential uses. Several organizations such as the Microarray Gene Expression Data (MGED) Society and the European Bioinformatics Institute (EBI) have established guidelines to aid researchers in the design and implementation of microarray experiments [8, 9, 16] . As mentioned earlier, verification is critical in order to assign distinct expression patterns to specific genes with certainty (i.e. statistical significance) because of the inherent variability present in microarray data. To verify the results generated from microarray experiments, a combinatorial approach is usually needed; checking the statistical significance associated with the expression levels of specific genes, reviewing the literature, and conducting additional experiments such as RT-PCR or Northern blotting. A large number of microarray-related studies in the past have aimed to either characterize diseased cells in comparison to healthy cells or highlight the genes involved in a particular biological pathway [4, 8] . abstract: With advances in robotics, computational capabilities, and the fabrication of high quality glass slides coinciding with increased genomic information being available on public databases, microarray technology is increasingly being used in laboratories around the world. In fact, fields as varied as: toxicology, evolutionary biology, drug development and production, disease characterization, diagnostics development, cellular physiology and stress responses, and forensics have benefiting from its use. However, for many researchers not familiar with microarrays, current articles and reviews often address neither the fundamental principles behind the technology nor the proper designing of experiments. Although, microarray technology is relatively simple, conceptually, its practice does require careful planning and detailed understanding of the limitations inherently present. Without these considerations, it can be exceedingly difficult to ascertain valuable information from microarray data. Therefore, this text aims to outline key features in microarray technology, paying particular attention to current applications as outlined in recent publications, experimental design, statistical methods, and potential uses. Furthermore, this review is not meant to be comprehensive, but rather substantive; highlighting important concepts and detailing steps necessary to conduct and interpret microarray experiments. Collectively, the information included in this text will highlight the versatility of microarray technology and provide a glimpse of what the future may hold. url: https://www.ncbi.nlm.nih.gov/pubmed/17254338/ doi: 10.1186/1475-2859-6-4 id: cord-024503-f4ibgn9i author: Jawed, Shayan title: Self-supervised Learning for Semi-supervised Time Series Classification date: 2020-04-17 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Self-supervised learning is a promising new technique for learning representative features in the absence of manual annotations. It is particularly efficient in cases where labeling the training data is expensive and tedious, naturally linking it to the semi-supervised learning paradigm. In this work, we propose a new semi-supervised time series classification model that leverages features learned from the self-supervised task on unlabeled data. The idea is to exploit the unlabeled training data with a forecasting task which provides a strong surrogate supervision signal for feature learning. We draw from established multi-task learning approaches and model forecasting as an auxiliary task to be optimized jointly with the main task of classification. We evaluate our proposed method on benchmark time series classification datasets in semi-supervised setting and are able to show that it significantly outperforms the state-of-the-art baselines. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7206263/ doi: 10.1007/978-3-030-47426-3_39 id: cord-300399-21xozruq author: Jayamohan, Harikrishnan title: SARS-CoV-2 pandemic: a review of molecular diagnostic tools including sample collection and commercial response with associated advantages and limitations date: 2020-10-18 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The unprecedented global pandemic known as SARS-CoV-2 has exercised to its limits nearly all aspects of modern viral diagnostics. In doing so, it has illuminated both the advantages and limitations of current technologies. Tremendous effort has been put forth to expand our capacity to diagnose this deadly virus. In this work, we put forth key observations in the functionality of current methods for SARS-CoV-2 diagnostic testing. These methods include nucleic acid amplification–, CRISPR-, sequencing-, antigen-, and antibody-based detection methods. Additionally, we include analysis of equally critical aspects of COVID-19 diagnostics, including sample collection and preparation, testing models, and commercial response. We emphasize the integrated nature of assays, wherein issues in sample collection and preparation could impact the overall performance in a clinical setting. url: https://www.ncbi.nlm.nih.gov/pubmed/33073312/ doi: 10.1007/s00216-020-02958-1 id: cord-321549-r7bmtloy author: Jendrny, Paula title: Scent dog identification of samples from COVID-19 patients – a pilot study date: 2020-07-23 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: As the COVID-19 pandemic continues to spread, early, ideally real-time, identification of SARS-CoV-2 infected individuals is pivotal in interrupting infection chains. Volatile organic compounds produced during respiratory infections can cause specific scent imprints, which can be detected by trained dogs with a high rate of precision. METHODS: Eight detection dogs were trained for 1 week to detect saliva or tracheobronchial secretions of SARS-CoV-2 infected patients in a randomised, double-blinded and controlled study. RESULTS: The dogs were able to discriminate between samples of infected (positive) and non-infected (negative) individuals with average diagnostic sensitivity of 82.63% (95% confidence interval [CI]: 82.02–83.24%) and specificity of 96.35% (95% CI: 96.31–96.39%). During the presentation of 1012 randomised samples, the dogs achieved an overall average detection rate of 94% (±3.4%) with 157 correct indications of positive, 792 correct rejections of negative, 33 incorrect indications of negative or incorrect rejections of 30 positive sample presentations. CONCLUSIONS: These preliminary findings indicate that trained detection dogs can identify respiratory secretion samples from hospitalised and clinically diseased SARS-CoV-2 infected individuals by discriminating between samples from SARS-CoV-2 infected patients and negative controls. This data may form the basis for the reliable screening method of SARS-CoV-2 infected people. url: https://www.ncbi.nlm.nih.gov/pubmed/32703188/ doi: 10.1186/s12879-020-05281-3 id: cord-346906-1wmp43ti author: Lewandowski, Kuiama title: Metagenomic Nanopore Sequencing of Influenza Virus Direct from Clinical Respiratory Samples date: 2019-12-23 words: 6766.0 sentences: 328.0 pages: flesch: 43.0 cache: ./cache/cord-346906-1wmp43ti.txt txt: ./txt/cord-346906-1wmp43ti.txt summary: We determine its sensitivity compared to that of existing diagnostic methods and its accuracy compared to short-read (Illumina) sequencing, using clinical samples from hospital patients during an influenza season and samples from a controlled laboratory infection in ferrets. During the study, respiratory samples submitted to the clinical diagnostic laboratory were routinely tested by a PCR-based test using the GeneXpert assay (Cepheid) to detect influenza A and B viruses and respiratory syncytial virus (RSV). Comparing this final method with our original protocol, using triplicate extractions from the pooled set of influenza A virus-positive samples demonstrated no significant loss in performance in the more rapid protocol (Fig. S3) , and we adopted this approach as our routine protocol, giving a wet-lab processing time of ϳ8 h. Future application of this method will involve real-time laboratory testing of respiratory samples, running the platform head to head with existing clinical diagnostics to further assess sensitivity and specificity, and using influenza virus sequence data to investigate transmission events. abstract: Influenza is a major global public health threat as a result of its highly pathogenic variants, large zoonotic reservoir, and pandemic potential. Metagenomic viral sequencing offers the potential for a diagnostic test for influenza virus which also provides insights on transmission, evolution, and drug resistance and simultaneously detects other viruses. We therefore set out to apply the Oxford Nanopore Technologies sequencing method to metagenomic sequencing of respiratory samples. We generated influenza virus reads down to a limit of detection of 10(2) to 10(3) genome copies/ml in pooled samples, observing a strong relationship between the viral titer and the proportion of influenza virus reads (P = 4.7 × 10(−5)). Applying our methods to clinical throat swabs, we generated influenza virus reads for 27/27 samples with mid-to-high viral titers (cycle threshold [C(T)] values, <30) and 6/13 samples with low viral titers (C(T) values, 30 to 40). No false-positive reads were generated from 10 influenza virus-negative samples. Thus, Nanopore sequencing operated with 83% sensitivity (95% confidence interval [CI], 67 to 93%) and 100% specificity (95% CI, 69 to 100%) compared to the current diagnostic standard. Coverage of full-length virus was dependent on sample composition, being negatively influenced by increased host and bacterial reads. However, at high influenza virus titers, we were able to reconstruct >99% complete sequences for all eight gene segments. We also detected a human coronavirus coinfection in one clinical sample. While further optimization is required to improve sensitivity, this approach shows promise for the Nanopore platform to be used in the diagnosis and genetic analysis of influenza virus and other respiratory viruses. url: https://doi.org/10.1128/jcm.00963-19 doi: 10.1128/jcm.00963-19 id: cord-333413-8buawes0 author: Liebing, J. title: Health status of free-ranging ring-necked pheasant chicks (Phasianus colchicus) in North-Western Germany date: 2020-06-16 words: 5556.0 sentences: 306.0 pages: flesch: 51.0 cache: ./cache/cord-333413-8buawes0.txt txt: ./txt/cord-333413-8buawes0.txt summary: Being a typical ground-breeding bird of the agricultural landscape in Germany, the pheasant has experienced a strong and persistent population decline with a hitherto unexplained cause. In the present study, 62 free-ranging pheasant chicks were caught within a two-year period in three federal states of Germany; Lower Saxony, North Rhine-Westphalia and Schleswig-Holstein. Pheasant chick deaths may often have been triggered by poor nutritional status, probably in association with inflammatory changes in various tissues and organs as well as bacterial and parasitic pathogens. In 2014 and 2015, the Institute for Terrestrial and Aquatic Wildlife Research (ITAW), University of Veterinary Medicine Hannover, Foundation, Hannover and the Wildlife Research Institute, State Office for Nature, Environment and Consumer Protection of North Rhine-Westphalia caught free-living Ring-necked Pheasant chicks from Lower Saxony (Cuxhaven, Grafschaft Bentheim, Emsland, Osnabrück, Vechta), North Rhine-Westphalia (Coesfeld, Warendorf) and Schleswig-Holstein (Dithmarschen) to assess the health state by means of pathological, microbiological, virological, parasitological and toxicological investigations. abstract: Being a typical ground-breeding bird of the agricultural landscape in Germany, the pheasant has experienced a strong and persistent population decline with a hitherto unexplained cause. Contributing factors to the ongoing negative trend, such as the effects of pesticides, diseases, predation, increase in traffic and reduced fallow periods, are currently being controversially discussed. In the present study, 62 free-ranging pheasant chicks were caught within a two-year period in three federal states of Germany; Lower Saxony, North Rhine-Westphalia and Schleswig-Holstein. The pheasant chicks were divided into three age groups to detect differences in their development and physical constitution. In addition, pathomorphological, parasitological, virological, bacteriological and toxicological investigations were performed. The younger chicks were emaciated, while the older chicks were of moderate to good nutritional status. However, the latter age group was limited to a maximum of three chicks per hen, while the youngest age class comprised up to ten chicks. The majority of chicks suffered from dermatitis of the periocular and caudal region of the head (57–94%) of unknown origin. In addition, intestinal enteritis (100%), pneumonia (26%), hepatitis (24%), perineuritis (6%), tracheitis (24%), muscle degeneration (1%) and myositis (1%) were found. In 78% of the cases, various Mycoplasma spp. were isolated. Mycoplasma gallisepticum (MG) was not detected using an MG-specific PCR. Parasitic infections included Philopteridae (55%), Coccidia (48%), Heterakis/Ascaridia spp. (8%) and Syngamus trachea (13%). A total of 8% of the chicks were Avian metapneumovirus (AMPV) positive using RT-PCR, 16% positive for infectious bronchitis virus (IBV) using RT-PCR, and 2% positive for haemorrhagic enteritis virus (HEV) using PCR. All samples tested for avian encephalomyelitis virus (AEV), infectious bursal disease virus (IBDV) or infectious laryngotracheitis virus (ILTV) were negative. The pool samples of the ten chicks were negative for all acid, alkaline-free and derivative substances, while two out of three samples tested were positive for the herbicide glyphosate. Pheasant chick deaths may often have been triggered by poor nutritional status, probably in association with inflammatory changes in various tissues and organs as well as bacterial and parasitic pathogens. Theses impacts may have played a major role in the decline in pheasant populations. url: https://www.ncbi.nlm.nih.gov/pubmed/32544211/ doi: 10.1371/journal.pone.0234044 id: cord-290722-neqj85xf author: Lojkić, Ivana title: Faecal virome of red foxes from peri-urban areas date: 2016-01-29 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Red foxes (Vulpes vulpes) are the most abundant carnivore species in the Northern Hemisphere. Since their populations are well established in peri-urban and urban areas, they represent a potential reservoir of viruses that transmit from wildlife to humans or domestic animals. In this study, we evaluated the faecal virome of juvenile and adult foxes from peri-urban areas in central Croatia. The dominating mammalian viruses were fox picobirnavirus and parvovirus. The highest number of viral reads (N = 1412) was attributed to a new fox circovirus and complete viral genome was de novo assembled from the high-throughput sequencing data. Fox circovirus is highly similar to dog circoviruses identified in diseased dogs in USA and Italy, and to a recently discovered circovirus of foxes with neurologic disease from the United Kingdom. Our fox picobirnavirus was more closely related to the porcine and human picobirnaviruses than to known fox picobirnaviruses. url: https://www.sciencedirect.com/science/article/pii/S0147957116300121 doi: 10.1016/j.cimid.2016.01.005 id: cord-011444-6jh3lvm3 author: Loureiro, Natália I. V. title: Solving an ethical issue involved in experimentation with animals in a brazilian teaching laboratory date: 2006-11-03 words: 2829.0 sentences: 130.0 pages: flesch: 44.0 cache: ./cache/cord-011444-6jh3lvm3.txt txt: ./txt/cord-011444-6jh3lvm3.txt summary: These were i) avoid the use of laboratory animals that would be sacrificed; ii) the inclusion of other topics of metabolism such as glycolysis, citric acid cycle, fatty acid and amino acid synthesis and catabolism, and ketogenesis in the experimental discussion; iii) the experiment should have low cost and be performed after the relevant theory material is studied; and finally iv) it also should be easy and fast, due to the limited time of the practical class. In this article, we will present the protocol and approach used in this practice class, also including the evaluation by student teaching assistants and undergraduate students from nine different courses ("Biological Science," "Pharmacy," "Medicine," "Veterinary Medicine," "Nutrition," "Nursing," "Odontology," "Chemistry," and "Industrial Chemistry"). After the preparation of the protocol and arranging all necessary laboratory material including the guarurine, it was possible to evaluate this new practical class with the group of student teaching assistants from the Biochemistry discipline (n ϭ 6). abstract: Changes are occurring within Brazilian institutes of higher education; currently several universities are reviewing their course offerings and teaching approaches to determine if they meet the needs of today's undergraduate students. When changes are made to the curriculum of experimental courses, there should be an understood guarantee that all efforts to avoid ethical and biosafety issues have been diligently considered. Ethical considerations lead us to create an alternative experimental session to be conducted that eliminated the use of rats, the conventional in vivo model employed for learning metabolism of glycogen in our university. To avoid possible biosafety issues, we prepared an alternative sample to simulate human urine, which we called guarurine. Using our new method, it is possible to verify positive results imitating a diabetic and starving people samples for detection of glucose and ketone. The alternative tool described herein is not only particularly suited to bypass the ethics of using animals for teaching, but also permits the discussion of significant aspects of pathological and physiological situations such as diabetics and starvation in a simple, safe, and interesting way. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7232745/ doi: 10.1002/bmb.2004.494032060404 id: cord-030409-bwxkxvsl author: Mamontov, Eugene title: Effect of Hydration on the Molecular Dynamics of Hydroxychloroquine Sulfate date: 2020-08-10 words: 6127.0 sentences: 275.0 pages: flesch: 49.0 cache: ./cache/cord-030409-bwxkxvsl.txt txt: ./txt/cord-030409-bwxkxvsl.txt summary: When hydration, even at a low level, results in a disordered structure, as opposed to the highly ordered structure of dry hydroxychloroquine sulfate, the activation barriers for the rotation of methyl groups in the drug molecules become randomized and, on average, significantly reduced. The free base HCQ and more ordered hydrated HCQS also show the methyl rotation peak at the same position, in agreement with their similar activation energies (for the broad dynamic component) presented in Figure 7 . This suggests that the effect of hydration on the activation energy for the methyl group rotation may be due to the disorder introduced by the water molecules in the main hydrated and less ordered hydrated HCQS samples. While the upper panels of Figures 10 and 11 show the measured spectra, the lower panels present a comparison of the difference spectra between the main hydrated and dry HCQS samples to the spectra of H 2 O ice-Ih (5 K) and liquid water (295 K) as well as the structural H 2 O in WO 3 ·H 2 O data. abstract: [Image: see text] Chloroquine and its derivative hydroxychloroquine are primarily known as antimalaria drugs. Here, we investigate the influence of hydration water on the molecular dynamics in hydroxychloroquine sulfate, a commonly used solubilized drug form. When hydration, even at a low level, results in a disordered structure, as opposed to the highly ordered structure of dry hydroxychloroquine sulfate, the activation barriers for the rotation of methyl groups in the drug molecules become randomized and, on average, significantly reduced. The facilitated stochastic motions of the methyl groups may benefit the biomolecular activity due to the more efficient sampling of the energy landscape in the disordered hydration environment experienced by the drug molecules in vivo. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7423024/ doi: 10.1021/acsomega.0c03091 id: cord-314753-xflhxb13 author: Manso, Carmen F. title: Efficient and unbiased metagenomic recovery of RNA virus genomes from human plasma samples date: 2017-06-23 words: 6333.0 sentences: 296.0 pages: flesch: 48.0 cache: ./cache/cord-314753-xflhxb13.txt txt: ./txt/cord-314753-xflhxb13.txt summary: The percentage of reads mapping to RNA virus genomes in the rRNA-depleted BBV Panel samples was between 40 and 150-fold higher than in corresponding untreated controls. The depth plots in Fig. 3 again show unbiased and even coverages across both genomes, and the percentages of reads mapping to viral targets was again much higher in the rRNA-depleted sample than in the untreated comparator (61-fold and 85-fold for HCV and HPgV respectively). By depleting host-derived nucleic acids and making modifications to an existing library preparation protocol to account for ultra-low RNA input quantities, we have been able to reconstruct effectively full-length genomes of HCV, HEV and HIV from plasma samples with viral loads of 10 4 IU/ml (copies/ml for HIV) and substantial fractions of complete genomes at 10 3 IU/ml. Additionally, our system was able to recover viral sequences from a panel of diverse RNA viruses diluted in human plasma, with a broad correlation between the genomic coverage and depth metrics and approximate concentration. abstract: RNA viruses cause significant human pathology and are responsible for the majority of emerging zoonoses. Mainstream diagnostic assays are challenged by their intrinsic diversity, leading to false negatives and incomplete characterisation. New sequencing techniques are expanding our ability to agnostically interrogate nucleic acids within diverse sample types, but in the clinical setting are limited by overwhelming host material and ultra-low target frequency. Through selective host RNA depletion and compensatory protocol adjustments for ultra-low RNA inputs, we are able to detect three major blood-borne RNA viruses – HIV, HCV and HEV. We recovered complete genomes and up to 43% of the genome from samples with viral loads of 10(4) and 10(3) IU/ml respectively. Additionally, we demonstrated the utility of this method in detecting and characterising members of diverse RNA virus families within a human plasma background, some present at very low levels. By applying this method to a patient sample series, we have simultaneously determined the full genome of both a novel subtype of HCV genotype 6, and a co-infecting human pegivirus. This method builds upon earlier RNA metagenomic techniques and can play an important role in the surveillance and diagnostics of blood-borne viruses. url: https://www.ncbi.nlm.nih.gov/pubmed/28646219/ doi: 10.1038/s41598-017-02239-5 id: cord-002178-ggtxuulg author: Mauk, Michael G. title: Integrated Microfluidic Nucleic Acid Isolation, Isothermal Amplification, and Amplicon Quantification date: 2015-10-20 words: 5753.0 sentences: 257.0 pages: flesch: 39.0 cache: ./cache/cord-002178-ggtxuulg.txt txt: ./txt/cord-002178-ggtxuulg.txt summary: A portable, miniaturized POC NAAT with performance comparable to conventional PCR (polymerase-chain reaction)-based tests in clinical laboratories can be realized with a disposable, palm-sized, plastic microfluidic chip in which: (1) nucleic acids (NAs) are extracted from relatively large (~mL) volume sample lysates using an embedded porous silica glass fiber or cellulose binding phase ("membrane") to capture sample NAs in a flow-through, filtration mode; (2) NAs captured on the membrane are isothermally (~65 °C) amplified; (3) amplicon production is monitored by real-time fluorescence detection, such as with a smartphone CCD camera serving as a low-cost detector; and (4) paraffin-encapsulated, lyophilized reagents for temperature-activated release are pre-stored in the chip. abstract: Microfluidic components and systems for rapid (<60 min), low-cost, convenient, field-deployable sequence-specific nucleic acid-based amplification tests (NAATs) are described. A microfluidic point-of-care (POC) diagnostics test to quantify HIV viral load from blood samples serves as a representative and instructive example to discuss the technical issues and capabilities of “lab on a chip” NAAT devices. A portable, miniaturized POC NAAT with performance comparable to conventional PCR (polymerase-chain reaction)-based tests in clinical laboratories can be realized with a disposable, palm-sized, plastic microfluidic chip in which: (1) nucleic acids (NAs) are extracted from relatively large (~mL) volume sample lysates using an embedded porous silica glass fiber or cellulose binding phase (“membrane”) to capture sample NAs in a flow-through, filtration mode; (2) NAs captured on the membrane are isothermally (~65 °C) amplified; (3) amplicon production is monitored by real-time fluorescence detection, such as with a smartphone CCD camera serving as a low-cost detector; and (4) paraffin-encapsulated, lyophilized reagents for temperature-activated release are pre-stored in the chip. Limits of Detection (LOD) better than 10(3) virons/sample can be achieved. A modified chip with conduits hosting a diffusion-mode amplification process provides a simple visual indicator to readily quantify sample NA template. In addition, a companion microfluidic device for extracting plasma from whole blood without a centrifuge, generating cell-free plasma for chip-based molecular diagnostics, is described. Extensions to a myriad of related applications including, for example, food testing, cancer screening, and insect genotyping are briefly surveyed. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4996405/ doi: 10.3390/microarrays4040474 id: cord-003640-psnec2qp author: Mbareche, Hamza title: Bioaerosols Play a Major Role in the Nasopharyngeal Microbiota Content in Agricultural Environment date: 2019-04-16 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Background: Bioaerosols are a major concern for public health and sampling for exposure assessment purposes is challenging. The nasopharyngeal region could be a potent carrier of long-term bioaerosol exposure agents. This study aimed to evaluate the correlation between nasopharyngeal bacterial flora of swine workers and the swine barns bioaerosol biodiversity. Methods: Air samples from eight swine barns as well as nasopharyngeal swabs from pig workers (n = 25) and from a non-exposed control group (n = 29) were sequenced using 16S rRNA gene high-throughput sequencing. Wastewater treatment plants were used as the industrial, low-dust, non-agricultural environment control to validate the microbial link between the bioaerosol content (air) and the nasopharynxes of workers. Results: A multivariate analysis showed air samples and nasopharyngeal flora of pig workers cluster together, compared to the non-exposed control group. The significance was confirmed with the PERMANOVA statistical test (p-value of 0.0001). Unlike the farm environment, nasopharynx samples from wastewater workers did not cluster with air samples from wastewater treatment plants. The difference in the microbial community of nasopharynx of swine workers and a control group suggest that swine workers are carriers of germs found in bioaerosols. Conclusion: Nasopharynx sampling and microbiota could be used as a proxy of air sampling for exposure assessment studies or for the determination of exposure markers in highly contaminated agricultural environments. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6518280/ doi: 10.3390/ijerph16081375 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-288202-r3r2bc7v author: Morel, Noelia title: A Monoclonal Antibody-Based Copro-ELISA Kit for Canine Echinococcosis to Support the PAHO Effort for Hydatid Disease Control in South America date: 2013-01-10 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Cystic echinococcosis is still a major concern in South America. While some regions show advances in the control of the disease, others have among the highest incidence in the world. To reverse this situation the Pan American Health Organization (PAHO) has launched a regional project on cystic echinococcosis control and surveillance. An early concern of the program was the lack of a standardized diagnostic tool to monitor infection in dogs, a key target of control programs. Under this premise, we have developed a new copro-ELISA test after extensive screening of a large panel of monoclonal antibodies (MAbs) and polyclonal sera, which performs with high standards of sensitivity (92.6%) and specificity (86.4%) as established by necropsy diagnosis of dogs. The key component of the test, MAbEg9 has a convenient IgG isotype and reacts with a periodate-resistant epitope found in high molecular weight components of the worm. Time-course analysis of experimentally infected dogs showed that even animals with a very low number of parasites could be detected as early as day 20 post infection. The test was formulated in a ready-to-use kit format with proven stability of each component for a minimum of 3 months at room temperature. This characteristic facilitates its standardized use and shipping to other laboratories, which was demonstrated by the identical results obtained by two different laboratories in Peru and our own laboratory when a large number of field samples were analyzed independently in a blind fashion. url: https://www.ncbi.nlm.nih.gov/pubmed/23326610/ doi: 10.1371/journal.pntd.0001967 id: cord-002560-pue5q5wp author: Moreno, Paloma S. title: Characterisation of the canine faecal virome in healthy dogs and dogs with acute diarrhoea using shotgun metagenomics date: 2017-06-01 words: 5137.0 sentences: 265.0 pages: flesch: 50.0 cache: ./cache/cord-002560-pue5q5wp.txt txt: ./txt/cord-002560-pue5q5wp.txt summary: Recently, due to the advent of molecular enrichment protocols, high throughput sequencing and new metagenomic analytical methods we are now able to explore, identify and characterise viruses from different biological and environmental samples with a greater capacity [2, [5] [6] [7] [8] [9] [10] [11] In studies of human faeces, the virome has been shown to include viruses that infect eukaryotic organisms and viruses that infect prokaryotes (bacteriophages) [2, 5, [12] [13] [14] [15] [16] [17] [18] . Another eukaryotic viral family found in one healthy dog sample was Parvoviridae, genetic analysis of the 3 contigs/singletons showed a coverage of approximately 3.5% of the complete genome of canine parvovirus reference sequence (NC_001539), or 9.3% of the polyprotetin Ns1-Ns2. Nucleic acids from a single faecal sample from a dog with acute diarrhoea (DD1), which had 18 contigs/singletons of canine astrovirus (after tBLASTx analysis) was used to determine the complete genome sequence. abstract: The virome has been increasingly investigated in numerous animal species and in different sites of the body, facilitating the identification and discovery of a variety of viruses. In spite of this, the faecal virome of healthy dogs has not been investigated. In this study we describe the faecal virome of healthy dogs and dogs with acute diarrhoea in Australia, using a shotgun metagenomic approach. Viral sequences from a range of different virus families, including both RNA and DNA families, and known pathogens implicated in enteric disease were documented. Twelve viral families were identified, of which four were bacteriophages. Eight eukaryotic viral families were detected: Astroviridae, Coronaviridae, Reoviridae, Picornaviridae, Caliciviridae, Parvoviridae, Adenoviridae and Papillomaviridae. Families Astroviridae, Picornaviridae and Caliciviridae were found only in dogs with acute diarrhoea, with Astroviridae being the most common family identified in this group. Due to its prevalence, characterisation the complete genome of a canine astrovirus was performed. These studies indicate that metagenomic analyses are useful for the investigation of viral populations in the faeces of dogs. Further studies to elucidate the epidemiological and biological relevance of these findings are warranted. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5453527/ doi: 10.1371/journal.pone.0178433 id: cord-263831-7aj9ozpn author: Mutzel, P. title: Increasing Virus Test Capacity via Recursive Pool Testing with an Application to SARS-CoV-2 Testing date: 2020-07-04 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: In the context of adequate reactions to the current Covid-19 pandemic, Seifried, Ciesek et al. [6, 5] have proposed the application of SARS-CoV-2 pool testing in the pursuit of increasing testing capacity. We show how this method can be substantially improved in realistic scenarios, and we point out a possible impact on the ongoing discussion concerning the need of increased testing as a complementary measure to relaxed restrictions. url: https://doi.org/10.1101/2020.07.02.20144956 doi: 10.1101/2020.07.02.20144956 id: cord-326133-d46wbfrx author: Nakayasu, Ernesto S. title: MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses date: 2016-05-10 words: 6104.0 sentences: 271.0 pages: flesch: 39.0 cache: ./cache/cord-326133-d46wbfrx.txt txt: ./txt/cord-326133-d46wbfrx.txt summary: We then applied this methodology and integrated proteomic, lipidomic, and metabolomic analyses in the study of Middle East respiratory syndrome coronavirus (MERS-CoV) infections in a lung epithelial cell line, which showed the impact of viral infection on different host metabolic pathways. We then evaluated if these protein losses affected the ability to obtain useful proteomic data, since a method that can simultaneously extract multiple omics sources from the same sample would be extremely useful for systems biology experiments and subsequent integrated data analysis, as well as in cases where limited sample amounts are available (e.g., a survey of data from the National Cancer Institute showed that obtaining an adequate number of samples to conduct a study is a major difficulty facing researchers [21] ). abstract: Integrative multi-omics analyses can empower more effective investigation and complete understanding of complex biological systems. Despite recent advances in a range of omics analyses, multi-omic measurements of the same sample are still challenging and current methods have not been well evaluated in terms of reproducibility and broad applicability. Here we adapted a solvent-based method, widely applied for extracting lipids and metabolites, to add proteomics to mass spectrometry-based multi-omics measurements. The metabolite, protein, and lipid extraction (MPLEx) protocol proved to be robust and applicable to a diverse set of sample types, including cell cultures, microbial communities, and tissues. To illustrate the utility of this protocol, an integrative multi-omics analysis was performed using a lung epithelial cell line infected with Middle East respiratory syndrome coronavirus, which showed the impact of this virus on the host glycolytic pathway and also suggested a role for lipids during infection. The MPLEx method is a simple, fast, and robust protocol that can be applied for integrative multi-omic measurements from diverse sample types (e.g., environmental, in vitro, and clinical). IMPORTANCE In systems biology studies, the integration of multiple omics measurements (i.e., genomics, transcriptomics, proteomics, metabolomics, and lipidomics) has been shown to provide a more complete and informative view of biological pathways. Thus, the prospect of extracting different types of molecules (e.g., DNAs, RNAs, proteins, and metabolites) and performing multiple omics measurements on single samples is very attractive, but such studies are challenging due to the fact that the extraction conditions differ according to the molecule type. Here, we adapted an organic solvent-based extraction method that demonstrated broad applicability and robustness, which enabled comprehensive proteomics, metabolomics, and lipidomics analyses from the same sample. Author Video: An author video summary of this article is available. url: https://www.ncbi.nlm.nih.gov/pubmed/27822525/ doi: 10.1128/msystems.00043-16 id: cord-307874-0obomty2 author: Pardon, Bart title: Bovine Respiratory Disease Diagnosis: What Progress Has Been Made in Infectious Diagnosis? date: 2020-05-23 words: 7061.0 sentences: 388.0 pages: flesch: 43.0 cache: ./cache/cord-307874-0obomty2.txt txt: ./txt/cord-307874-0obomty2.txt summary: Evidence-based guidelines for precise interpretation of microbiologic tests results are lacking; however, approaches that have been practically useful for the management of bovine respiratory disease outbreaks are presented. However, naturally resistant to fluoroquinolones 71 Escherichia coli, Gallibacterium anatis, Enterobacter hormaechei, staphylococci, streptococci, fungi Secondary Single reports on cattle-specific strains isolated in pure culture in an outbreak of pneumonia in calves 52, [72] [73] [74] Multiple other bacterial species can be detected in the bovine respiratory tract. 10, 35, 54 However, with current knowledge on the interpretation of DNS results at the individual or group level, samples of the lower respiratory tract are likely a better option to evaluate potential involvement of opportunistic pathogens. In the example where the pathogen is causing the disease in 100% of affected calves, the risk of not finding an infected animal after sampling n cases is (1-Se)n , where Se is the test sensitivity. abstract: When it is desired to identify infectious agents involved in an outbreak of bovine respiratory disease, a variety of possible sampling methods may be used. For field use, the deep nasopharyngeal swab, transtracheal wash, and nonendoscopic bronchoalveolar lavage are most feasible. At present, bacterial culture and polymerase chain reaction testing are most commonly used to identify infectious agents. Interpretation of test results can be challenging, particularly for opportunistic pathogens. Evidence-based guidelines for precise interpretation of microbiologic tests results are lacking; however, approaches that have been practically useful for the management of bovine respiratory disease outbreaks are presented. url: https://api.elsevier.com/content/article/pii/S0749072020300220 doi: 10.1016/j.cvfa.2020.03.005 id: cord-254963-cnvxlv6h author: Paskey, Adrian C. title: Enrichment post-library preparation enhances the sensitivity of high-throughput sequencing-based detection and characterization of viruses from complex samples date: 2019-02-26 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Sequencing-based detection and characterization of viruses in complex samples can suffer from lack of sensitivity due to a variety of factors including, but not limited to, low titer, small genome size, and contribution of host or environmental nucleic acids. Hybridization-based target enrichment is one potential method for increasing the sensitivity of viral detection via high-throughput sequencing. RESULTS: This study expands upon two previously developed panels of virus enrichment probes (for filoviruses and for respiratory viruses) to include other viruses of biodefense and/or biosurveillance concern to the U.S. Department of Defense and various international public health agencies. The newly expanded and combined panel is tested using carefully constructed synthetic metagenomic samples that contain clinically relevant amounts of viral genetic material. Target enrichment results in a dramatic increase in sensitivity for virus detection as compared to shotgun sequencing, yielding full, deeply covered viral genomes from materials with Ct values suggesting that amplicon sequencing would be likely to fail. Increased pooling to improve cost- and time-effectiveness does not negatively affect the ability to obtain full-length viral genomes, even in the case of co-infections, although as expected, it does decrease depth of coverage. CONCLUSIONS: Hybridization-based target enrichment is an effective solution to obtain full-length viral genomes for samples from which virus detection would fail via unbiased, shotgun sequencing or even via amplicon sequencing. As the development and testing of probe sets for viral target enrichment expands and continues, the application of this technique, in conjunction with deeper pooling strategies, could make high-throughput sequencing more economical for routine use in biosurveillance, biodefense and outbreak investigations. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-019-5543-2) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1186/s12864-019-5543-2 doi: 10.1186/s12864-019-5543-2 id: cord-319685-dw0qsl4s author: Porter, Emily title: Amino acid changes in the spike protein of feline coronavirus correlate with systemic spread of virus from the intestine and not with feline infectious peritonitis date: 2014-04-25 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Recent evidence suggests that a mutation in the spike protein gene of feline coronavirus (FCoV), which results in an amino acid change from methionine to leucine at position 1058, may be associated with feline infectious peritonitis (FIP). Tissue and faecal samples collected post mortem from cats diagnosed with or without FIP were subjected to RNA extraction and quantitative reverse-transcriptase polymerase chain reaction (qRT-PCR) to detect FCoV RNA. In cats with FIP, 95% of tissue, and 81% of faecal samples were PCR-positive, as opposed to 22% of tissue, and 60% of faecal samples in cats without FIP. Relative FCoV copy numbers were significantly higher in the cats with FIP, both in tissues (P < 0.001) and faeces (P = 0.02). PCR-positive samples underwent pyrosequencing encompassing position 1058 of the FCoV spike protein. This identified a methionine codon at position 1058, consistent with the shedding of an enteric form of FCoV, in 77% of the faecal samples from cats with FIP, and in 100% of the samples from cats without FIP. In contrast, 91% of the tissue samples from cats with FIP and 89% from cats without FIP had a leucine codon at position 1058, consistent with a systemic form of FCoV. These results suggest that the methionine to leucine substitution at position 1058 in the FCoV spike protein is indicative of systemic spread of FCoV from the intestine, rather than a virus with the potential to cause FIP. url: https://www.ncbi.nlm.nih.gov/pubmed/24767677/ doi: 10.1186/1297-9716-45-49 id: cord-313887-8sabsrgy author: Quandt, Sara A. title: COVID-19 Pandemic among Latinx Farmworker and Nonfarmworker Families in North Carolina: Knowledge, Risk Perceptions, and Preventive Behaviors date: 2020-08-10 words: 7451.0 sentences: 353.0 pages: flesch: 50.0 cache: ./cache/cord-313887-8sabsrgy.txt txt: ./txt/cord-313887-8sabsrgy.txt summary: Taken together, the rapidly changing messages, coupled with public concern, and limited availability of up-to-date information in formats for those with limited English proficiency created a situation in the USA in which Latinx workers such as farmworkers were likely to lack consistent and accurate information and, as a result, practice ineffective behaviors to protect themselves and prevent spreading disease to their social network. This study was designed to describe the knowledge, perceived risk and susceptibility, and preventive behaviors reported by Latinx immigrant farmworker and nonfarmworker families in North Carolina during the first months of the COVID-19 pandemic. In total, these results indicate that, despite relatively high knowledge, strong perceptions of risk from COVID-19, and claims of avoiding situations where contracting or spreading infection might be likely, many of the farmworker families included here do not practice safe physical distancing measures as recommended; and their use of masks appears to be confined to work settings. abstract: (1) Background: The COVID-19 pandemic poses substantial threats to Latinx farmworkers and other immigrants in food production and processing. Classified as essential, such workers cannot shelter at home. Therefore, knowledge and preventive behaviors are important to reduce COVID-19 spread in the community. (2) Methods: Respondents for 67 families with at least one farmworker (FWF) and 38 comparable families with no farmworkers (nonFWF) in North Carolina completed a telephone survey in May 2020. The survey queried knowledge of COVID-19, perceptions of its severity, self-efficacy, and preventive behaviors. Detailed data were collected to document household members’ social interaction and use of face coverings. (3) Results: Knowledge of COVID-19 and prevention methods was high in both groups, as was its perceived severity. NonFWF had higher self-efficacy for preventing infection. Both groups claimed to practice preventive behaviors, though FWF emphasized social avoidance and nonFWF emphasized personal hygiene. Detailed social interactions showed high rates of inter-personal contact at home, at work, and in the community with more mask use in nonFWF than FWF. (4) Conclusions: Despite high levels of knowledge and perceived severity for COVID-19, these immigrant families were engaged in frequent interpersonal contact that could expose community members and themselves to COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32785108/ doi: 10.3390/ijerph17165786 id: cord-303647-c4umbcvn author: Reed, Patricia E. title: A New Approach for Monitoring Ebolavirus in Wild Great Apes date: 2014-09-18 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Central Africa is a “hotspot” for emerging infectious diseases (EIDs) of global and local importance, and a current outbreak of ebolavirus is affecting multiple countries simultaneously. Ebolavirus is suspected to have caused recent declines in resident great apes. While ebolavirus vaccines have been proposed as an intervention to protect apes, their effectiveness would be improved if we could diagnostically confirm Ebola virus disease (EVD) as the cause of die-offs, establish ebolavirus geographical distribution, identify immunologically naïve populations, and determine whether apes survive virus exposure. METHODOLOGY/PRINCIPAL FINDINGS: Here we report the first successful noninvasive detection of antibodies against Ebola virus (EBOV) from wild ape feces. Using this method, we have been able to identify gorillas with antibodies to EBOV with an overall prevalence rate reaching 10% on average, demonstrating that EBOV exposure or infection is not uniformly lethal in this species. Furthermore, evidence of antibodies was identified in gorillas thought previously to be unexposed to EBOV (protected from exposure by rivers as topological barriers of transmission). CONCLUSIONS/SIGNIFICANCE: Our new approach will contribute to a strategy to protect apes from future EBOV infections by early detection of increased incidence of exposure, by identifying immunologically naïve at-risk populations as potential targets for vaccination, and by providing a means to track vaccine efficacy if such intervention is deemed appropriate. Finally, since human EVD is linked to contact with infected wildlife carcasses, efforts aimed at identifying great ape outbreaks could have a profound impact on public health in local communities, where EBOV causes case-fatality rates of up to 88%. url: https://www.ncbi.nlm.nih.gov/pubmed/25232832/ doi: 10.1371/journal.pntd.0003143 id: cord-305282-x2zzzw43 author: SUEN, C. Y. title: Feasibility of Reusing Surgical Mask Under Different Disinfection Treatments date: 2020-05-20 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The possibility to extend the lifespan or even reuse one-off personal protective equipment, especially for N95 respirator and surgical mask become critical during pandemic. World Health Organization has confirmed that wearing surgical mask is effective in controlling the spread of respiratory diseases in the community, but the supply may not be able to satisfy all the demands created all over the world in a short period of time. This investigation found that dry heat and UVC irradiance could effectively disinfect the mask material without creating significant damage to surgical mask. url: http://medrxiv.org/cgi/content/short/2020.05.16.20102178v1?rss=1 doi: 10.1101/2020.05.16.20102178 id: cord-001207-yjaiybwf author: Sachsenröder, Jana title: The General Composition of the Faecal Virome of Pigs Depends on Age, but Not on Feeding with a Probiotic Bacterium date: 2014-02-19 words: 5919.0 sentences: 302.0 pages: flesch: 49.0 cache: ./cache/cord-001207-yjaiybwf.txt txt: ./txt/cord-001207-yjaiybwf.txt summary: faecium) NCIMB 10415 on the pig faecal virome composition was analysed in a pig feeding trial with sows and their piglets, which received either the probiotic bacterium or not. RESULTS: From 8 pooled faecal samples derived from the feeding trial, DNA and RNA virus particles were prepared and subjected to process-controlled Next Generation Sequencing resulting in 390,650 sequence reads. However, it is not known so far, whether probiotic bacteria can also influence the general composition of the faecal virome, e.g. by changing the composition of the bacterial community, which represents the host population for bacteriophages, or by direct interactions with specific viruses. Faecal samples from sows and their piglets experimentally fed with or without the probiotic bacterium were analyzed using a process-controlled deep sequencing method. As the detection rate of the bacteriophages is -besides technical factors -also dependent on the amount of viruses initially present in the analyzed sample, improved deep sequencing methods enabling quantitative analyses should be developed in future for comparative virome investigations. abstract: BACKGROUND: The pig faecal virome, which comprises the community of viruses present in pig faeces, is complex and consists of pig viruses, bacteriophages, transiently passaged plant viruses and other minor virus species. Only little is known about factors influencing its general composition. Here, the effect of the probiotic bacterium Enterococcus faecium (E. faecium) NCIMB 10415 on the pig faecal virome composition was analysed in a pig feeding trial with sows and their piglets, which received either the probiotic bacterium or not. RESULTS: From 8 pooled faecal samples derived from the feeding trial, DNA and RNA virus particles were prepared and subjected to process-controlled Next Generation Sequencing resulting in 390,650 sequence reads. In average, 14% of the reads showed significant sequence identities to known viruses. The percentage of detected mammalian virus sequences was highest (55–77%) in the samples of the youngest piglets and lowest (8–10%) in the samples of the sows. In contrast, the percentage of bacteriophage sequences increased from 22–44% in the youngest piglets to approximately 90% in the sows. The dominating mammalian viruses differed remarkably among 12 day-old piglets (kobuvirus), 54 day-old piglets (boca-, dependo- and pig stool-associated small circular DNA virus [PigSCV]) and the sows (PigSCV, circovirus and “circovirus-like” viruses CB-A and RW-A). In addition, the Shannon index, which reflects the diversity of sequences present in a sample, was generally higher for the sows as compared to the piglets. No consistent differences in the virome composition could be identified between the viromes of the probiotic bacterium-treated group and the control group. CONCLUSION: The analysis indicates that the pig faecal virome shows a high variability and that its general composition is mainly dependent on the age of the pigs. Changes caused by feeding with the probiotic bacterium E. faecium could not be demonstrated using the applied metagenomics method. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3929612/ doi: 10.1371/journal.pone.0088888 id: cord-275360-uphdzj5l author: Sahajpal, Nikhil Shri title: Proposal of Reverse Transcription-PCR–Based Mass Population Screening for SARS-CoV-2 (COVID-19) date: 2020-07-30 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Testing for SARS-CoV-2 has lagged behind in many countries due to lack of adequate test kits and bottlenecks in the analytical process. The aim of this study was to investigate the feasibility and accuracy of a sample pooling approach for wide-scale population screening for COVID-19. A total of 940 nasopharyngeal-swab samples (934 negative and 6 positive) previously tested for SARS-CoV-2 were de-identified and assigned random numbers for analysis. From this, 94 pools of 10 samples each were created. Automated RNA extraction followed by RT-PCR was carried out in a 96 well plate. Positive pools were identified and the individual samples were re-analyzed. url: https://www.sciencedirect.com/science/article/pii/S1525157820304074?v=s5 doi: 10.1016/j.jmoldx.2020.07.001 id: cord-301991-n87le8ix author: Saxena, Abhishek title: Diatoms recovery from wastewater: Overview from an ecological and economic perspective date: 2020-10-16 words: 9968.0 sentences: 533.0 pages: flesch: 40.0 cache: ./cache/cord-301991-n87le8ix.txt txt: ./txt/cord-301991-n87le8ix.txt summary: Because diatoms produce organic matter to a large extent that permits natural inbuilt capacity to withstand toxicity levels in water bodies, extended survival rate, short regeneration time than microalgae, fishes, and other micro invertebrates thus making them one of the best candidate for water quality monitoring, and excellent bioindicators of aquatic biological integrity [12, 13] . Isolation and identification of benthic diatoms are problematic in comparison with planktonic species due to difficulties in sample treatment, sampling, and microscopic observation though benthic diatoms play the main role as bioindicators in the aquatic ecosystem because they attached to the substratum with secreted mucilage from their cell wall [44, 45] . An outline of isolation of pure diatom species getting affected by the surrounding contaminants is challenging since they get heavily occupied with different interfering organisms, which pose a significant threat in obtaining axenic culture, as presented in Fig. 3 . abstract: Alarming water pollution is toxic to the aquatic ecosystem leading to a sharp decline in species diversity. Diatoms have great potency to survive in contaminated water bodies, hence they can be compelling bioindicators to monitor the change in the environmental matrices effectively. Around the globe, researchers are intended to evaluate the impact of pollution on the diatoms recovery and techniques used for the assessment. The diatoms are precious for futuristic need viz. value-added products, energy generation, pharmaceuticals, and aquaculture feedstocks. All these applications led to a significant rise in diatoms research among the scientific community. This review presents different isolation practices, cultivation, and other challenges associated with the diatoms. A precise focus is given to diatoms isolation techniques from highly polluted water bodies with the main thrust towards obtaining an axenic culture to elucidate the significance of pure diatom cultures. Recovery of “jewels of the sea” from polluted water signifies the prospective ecological and economic aspects. url: https://www.sciencedirect.com/science/article/pii/S2214714420305833 doi: 10.1016/j.jwpe.2020.101705 id: cord-336103-ufvq0ngl author: Sharma, R. title: Optimal sample pooling: an efficient tool against SARS-CoV-2 date: 2020-07-04 words: 1563.0 sentences: 125.0 pages: flesch: 64.0 cache: ./cache/cord-336103-ufvq0ngl.txt txt: ./txt/cord-336103-ufvq0ngl.txt summary: 2, 3 To identify such cases, the World Health Organization has stressed on multiple occasions the significant role of sample testing. While the current guidelines from ICMR state that up to 5 samples can be pooled, 20 multiple studies have confirmed that the pooling size of up to 8 does not harm the specificity and the sensitivity of the test. The determination of sample pool size for each lab using its prevalence rate would yield desired efficiency and be easy to implement. Strategizing to have a common sample pool size across the nation would not yield optimum results as the variance of prevalence rates is extremely high. Hence, sample pool size should be decided individually for a testing facility using the prevalence rates recorded by the same lab. This prevalence rate can then be looked up on the decision matrix table to arrive at the optimal sample pool size. Pooled Sample Testing for SARS-CoV-2 abstract: The SARS-CoV-2 pandemic situation has presented multiple imminent challenges to the nations around the globe. While health agencies around the world are exploring various options to contain the spread of this fatal viral infection, multiple strategies and guidelines are being issued to boost the fight against the disease. Identifying and isolating infected individuals at an early phase of the disease has been a very successful approach to stop the chain of transmission. But this approach faces a practical challenge of limited resources. Sample pooling solves this enigma by significantly improving the testing capacity and result turn around time while using no extra resources. However, the general sample pooling method also has the scope of significant improvements. This article describes a process to further optimize the resources with optimal sample pooling. This is a user-friendly technique, scalable on a national or international scale. A mathematical model has been built and validated for its performance using clinical data. url: http://medrxiv.org/cgi/content/short/2020.07.03.20145953v1?rss=1 doi: 10.1101/2020.07.03.20145953 id: cord-313107-6cfenpxm author: Singh, Anirudh K. title: Evaluation of pooled sample analysis strategy in expediting case detection in areas with emerging outbreaks of COVID-19: A pilot study date: 2020-09-22 words: 2889.0 sentences: 124.0 pages: flesch: 50.0 cache: ./cache/cord-313107-6cfenpxm.txt txt: ./txt/cord-313107-6cfenpxm.txt summary: In this context, a pooled sample testing strategy was evaluated in the setting of emerging disease outbreak in 3 central Indian districts to assess if the cost of the test and turn-around time could be reduced without compromising its diagnostic characteristics and thus lead to early containment of the outbreak. At the reported point prevalence of 4.8% in this study, the negative predictive value of qRT-PCR on pooled samples was around 96% suggesting that the adoption of this strategy as an effective screening tool for COVID-19 needs to be carefully evaluated. We hypothesized that testing of pooled respiratory samples, collected from potentially infected individuals, could lead to faster laboratory confirmation and quicker containment of the emerging infection in these districts and, thus, undertook this study to evaluate the diagnostic concordance between the strategies of pooled vs. abstract: Timely diagnosis of COVID-19 infected individuals and their prompt isolation are essential for controlling the transmission of SARS-CoV-2. Though quantitative reverse transcriptase PCR (qRT-PCR) is the method of choice for COVID-19 diagnostics, the resource-intensive and time-consuming nature of the technique impairs its wide applicability in resource-constrained settings and calls for novel strategies to meet the ever-growing demand for more testing. In this context, a pooled sample testing strategy was evaluated in the setting of emerging disease outbreak in 3 central Indian districts to assess if the cost of the test and turn-around time could be reduced without compromising its diagnostic characteristics and thus lead to early containment of the outbreak. From 545 nasopharyngeal and oropharyngeal samples received from the three emerging districts, a total of 109 pools were created with 5 consecutive samples in each pool. The diagnostic performance of qRT-PCR on pooled sample was compared with that of individual samples in a blinded manner. While pooling reduced the cost of diagnosis by 68% and the laboratory processing time by 66%, 5 of the 109 pools showed discordant results when compared with induvial samples. Four pools which tested negative contained 1 positive sample and 1 pool which was positive did not show any positive sample on deconvolution. Presence of a single infected sample with Ct value of 34 or higher, in a pool of 5, was likely to be missed in pooled sample analysis. At the reported point prevalence of 4.8% in this study, the negative predictive value of qRT-PCR on pooled samples was around 96% suggesting that the adoption of this strategy as an effective screening tool for COVID-19 needs to be carefully evaluated. url: https://www.ncbi.nlm.nih.gov/pubmed/32960929/ doi: 10.1371/journal.pone.0239492 id: cord-301823-fbeb1nw1 author: Sridhar, Sushmita title: A blueprint for the implementation of a validated approach for the detection of SARS-Cov2 in clinical samples in academic facilities date: 2020-10-21 words: 6118.0 sentences: 309.0 pages: flesch: 51.0 cache: ./cache/cord-301823-fbeb1nw1.txt txt: ./txt/cord-301823-fbeb1nw1.txt summary: Here we describe our experience in establishing a COVID-19 diagnostics laboratory in an academic containment level 2 (CL2) research facility (UK) in which we validated and established a real-time PCR workflow to detect SARS-CoV2 in nose and throat swabs from HCWs. We developed an assay and workflow over eight working days (set-up to validation to screening) that can produce a quantitative diagnostic result ~4 hours after swabbing. Establishing and validating the workflow in our setting Establishing a workflow for SARS-Cov2 qRT-PCR Upon the decision to rapidly establish the qRT-PCR assay we identified several challenges, and these included: a) establishment and validation of a method suitable for diagnostic reporting, b) safe extraction of nucleic acid from a highly transmissible virus, c) accessing reagents required for performing extractions and amplifications, d) establishing a "clean" diagnostic workflow to minimise the risk of contamination, and e) creating a system in which HCWs could be swabbed and the data reported confidentially within a specified timeframe. abstract: The COVID-19 pandemic is expanding at an unprecedented rate. As a result, diagnostic services are stretched to their limit, and there is a clear need for the provision of additional diagnostic capacity. Academic laboratories, many of which are closed due to governmental lockdowns, may be in a position to support local screening capacity by adapting their current laboratory practices. Here, we describe the process of developing a SARS-Cov2 diagnostic workflow in a conventional academic Containment Level 2 laboratory. Our outline includes simple SARS-Cov2 deactivation upon contact, the method for a quantitative real-time reverse transcriptase PCR detecting SARS-Cov2, a description of process establishment and validation, and some considerations for establishing a similar workflow elsewhere. This was achieved under challenging circumstances through the collaborative efforts of scientists, clinical staff, and diagnostic staff to mitigate to the ongoing crisis. Within 14 days, we created a validated COVID-19 diagnostics service for healthcare workers in our local hospital. The described methods are not exhaustive, but we hope may offer support to other academic groups aiming to set up something comparable in a short time frame. url: https://www.ncbi.nlm.nih.gov/pubmed/33134554/ doi: 10.12688/wellcomeopenres.15937.2 id: cord-130198-pyg81vwb author: Tabak, Tom title: Temporal Mental Health Dynamics on Social Media date: 2020-08-30 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: We describe a set of experiments for building a temporal mental health dynamics system. We utilise a pre-existing methodology for distant-supervision of mental health data mining from social media platforms and deploy the system during the global COVID-19 pandemic as a case study. Despite the challenging nature of the task, we produce encouraging results, both explicit to the global pandemic and implicit to a global phenomenon, Christmas Depression, supported by the literature. We propose a methodology for providing insight into temporal mental health dynamics to be utilised for strategic decision-making. url: https://arxiv.org/pdf/2008.13121v3.pdf doi: nan id: cord-294062-3esrg1jw author: Tam, Clarence C. title: Association between semi-quantitative microbial load and respiratory symptoms among Thai military recruits: a prospective cohort study date: 2018-09-14 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Multiplex real-time polymerase chain reaction assays have improved diagnostic sensitivity for a wide range of pathogens. However, co-detection of multiple agents and bacterial colonization make it difficult to distinguish between asymptomatic infection or illness aetiology. We assessed whether semi-quantitative microbial load data can differentiate between symptomatic and asymptomatic states for common respiratory pathogens. METHODS: We obtained throat and nasal swab samples from military trainees at two Thai Army barracks. Specimens were collected at the start and end of 10-week training periods (non-acute samples), and from individuals who developed upper respiratory tract infection during training (acute samples). We analysed the samples using a commercial multiplex respiratory panel comprising 33 bacterial, viral and fungal targets. We used random effects tobit models to compare cycle threshold (Ct) value distributions from non-acute and acute samples. RESULTS: We analysed 341 non-acute and 145 acute swab samples from 274 participants. Haemophilus influenzae type B was the most commonly detected microbe (77.4% of non-acute and 64.8% of acute samples). In acute samples, nine specific microbe pairs were detected more frequently than expected by chance. Regression models indicated significantly lower microbial load in non-acute relative to acute samples for H. influenzae non-type B, Streptococcus pneumoniae and rhinovirus, although it was not possible to identify a Ct-value threshold indicating causal etiology for any of these organisms. CONCLUSIONS: Semi-quantitative measures of microbial concentration did not reliably differentiate between illness and asymptomatic colonization, suggesting that clinical symptoms may not always be directly related to microbial load for common respiratory infections. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12879-018-3358-4) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1186/s12879-018-3358-4 doi: 10.1186/s12879-018-3358-4 id: cord-017543-60q9iecq author: Tian, Wei-Chang title: Microfluidic Applications in Biodefense date: 2008-08-23 words: 16557.0 sentences: 831.0 pages: flesch: 37.0 cache: ./cache/cord-017543-60q9iecq.txt txt: ./txt/cord-017543-60q9iecq.txt summary: Sections cover microscale sample preparation methods; immunomagnetic separations and immunoassays; proteomics; polymerase chain reaction (PCR), quantitative PCR (qPCR) and other nucleic acid amplification methods; DNA microarrays, microelectrophoresis, and finally integrated Lab-on-a-Chip systems. The intent of JBAIDS Block III, Next Generation Diagnostics (NGD), is to establish a new system incorporating the capabilities of Block I and Block II capabilities (Table 10 .1) and adding immunoassay capabilities and the ability to identify up to 50 agents including toxins in 15 minutes using automated, miniaturized sample preparation integrated with analysis for nucleic acids and proteins, in a hand held or smaller format. They will need to be completely automated or simple to use; incorporate advanced technologies including sample preparation starting from primary samples (aerosols, blood, etc.), molecular detection, automation, microfluidics, and bioinformatics; reduce reagent consumption and space requirements; and provide cost and performance advantages compared to present systems. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122129/ doi: 10.1007/978-0-387-09480-9_10 id: cord-317213-vhprfb1o author: Tram, Dai Thien Nhan title: Advances in nanomaterials and their applications in point of care (POC) devices for the diagnosis of infectious diseases date: 2016-09-26 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Nanotechnology has gained much attention over the last decades, as it offers unique opportunities for the advancement of the next generation of sensing tools. Point-of-care (POC) devices for the selective detection of biomolecules using engineered nanoparticles have become a main research thrust in the diagnostic field. This review presents an overview on how the POC-associated nanotechnology, currently applied for the identification of nucleic acids, proteins and antibodies, might be further exploited for the detection of infectious pathogens: although still premature, future integrations of nanoparticles with biological markers that target specific microorganisms will enable timely therapeutic intervention against life-threatening infectious diseases. url: https://www.ncbi.nlm.nih.gov/pubmed/27686397/ doi: 10.1016/j.biotechadv.2016.09.003 id: cord-310061-nro623aa author: Valitutto, Marc T. title: Detection of novel coronaviruses in bats in Myanmar date: 2020-04-09 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The recent emergence of bat-borne zoonotic viruses warrants vigilant surveillance in their natural hosts. Of particular concern is the family of coronaviruses, which includes the causative agents of severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), and most recently, Coronavirus Disease 2019 (COVID-19), an epidemic of acute respiratory illness originating from Wuhan, China in December 2019. Viral detection, discovery, and surveillance activities were undertaken in Myanmar to identify viruses in animals at high risk contact interfaces with people. Free-ranging bats were captured, and rectal and oral swabs and guano samples collected for coronaviral screening using broadly reactive consensus conventional polymerase chain reaction. Sequences from positives were compared to known coronaviruses. Three novel alphacoronaviruses, three novel betacoronaviruses, and one known alphacoronavirus previously identified in other southeast Asian countries were detected for the first time in bats in Myanmar. Ongoing land use change remains a prominent driver of zoonotic disease emergence in Myanmar, bringing humans into ever closer contact with wildlife, and justifying continued surveillance and vigilance at broad scales. url: https://www.ncbi.nlm.nih.gov/pubmed/32271768/ doi: 10.1371/journal.pone.0230802 id: cord-273495-hruq0hdw author: Waffo Tchounga, C.A. title: Composition analysis of falsified chloroquine phosphate samples seized during the COVID-19 pandemic date: 2020-11-12 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The proliferation of falsified medicines can cause serious public health issues, particularly in the context of a global pandemic such as the actual COVID-19 pandemic. Our study involved eight chloroquine phosphate medicines seized in Cameroon, Democratic Republic of Congo and Niger during March and May 2020. These suspect samples were first analyzed in a screening phase using field tools such as handheld Raman spectroscopy (TruScan) and then in a confirmation phase using laboratory tools such as hyperspectral Raman imaging and High Performance Liquid Chromatography (HPLC). The results confirmed the falsified nature of the samples, highlighting the presence of metronidazole at low dose in four samples (16.6, 15.2, 15.2 and 14.5 mg/tab), too low levels of chloroquine in two samples (2.4 and 20.2 mg/tab), and substitution of chloroquine phosphate by paracetamol in one sample (255.7 mg/tab). The results also confirmed that four samples had been adulterated with paracetamol in trace amounts and two of them presented traces of chloramphenicol. url: https://www.sciencedirect.com/science/article/pii/S0731708520316472?v=s5 doi: 10.1016/j.jpba.2020.113761 id: cord-004133-32w6g7qk author: Walker, Faye M. title: Advances in Directly Amplifying Nucleic Acids from Complex Samples date: 2019-09-30 words: 13585.0 sentences: 664.0 pages: flesch: 42.0 cache: ./cache/cord-004133-32w6g7qk.txt txt: ./txt/cord-004133-32w6g7qk.txt summary: Studies were included if they involved direct amplification and detection of genetic material from one of six representative sample types: blood, dried blood spot, serum and plasma, saliva and sputum, swabs, urine, and stool. However, it is important to note that the sensitivity does not necessarily suffer in much more concentrated samples-in Liu et al.''s highly robust two-step amplification process with direct hairpin assembly and HCR-based detection of SNP DNA sequences in 50% (v/v) serum, they achieved a very low LOD of 100 pg [119] . However, it is important to note that the sensitivity does not necessarily suffer in much more concentrated samples-in Liu et al.''s highly robust two-step amplification process with direct hairpin assembly and HCR-based detection of SNP DNA sequences in 50% (v/v) serum, they achieved a very low LOD of 100 pg [119] . abstract: Advances in nucleic acid amplification technologies have revolutionized diagnostics for systemic, inherited, and infectious diseases. Current assays and platforms, however, often require lengthy experimental procedures and multiple instruments to remove contaminants and inhibitors from clinically-relevant, complex samples. This requirement of sample preparation has been a bottleneck for using nucleic acid amplification tests (NAATs) at the point of care (POC), though advances in “lab-on-chip” platforms that integrate sample preparation and NAATs have made great strides in this space. Alternatively, direct NAATs—techniques that minimize or even bypass sample preparation—present promising strategies for developing POC diagnostic tools for analyzing real-world samples. In this review, we discuss the current status of direct NAATs. Specifically, we surveyed potential testing systems published from 1989 to 2017, and analyzed their performances in terms of robustness, sensitivity, clinical relevance, and suitability for POC diagnostics. We introduce bubble plots to facilitate our analysis, as bubble plots enable effective visualization of the performances of these direct NAATs. Through our review, we hope to initiate an in-depth examination of direct NAATs and their potential for realizing POC diagnostics, and ultimately transformative technologies that can further enhance healthcare. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6955841/ doi: 10.3390/bios9040117 id: cord-348464-1c08mb2k author: Winter, Taylor title: Evaluation of the English Version of the Fear of COVID-19 Scale and Its Relationship with Behavior Change and Political Beliefs date: 2020-06-15 words: 3455.0 sentences: 185.0 pages: flesch: 54.0 cache: ./cache/cord-348464-1c08mb2k.txt txt: ./txt/cord-348464-1c08mb2k.txt summary: Consistent with the earlier validation studies, the FCV-19S displayed a moderately strong relationship with the perceived infectability and germ aversion subscales of the perceived vulnerability to disease scale (PVDS). With respect to the motivating role of fear, there was a significant relationship between FCV-19S scores and adherence to the lockdown rules that were implemented in New Zealand. Finally, consistent with recent reports on the politicization of the COVID-19 pandemic, an exploratory question found that participants who rated themselves as more conservative tended to report lower FCV-19S scores. The current study demonstrates that the English version of the COVID-19S is a sound unidimensional scale with robust psychometric properties that can be used with confidence Also shown is the association between FCV-19S and adherence to each rule among English-speaking populations. Validation and psychometric evaluation of the Italian version of the fear of COVID-19 scale abstract: The COVID-19 pandemic has many individuals around the world fearing for their lives. The constant news coverage, rapid transmission, and relatively high mortality rate, make fearfulness a natural response. To assess the fear of COVID-19, the Fear of COVID-19 Scale (FCV-19S) was developed. The primary aim of the present study was to conduct the first psychometric assessment and validation of the English version of the FCV-19S. Two samples were collected in New Zealand. Sample 1 comprised 1624 participants of which 1397 completed all questions and were used in the analyses. Sample 2 comprised 1111 participants of which 1023 completed all questions and were used in the analyses. Several psychometric tests were conducted to ascertain the scale’s reliability and validity. Across both samples, the FCV-19S had high internal consistency. Consistent with the earlier validation studies, the FCV-19S displayed a moderately strong relationship with the perceived infectability and germ aversion subscales of the perceived vulnerability to disease scale (PVDS). Furthermore, FCV-19S scores were negatively correlated with the Warwick-Edinburgh Mental Wellbeing Scale (WEMWBS) scores. With respect to the motivating role of fear, there was a significant relationship between FCV-19S scores and adherence to the lockdown rules that were implemented in New Zealand. Finally, consistent with recent reports on the politicization of the COVID-19 pandemic, an exploratory question found that participants who rated themselves as more conservative tended to report lower FCV-19S scores. The English version of the COVID-19S is a sound unidimensional scale with robust psychometric properties and can be used with confidence among English-speaking populations. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s11469-020-00342-9) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1007/s11469-020-00342-9 doi: 10.1007/s11469-020-00342-9 id: cord-102471-dtukacm7 author: Xu, Y. title: Nanopore metagenomic sequencing of influenza virus directly from respiratory samples: diagnosis, drug resistance and nosocomial transmission date: 2020-04-22 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Background: Influenza virus presents a significant challenge to public health by causing seasonal epidemics and occasional pandemics. Nanopore metagenomic sequencing has the potential to be deployed for near-patient testing, providing rapid diagnosis of infection, rationalising antimicrobial therapy, and supporting interventions for infection control. This study aimed to evaluate the applicability of this sequencing approach as a routine laboratory test for influenza in clinical settings. Methods: We conducted Nanopore metagenomic sequencing for 180 respiratory samples from a UK hospital during the 2018/19 influenza season, and compared results to routine molecular diagnostic testing. We investigated drug resistance, genetic diversity, and nosocomial transmission using influenza sequence data. Results: Metagenomic sequencing was 83% (75/90) sensitive and 93% (84/90) specific for detecting influenza A viruses compared with the diagnostic standard (Cepheid Xpress/BioFire FilmArray Respiratory Panel). We identified a H3N2 genome with the oseltamivir resistant S331R mutation in the NA protein, potentially associated with the emergence of a distinct intra-subtype reassortant. Whole genome phylogeny refuted suspicions of a transmission cluster in the infectious diseases ward, but identified two other clusters that likely reflected nosocomial transmission, associated with a predominant strain circulating in the community. We also detected a range of other potentially pathogenic viruses and bacteria from the metagenome. Conclusion: Nanopore metagenomic sequencing can detect the emergence of novel variants and drug resistance, providing timely insights into antimicrobial stewardship and vaccine design. Generation of full genomes can contribute to the investigation and management of nosocomial outbreaks. url: http://medrxiv.org/cgi/content/short/2020.04.21.20073072v1?rss=1 doi: 10.1101/2020.04.21.20073072 id: cord-011485-15wtv6bt author: Yang, Wenbo title: An immunoassay cassette with a handheld reader for HIV urine testing in point-of-care diagnostics date: 2020-05-21 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Currently, most HIV tests are performed with blood samples, or alternatively saliva samples are used for HIV testing. Simple HIV tests need to be performed in hospitals or other medical agencies instead of more invasive HIV blood tests. To enable point-of-care (POC) HIV diagnostics, based on a recently developed lateral flow strip for HIV urine testing, a microfluidic immunoassay cassette with a handheld optical reader is developed. Based on lateral flow strip with gold colloid reporter, the integrated immunoassay cassette can perform sample introduction, metering, discharging, applying and detection which simplifies HIV testing. An indicator is incorporated into the cassette to guide sample introduction based on color change, and further, the excess test sample is stored inside the sealed cassette to avoid any contamination. The low-cost handheld optical reader can provide a test result within a few seconds, which is useful for simple, sensitive and affordable HIV onsite detection. Instead of using normal white LEDs, a customized back light module embedded with green LEDs is adopted to illuminate the lateral flow strip with an appropriate working current to achieve optimal performance. Compared to the standard lateral flow strips using a benchtop reader, with the disposable immunoassay cassette assisted by the handheld optical reader, more convenient, easier-to-operate, and more affordable HIV urine testing can be achieved in POC diagnostics. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7239691/ doi: 10.1007/s10544-020-00494-4 id: cord-323973-wszo9s3d author: Zhu, Hanliang title: The vision of point-of-care PCR tests for the COVID-19 pandemic and beyond date: 2020-07-20 words: 9784.0 sentences: 493.0 pages: flesch: 50.0 cache: ./cache/cord-323973-wszo9s3d.txt txt: ./txt/cord-323973-wszo9s3d.txt summary: [9] The analysis of larger volumes of biological fluids with a low viral load is likely to reduce the risk of false-negative results, but microfluidic point-of-care (POC) devices are typically unable to handle mL-scale volumes in a short time due to the requirement of slow flow rates. [15] The PCR test on samples prepared from blood and urine specimens is capable of detecting the virus in the early stages of the disease, resulting in early diagnosis and subsequent isolation of infected patients to block transmission. The total reaction time depends on a series of parameters, such as the chip size, the PCR master mix volume determining the value of C, the thermal conductivity of the substrate (G), and the temperature cycling rate. A number of fully integrated systems have so far been developed, starting with the non-portable GenExpert from Cepheid, which was first utilized for anthrax detection by the United States Postal Service, [64] and then with different primers to perform HIV and tuberculosis diagnostics in South Africa. abstract: Infectious diseases, such as the most recent case of COVID-19, have brought the prospect of point-of-care (POC) diagnostic tests into the spotlight. A rapid, accurate, low-cost, and easy-to-use test in the field could stop epidemics before they develop into full-blown pandemics. Unfortunately, despite all the advances, it still does not exist. Here, we critically review the limited number of prototypes demonstrated to date that is based on a polymerase chain reaction (PCR) and has come close to fulfilling this vision. We summarize the requirements for the POC-PCR tests and then go on to discuss the PCR product-detection methods, the integration of their functional components, the potential applications, and other practical issues related to the implementation of lab-on-a-chip technologies. We conclude our review with a discussion of the latest findings on nucleic acid-based diagnosis. url: https://api.elsevier.com/content/article/pii/S0165993620302132 doi: 10.1016/j.trac.2020.115984 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-017248-a37t31u1 author: nan title: Alphabetic Listing of Diseases and Conditions date: 2010-05-17 words: 48753.0 sentences: 4281.0 pages: flesch: 41.0 cache: ./cache/cord-017248-a37t31u1.txt txt: ./txt/cord-017248-a37t31u1.txt summary: Possible Associated Conditions: Disseminated intravascular coagulation;* eclampsia;* glucose-6-phosphatase deficiency (G6PD); hemolytic uremic syndrome;* malignant hypertension; lymphoma* and other malignancies; paroxysmal nocturnal hemo-globinuria; sickle cell disease;*thalassemia;* thrombotic thrombocytopenic purpura.* (See also below under "NOTE.") NOTE: Hemolysis also may be caused by conditions such as poisoning with chemicals or drugs, heat injury, snake bite,* or infections or may develop as a transfusion reaction* or be secondary to adenocarcinoma, heart valve prostheses (see below), liver disease (see below), renal disease, or congenital erythropoietic porphyria. Unusual under-lying or associated conditions include chronic aortic stenosis or regurgitation; coronary artery anomalies; coronary artery dissection; coronary embolism; coronary ostial stenosis (due to calcification of aortic sinotubular junction or, rarely, to syphilitic aortitis); coronary vasculitis (for instance, in polyarteritis nodosa* or acute hypersensitivity arteritis); hyperthyroidism,* gastrointestinal hemorrhage; * hypothyroidism, * idiopathic arterial calcification of infancy; intramural coronary amyloidosis; pheochromocytoma, polycythemia vera; * pseudoxanthoma elasticum,* radiationinduced coronary stenosis; severe pulmonary hypertension (with right ventricular ischemia); sickle cell disease;* and others. abstract: Part II begins with a list of special histologic stains, their for use and their corresponding references. At the end of this list is a procedure for removal of formalin precipitate from tissue sections. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121759/ doi: 10.1007/978-1-59745-127-7_17 id: cord-022147-istz1iql author: nan title: Procedures to Investigate Waterborne Illness date: 2016-07-13 words: 38204.0 sentences: 1874.0 pages: flesch: 50.0 cache: ./cache/cord-022147-istz1iql.txt txt: ./txt/cord-022147-istz1iql.txt summary: • Identifying illness associated with an exposure and verifying that the causative agent is waterborne • Detecting all cases, the causative agent, and the place of exposure • Determining the water source, mode of contamination, processes, or practices by which proliferation and/or survival of the etiological agent occurred • Implementing emergency measures to control the spread of the outbreak • Gathering information on the epidemiology of waterborne diseases and the etiology of the causative agents that can be used for education, training, and program planning, thereby impacting on the prevention of waterborne illness • Determining if the outbreak under investigation is part of a larger outbreak by immediately reporting to state/provincial/national epidemiologists In the instance of a bottled water outbreak, halting of distribution and sale of product and recall of product, some of which may already be in consumers'' homes, are necessary to prevent further illness. abstract: Humanity could not survive without a reliably clean, safe, and steady flow of drinking water. Since the early 1900s when typhoid fever and cholera were frequently causes of waterborne illness in developed countries, drinking water supplies have been protected and treated to ensure water safety, quality, and quantity. Having access to safe drinking water has always been one of the cornerstones of good public health. Not only safe water is limited to drinking water, but recreational water can also be a source for waterborne illness—both from treated waters such as in swimming pools, whirlpools, or splash pads and from non-treated surface waters such as lakes, rivers, streams and ponds. Recreational waters may cause illness not only from ingestion of pathogens, but also when in contact with eyes, ears, or skin. Some pathogens in water can be acquired by inhalation of aerosols from water that is agitated or sprayed such as in humidifiers, fountains, or misting of produce. This poses a potential risk to those exposed, particularly if they are immunocompromised. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7153435/ doi: 10.1007/978-3-319-26027-3_1 id: cord-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-023442-4vzwc2d2 author: nan title: Proceedings of SCANNING 94/SEEMS 94 Charleston, South Carolina, USA date: 2006-12-05 words: 55552.0 sentences: 2821.0 pages: flesch: 48.0 cache: ./cache/cord-023442-4vzwc2d2.txt txt: ./txt/cord-023442-4vzwc2d2.txt summary: IV-4 Scanning Vol. 16, Supplement IV (1994) Simulation of image formation and detection systems in the SEM is a vital link in performing image analysis to obtain precise measurements, to provide the necessary connection between image parameters and structural dimensions, and to reflect important microscope beam and detector parameters. By knowing the transfer function, noise, and distortion figure in digital form, it is relatively easy to obtain more accurate comparison of the measured and calculated signal (Fig. 1 The calculation of image contrast in the scanning electron microscope (SEM) can be done using Monte Carlo techniques if the electron trajectories can be calculated through the composition profiles in the specimen. Specimens providing IV-18 Scanning Vol. 16, Supplement IV (1994) FIG highly redundant structures and relatively smooth fractures, such as cell suspensions or o/w emulsions, were investigated using freeze fracture/replication and ambient temperature transmission electron microscopy (AT-TEM). abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7169609/ doi: 10.1002/sca.4950160315 id: cord-030725-876arxiu author: nan title: September 2020 New in Review date: 2020-08-20 words: 2743.0 sentences: 170.0 pages: flesch: 47.0 cache: ./cache/cord-030725-876arxiu.txt txt: ./txt/cord-030725-876arxiu.txt summary: Researchers assessed nutritional risks among older patients diagnosed with COVID-19 along with their associated clinical outcomes. The NRS 2002 was designed to predict clinical effects of nutritional treatment in hospital settings with two levels: level 1 and level 2 contained factors of BMI status, weight loss history, nutritional intake, and disease severity. Association of work requirements with Supplemental Nutrition Assistance Program participation by race/ ethnicity and disability status, 2013-2017. Dietary patterns studied included the Alternative Healthy Eating Index, Dietary Approaches to Stop Hypertension diet score, and Mediterranean-style, adherence to which was determined via the food frequency questionnaire. Association between lifestyle factors, vitamin and garlic supplementation, and gastric cancer outcomes: A secondary analysis of a randomized clinical trial. A secondary analysis of a randomized controlled trial was performed to examine this issue using a sample of 3,365 participants. Demographic variables taken included age, sex, race/ethnicity, participation in the Supplemental Nutrition Assistance Program, family income level, education of parents, and health insurance status. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7440878/ doi: 10.1016/j.jand.2020.07.010 id: cord-031907-ilhr3iu5 author: nan title: ISEV2020 Abstract Book date: 2020-07-15 words: 200999.0 sentences: 11528.0 pages: flesch: 44.0 cache: ./cache/cord-031907-ilhr3iu5.txt txt: ./txt/cord-031907-ilhr3iu5.txt summary: L.M., and the National Institutes of Health (R35GM119623) to T.R.G. The addition of a size exclusion chromatography step to various urinary extracellular vesicle concentrating methods reveals differences in the small RNA profile Introduction: Urinary extracellular vesicles (EVs) and their RNA cargo are a novel source of biomarkers for various diseases, however non-vesicular RNA (e.g. associated with proteins) is also present within urine. We then evaluated efficiency of heart targeting for eAAV9 or eAAV6 and standard AAV9 or AAV6 encoding for EGFP, mCherry or firefly luciferase in different human cell lines in vitro, in black mouse and in passive immunity nude mouse model in vivo using flow cytometry, confocal microscopy, Langendorff perfusion system and Methods: HLHS patients (n = 3) after Glenn procedure and swine (n = 3) after PAB were given RV injections of allogeneic/xenogeneic MSCs. Donor-specific, HLA-I+, exosomes were isolated from plasma. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7480431/ doi: 10.1080/20013078.2020.1784511 id: cord-032379-pelz3ygf author: nan title: October 2020 New in Review date: 2020-09-21 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7503137/ doi: 10.1016/j.jand.2020.08.011 id: cord-291540-raksomda author: nan title: July 2020 New in Review date: 2020-07-31 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.sciencedirect.com/science/article/pii/S2212267220304494 doi: 10.1016/j.jand.2020.05.005 ==== 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