Summary of your 'study carrel' ============================== This is a summary of your Distant Reader 'study carrel'. The Distant Reader harvested & cached your content into a collection/corpus. It then applied sets of natural language processing and text mining against the collection. The results of this process was reduced to a database file -- a 'study carrel'. The study carrel can then be queried, thus bringing light specific characteristics for your collection. These characteristics can help you summarize the collection as well as enumerate things you might want to investigate more closely. This report is a terse narrative report, and when processing is complete you will be linked to a more complete narrative report. Eric Lease Morgan Number of items in the collection; 'How big is my corpus?' ---------------------------------------------------------- 85 Average length of all items measured in words; "More or less, how big is each item?" ------------------------------------------------------------------------------------ 27252 Average readability score of all items (0 = difficult; 100 = easy) ------------------------------------------------------------------ 48 Top 50 statistically significant keywords; "What is my collection about?" ------------------------------------------------------------------------- 85 sample 21 PCR 15 dna 13 RNA 12 SARS 8 study 7 Fig 6 patient 6 HIV 5 result 5 figure 5 dog 5 cell 4 virus 4 test 4 respiratory 4 method 4 detection 4 blood 4 analysis 4 amplification 3 tissue 3 system 3 pool 3 group 3 disease 3 cat 3 University 3 POC 3 Illumina 3 HCV 3 ELISA 3 COVID-19 2 water 2 viral 2 type 2 surface 2 specie 2 procedure 2 platelet 2 non 2 influenza 2 high 2 expression 2 donor 2 death 2 day 2 covid-19 2 conclusion 2 chip Top 50 lemmatized nouns; "What is discussed?" --------------------------------------------- 8059 sample 7477 % 6055 blood 5420 cell 4057 patient 3873 study 3822 method 3622 ev 3554 result 3101 donor 2603 time 2507 transfusion 2480 analysis 2452 group 2265 disease 2068 test 1987 virus 1950 datum 1907 dog 1896 platelet 1820 detection 1800 system 1758 p 1749 number 1743 level 1702 plasma 1696 day 1682 protein 1651 antibody 1648 case 1473 infection 1421 assay 1404 control 1383 concentration 1373 type 1352 testing 1336 treatment 1318 unit 1241 use 1228 conclusion 1219 water 1184 effect 1164 risk 1161 product 1094 sequence 1089 procedure 1087 donation 1070 reaction 1065 sequencing 1059 rate Top 50 proper nouns; "What are the names of persons or places?" -------------------------------------------------------------- 1356 PCR 1187 RNA 1033 Summary 886 RBC 848 al 705 EV 687 et 660 C 632 . 579 SARS 567 Study 558 AE 537 Background 531 Design 525 HIV 519 mg 491 Case 489 Blood 488 Studies 453 Conclusions 443 Fig 443 ABO 429 CoV-2 428 University 415 RT 403 A 398 - 349 RHD 347 DNA 346 Hb 324 T 311 D 309 EVs 307 MSC 305 USA 291 B 282 Health 279 HCV 268 L 262 Transfusion 260 MS 258 Table 258 COVID-19 247 Rh 247 HLA 240 • 240 M 231 S 227 National 224 PLT Top 50 personal pronouns nouns; "To whom are things referred?" ------------------------------------------------------------- 4209 we 2472 it 886 they 362 them 328 i 132 us 118 he 91 you 86 she 77 one 51 themselves 46 itself 8 her 5 yourself 3 ourselves 3 me 3 him 2 s 2 ours 2 igg4 2 his 2 himself 1 ™ 1 u 1 srbcs 1 sevs 1 o139 1 o103 1 nsp(+)-evs 1 mrnas 1 microev 1 magpixv 1 herself 1 grch37 1 em 1 clustalx 1 ccrcc 1 casp3-/mice 1 casp3-/-mice 1 c.1136c 1 's Top 50 lemmatized verbs; "What do things do?" --------------------------------------------- 50734 be 7160 have 7153 use 2188 show 2021 include 1954 perform 1940 base 1759 compare 1715 identify 1573 detect 1572 increase 1453 do 1451 associate 1366 determine 1351 find 1282 collect 1249 follow 1200 test 1168 provide 1080 report 1063 obtain 1041 require 1025 evaluate 998 develop 963 see 909 reduce 881 derive 873 make 869 observe 827 contain 818 demonstrate 794 treat 780 suggest 756 result 755 isolate 750 indicate 743 describe 740 assess 732 allow 720 measure 712 aim 706 confirm 702 give 648 take 639 receive 623 relate 622 know 620 consider 620 cause 599 investigate Top 50 lemmatized adjectives and adverbs; "How are things described?" --------------------------------------------------------------------- 3921 - 3845 not 2681 high 2245 also 1963 other 1760 low 1736 more 1720 clinical 1668 positive 1486 different 1429 such 1381 however 1339 only 1305 well 1287 human 1270 most 1237 viral 1213 non 1193 specific 1176 anti 1132 significant 1131 negative 977 large 974 first 933 further 919 small 908 as 893 significantly 840 available 837 single 818 then 764 new 751 total 749 respiratory 738 respectively 737 red 734 possible 693 same 677 diagnostic 671 present 658 whole 657 molecular 649 bacterial 635 extracellular 609 several 608 many 603 similar 601 acute 586 common 580 normal Top 50 lemmatized superlative adjectives; "How are things described to the extreme?" ------------------------------------------------------------------------- 337 most 211 least 202 high 190 good 113 Most 68 low 64 large 33 great 20 late 16 small 14 close 12 young 11 long 9 strong 9 old 9 easy 9 bad 8 near 8 big 7 short 7 common 6 early 5 wide 5 simple 5 safe 5 fresh 4 few 4 fast 3 postt 2 weak 2 quick 2 deadly 2 cfDNA 2 AuNPs 1 ≤180 1 ® 1 thick 1 swD 1 strict 1 steep 1 sparse 1 soft 1 sharp 1 severe 1 remote 1 pure 1 poor 1 new 1 narrow 1 ky"-square Top 50 lemmatized superlative adverbs; "How do things do to the extreme?" ------------------------------------------------------------------------ 933 most 171 least 31 well 8 highest 2 hard 1 worst 1 strongest 1 shortest 1 s2&3 1 lowest 1 freshest 1 cm² 1 clustalw 1 close 1 cfdna Top 50 Internet domains; "What Webbed places are alluded to in this corpus?" ---------------------------------------------------------------------------- 71 doi.org 6 github.com 5 www.malariagen.net 5 bit.ly 4 creativecommons.org 3 www.ncbi.nlm.nih.gov 3 nextstrain.org 2 www.mdpi.com 2 www.gisaid.org 2 www.ebi.ac.uk 2 www.arb-silva.de 2 www.cdc.gov 2 www 2 dx.doi.org 2 chao.stat.nthu.edu.tw 1 zha 1 www.worldometers.info 1 www.who.int 1 www.ukev.org.uk 1 www.thingiverse 1 www.rcsb.org 1 www.protocols.io 1 www.nscc.sg 1 www.ncbi.nlm.inh.gov 1 www.microbiomeanalyst.ca 1 www.isbtweb.org 1 www.finngen.fi 1 www.fda.gov 1 www.expertmed.it 1 www.earthmicrobiome.org 1 www.compbio.dundee.ac.uk 1 www.cioms.ch 1 www.ada.org" 1 vakser.compbio.ku.edu 1 va 1 usegalaxy.eu 1 tree.bio.ed.ac.uk 1 sparks-lab.org 1 servicesn.mbi.ucla.edu 1 robetta.bakerlab.org 1 raptorx.uchicago.edu 1 qiita.ucsd.edu 1 qiime.org 1 pubs.acs.org 1 protein.ict.ac.cn 1 prosa.services.came.sb 1 predictprotein.org 1 panther.appliedbiosystems.com 1 mafft.cbrc.jp 1 eufrattool.ecdc.europa.eu Top 50 URLs; "What is hyperlinked from this corpus?" ---------------------------------------------------- 11 http://doi.org/10.1101/2020.09.21.20198838 8 http://doi.org/10.1101/2020.06.09.20126219 7 http://doi.org/10.1101/2020.06.21.20134882 6 http://doi.org/10.1101/2020.04 4 http://doi.org/10.1101/2020.07.02.20144956 4 http://creativecommons.org/licenses/by/4.0/ 3 http://doi.org/10.1101/2020.04.21.20073072 2 http://www.malariagen.net/resource/26 2 http://www.malariagen.net/data/ 2 http://www.ebi.ac.uk/ 2 http://www.arb-silva.de/documentation/release-132/ 2 http://www.CDC.gov 2 http://www 2 http://nextstrain.org/ 2 http://github.com/kern-lab/spaceness/blob/master/slim_recipes/spaceness.slim 2 http://doi.org/10.5281/zenodo.3892637 2 http://doi.org/10.1101/2020.04.23.20077727 2 http://chao.stat.nthu.edu.tw/wordpress/paper/119.pdf 1 http://zha 1 http://www.worldometers.info/coronavirus/#countries 1 http://www.who.int/csr/don/2010_08_06/en/index.html 1 http://www.ukev.org.uk/public-engagementmaterials/ 1 http://www.thingiverse 1 http://www.rcsb.org/structure/3nvq 1 http://www.protocols.io/view/one-pot-ligation-protocol-for-oxford-nanopore-libr 1 http://www.nscc.sg 1 http://www.ncbi.nlm.nih.gov/sra 1 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL13323 1 http://www.ncbi.nlm.nih.gov/ 1 http://www.ncbi.nlm.inh.gov/sra 1 http://www.microbiomeanalyst.ca 1 http://www.mdpi.com/2079-6374/9/4/117/s1 1 http://www.mdpi.com/1999-4915/12/8/841/s1 1 http://www.malariagen.net/data/ag1000g-phase1-ar3 1 http://www.isbtweb.org/working-parties/red-cell-immunogenetics-and-bloodgroup-terminology/ 1 http://www.gisaid.org/ 1 http://www.gisaid.org 1 http://www.finngen.fi/ 1 http://www.fda.gov/medical-devices/emergency-situations-medical-devices/emergencyuse-authorizations#COVID19ivd 1 http://www.expertmed.it 1 http://www.earthmicrobiome.org/emp-standard-protocols/16s/; 1 http://www.compbio.dundee.ac.uk/jpred4/ 1 http://www.cioms.ch/ 1 http://www.ada.org" 1 http://vakser.compbio.ku.edu/resources/gramm/grammx/ 1 http://va 1 http://usegalaxy.eu/ 1 http://tree.bio.ed.ac.uk/software/figtree/ 1 http://sparks-lab.org/server/SPIDER2/ 1 http://servicesn.mbi.ucla.edu/Verify3D/ Top 50 email addresses; "Who are you gonna call?" ------------------------------------------------- 1 kkhafizov@gmail.com Top 50 positive assertions; "What sentences are in the shape of noun-verb-noun?" ------------------------------------------------------------------------------- 12 samples were also 11 samples were not 11 samples were positive 8 study did not 7 cell derived evs 7 patient did not 6 % did not 6 % were female 6 % were male 6 cells were then 6 data are available 6 donors did not 6 levels were significantly 6 proteins were significantly 6 results are available 6 results are consistent 6 samples did not 6 samples were available 6 samples were negative 6 transfusion associated cost 5 cases were positive 5 donors were more 5 evs were also 5 evs were then 5 levels were not 5 methods are available 5 patients are not 5 sample was significantly 5 samples were further 5 samples were then 4 blood is not 4 cell derived vesicles 4 cells were also 4 data are not 4 data were also 4 disease has not 4 evs are able 4 evs were able 4 methods are not 4 patient was not 4 results were available 4 sample does not 4 samples detected positive 4 samples is not 4 samples were still 4 studies are available 4 studies are necessary 4 studies are not 4 studies are underway 4 tests were negative Top 50 negative assertions; "What sentences are in the shape of noun-verb-no|not-noun?" --------------------------------------------------------------------------------------- 3 disease has not yet 2 analysis showed no significant 2 data are not comparable 2 donor has not yet 2 donors were not able 2 levels were not significantly 2 methods are not available 2 patients were not subsequently 2 studies are not available 2 transfusion had no effect 1 % had no change 1 % had no clinical 1 % is not satisfactory 1 analysis showed no correlation 1 antibodies are not commercially 1 antibodies are not detectable 1 antibodies are not generally 1 antibody has not yet 1 antibody is not demonstrable 1 antibody was not reactive 1 blood identified no mutations 1 blood is not always 1 blood is not available 1 blood is not feasible 1 cases was not previously 1 cells are not available 1 cells is not fully 1 cells was not significantly 1 data are not available 1 data are not convenient 1 disease is not well 1 disease is not yet 1 diseases were not reactive 1 dogs had no alterations 1 dogs is not just 1 donor had no identifiable 1 donor reported no clinical 1 donor were not significant 1 donors are not constant 1 donors are not correctly 1 donors reported no significant 1 evs does not significantly 1 evs was not significantly 1 evs were not positive 1 group are not available 1 group is not evident 1 group was not significant 1 groups was not significantly 1 groups were not exactly 1 level is not such A rudimentary bibliography -------------------------- id = cord-103735-nil1vv6h author = Alfano, Niccolo title = Non-invasive surveys of mammalian viruses using environmental DNA date = 2020-03-29 keywords = PCR; RNA; Suppl; dna; sample 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. 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 keywords = PCR; primer; sample; viral 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. 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 keywords = SARS; sample summary = 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 keywords = Anopheles; Locator; figure; location; sample 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) . 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 keywords = respiratory; sample; viral 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. doi = 10.1186/s12879-016-1730-9 id = cord-018761-vm86d4mj author = Bradt, David A. title = Technical Annexes date = 2017-11-08 keywords = bias; case; disease; epidemic; sample summary = 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 keywords = Batrachochytrium; dna; edna; sample 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. doi = 10.1038/s41598-020-66280-7 id = cord-313670-tbah33ro author = Cannovo, Nunzia title = Regulation of Biobanks in Italy date = 2020-09-02 keywords = biological; material; sample 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) . 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 keywords = SARS; autopsy; death; patient; sample summary = 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 keywords = RNA; sample; tissue summary = 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 keywords = SARS; sample 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. 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 keywords = Illumina; PCR; R10.3; barcode; dna; sample summary = 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 keywords = GPS; method; sample summary = 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 keywords = HPV; Note; dna; sample summary = 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 keywords = OTA; biosensor; dna; electrochemical; sample summary = 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 keywords = AMR; Supp; city; figure; sample 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. 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 keywords = Caliciviridae; RNA; RSS; VF14; sample 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 . doi = 10.1080/03079457.2016.1193123 id = cord-345992-3ij1vbqp author = Drosten, Christian title = SARS Molecular Detection External Quality Assurance date = 2004-12-17 keywords = SARS; sample summary = 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 keywords = Fig; covid-19; sample; tissue 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. 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 keywords = group; sample; specie summary = 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 keywords = CADGMM; sample summary = 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 keywords = biopsy; blood; cat; catheter; dog; examination; figure; needle; patient; place; procedure; sample; skin; technique; tube 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. 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 keywords = influenza; sample; virus summary = 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 keywords = number; sample summary = 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 keywords = RNA; Threshold; sample 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. 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 keywords = SARS; peptide; sample; swab summary = 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 keywords = DRS; Illumina; RNA; sample 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%). 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 keywords = Fig; H1N1; PCR; Virochip; read; sample summary = 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 keywords = pool; sample summary = 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 keywords = DRS; E590; Illumina; RNA; sample summary = 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 keywords = AHS; dental; sample; surface summary = 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 keywords = sample 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 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 keywords = Korea; asian; sample summary = 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 keywords = PCR; respiratory; sample summary = 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 keywords = CoV-2; Netherlands; SARS; sample 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). 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 keywords = dna; expression; gene; microarray; sample 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] . 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 keywords = learning; sample; task summary = 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 keywords = CRISPR; CoV-2; PCR; RNA; SARS; covid-19; sample summary = 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 keywords = SARS; dog; sample summary = 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 keywords = Nanopore; influenza; sample; virus 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. 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 keywords = Germany; Mycoplasma; PCR; chick; pheasant; sample 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. 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 keywords = Fig; fox; sample summary = 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 keywords = animal; sample; student 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). 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 keywords = HCQS; figure; hydrated; sample 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. 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 keywords = HCV; HIV; Panel; RNA; sample 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. 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 keywords = PCR; amplification; chip; sample 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. 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 keywords = air; control; farmer; non; pig; sample summary = 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 keywords = Fig; PCR; POC; RNA; amplification; detection; diagnostic; dna; patient; sample; system; test 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). 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 keywords = ELISA; dog; sample summary = 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 keywords = PCR; canine; dog; sample 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. 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 keywords = pool; sample summary = 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 keywords = Fig; MERS; sample 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] ). 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 keywords = PCR; pathogen; respiratory; result; sample 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. 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 keywords = RNA; sample; sequencing; virus summary = 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 keywords = FIP; PCR; cat; sample summary = 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 keywords = COVID-19; family; farmworker; sample 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. 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 keywords = EBOV; Ebola; ape; sample summary = 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 keywords = mask; sample; surgical summary = 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 keywords = NCIMB; sample; virus 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. 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 keywords = SARS; sample summary = 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 keywords = cell; culture; diatom; isolation; microalgae; sample; specie; water 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 . 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 keywords = SARS; sample 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 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 keywords = PCR; pool; sample 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. 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 keywords = Cov2; PCR; SARS; sample 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. 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 keywords = classifier; mental; sample summary = 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 keywords = acute; non; respiratory; sample summary = doi = 10.1186/s12879-018-3358-4 id = cord-017543-60q9iecq author = Tian, Wei-Chang title = Microfluidic Applications in Biodefense date = 2008-08-23 keywords = PCR; amplification; bacillus; detection; device; dna; microfluidic; sample; system 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. 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 keywords = ECM; HIV; POC; detection; dna; lod; sample summary = 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 keywords = Myanmar; SARS; bat; sample summary = 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 keywords = COVID-19; Raman; sample summary = 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 keywords = LAMP; PCR; amplification; blood; detection; direct; dna; sample 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] . 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 keywords = COVID-19; fcv-19s; sample 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 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 keywords = IAV; Nanopore; sample summary = 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 keywords = Fig; HIV; sample; urine summary = 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 keywords = PCR; POC; RNA; chip; dna; sample; system 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. 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 keywords = ABO; AIHA; Alinity; Background; Blood; CD34; Conclusions; DAT; December; HBV; HCV; HDFN; HEV; HIV; HLA; Health; Hospital; January; NAT; National; PBM; PCR; PLT; RBC; RHD; RNA; Red; SCD; Service; Summary; Transfusion; aim; anti; cell; dna; donation; donor; group; method; patient; platelet; result; sample; study; test 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. 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 keywords = ABO; Anti; Background; Blood; CD36; Case; Center; DAT; DTT; Design; FDA; FFP; HBV; HCV; HIV; HLA; Hospital; IPC; MTP; Medical; Medicine; NAT; PCR; PLT; RBC; RHD; Red; Studies; Study; System; TPE; University; WBC; ZIKV; Zika; cd341; cell; conclusion; day; dna; donor; finding; method; patient; platelet; result; sample; table; test; transfusion; type 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). doi = 10.1111/trf.14286 id = cord-017248-a37t31u1 author = nan title = Alphabetic Listing of Diseases and Conditions date = 2010-05-17 keywords = Associated; Related; Synonyms; acute; aortic; artery; autopsy; blood; chapter; chronic; condition; death; disease; external; heart; lung; note; poisoning; possible; procedure; pulmonary; record; sample; study; syndrome; term; tissue; type 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. 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 keywords = Flint; Form; Giardia; Table; case; illness; outbreak; person; sample; source; water 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. 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 keywords = ACTH; CHF; CKCS; CKD; DMVD; ECG; ELISA; IBD; PCR; TLR5; University; Veterinary; blood; cat; concentration; day; disease; dna; dog; group; horse; sample; study; test; time; treatment 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] ! 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 keywords = Carlo; EPMA; Fig; Monte; Mott; SEM; Scanning; Supplement; TEM; USA; Vol; beam; cell; electron; figure; high; image; microscopy; result; sample; section; specimen; structure; study; surface 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). doi = 10.1002/sca.4950160315 id = cord-030725-876arxiu author = nan title = September 2020 New in Review date = 2020-08-20 keywords = analysis; hispanic; sample; study 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. doi = 10.1016/j.jand.2020.07.010 id = cord-031907-ilhr3iu5 author = nan title = ISEV2020 Abstract Book date = 2020-07-15 keywords = CD63; CD81; CD9; CDC; CRC; CSF; ELISA; Exo; Extracellular; GBM; HER2; HIV; Health; Institute; L1CAM; MDA; MSC; NIH; NTA; Nanoparticle; National; PCR; RNA; Research; SEC; TEM; Tau; USA; University; analysis; cancer; cell; conclusion; dna; exosome; expression; high; human; introduction; isolate; marker; method; patient; plasma; protein; result; sample; size; study; summary; vesicle; western 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. doi = 10.1080/20013078.2020.1784511 id = cord-032379-pelz3ygf author = nan title = October 2020 New in Review date = 2020-09-21 keywords = analysis; dietary; sample; study summary = doi = 10.1016/j.jand.2020.08.011 id = cord-291540-raksomda author = nan title = July 2020 New in Review date = 2020-07-31 keywords = analysis; sample; study summary = doi = 10.1016/j.jand.2020.05.005