item: #1 of 85 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: 5923 flesch: 45 summary: Most obvious are age-related differences in the proportion between pig viruses and bacteriophages as well as an increasing diversification of virus species by age. 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. keywords: bacteriophages; faecal; faecium; group; piglets; probiotic; reads; samples; sequences; species; virome; viruses cache: cord-001207-yjaiybwf.txt plain text: cord-001207-yjaiybwf.txt item: #2 of 85 id: cord-002178-ggtxuulg author: Mauk, Michael G. title: Integrated Microfluidic Nucleic Acid Isolation, Isothermal Amplification, and Amplicon Quantification date: 2015-10-20 words: 5757 flesch: 32 summary: Figure 2 shows the results for plasma samples spiked with three different concentrations of HIV virons plus a negative control, indicating a LOD (limit of detection) of 350 copies per mL of plasma sample. These instruments cost over $100,000 and their use is restricted to modern clinical laboratory facilities. Self-contained, fully integrated biochip for sample preparation, polymerase chain reaction amplification, and DNA microarray detection Monitoring systems and quantitative measurement of biomolecules for the management of trauma Microfluidic technology for molecular diagnostics Advances in microfluidic PCR for point-of-care infectious disease diagnostics Antibody production, design and use for biosensor-based applications Point-of-care diagnostics: An advancing sector with nontechnical issues Present technology and future trends in point-of-care microfluidic diagnostics Point-of-care technologies for molecular diagnostics using a drop of blood A handheld flow genetic analysis system (FGAS): Towards rapid, sensitive, quantitative and multiplex molecular diagnosis at the point-of-care level Smartphones for cell and biomolecular detection Microfluidic chip for molecular amplification of influenza A RNA in human respiratory specimens Miniaturized nucleic acid amplification systems for rapid and point-of-care diagnostics: A review Anal Chim Advances in developing HIV-1 viral load assays for resource-limited settings Elevating sampling Rapid development of nucleic acid diagnostics Point of care technologies for HIV Isothermal nucleic acid amplification technologies for point-of-care diagnostics: A critical review An isothermal amplification reactor with an integrated isolation membrane for point-of-care detection of infectious diseases Simultaneous quantification of multiple food-and waterborne pathogens by use of microfluidic quantitative PCR Lab-on-a-chip pathogen sensors for food safety A handheld point-of-care genomic diagnostic system Application of microfluidics in waterborne pathogen monitoring: A review Point-of-care diagnostics for ricin exposure A lab-on-a-chip for detection of nerve agent sarin in blood Capturing cancer: Emerging microfluidic technologies for the capture and characterization of circulating tumor cells Point-of-care rare cell cancer diagnostics Microfluidics for research and applications in oncology Nucleic-acid testing, new platforms and nanotechnology for point-of-decision diagnosis of animal pathogens A microfluidic technique for quantification of steroids in core needle biopsies Microfluidic biosensor for β-Hydroxybutyrate (βHBA) determination of subclinical ketosis diagnosis Microfluidics for food, agriculture and biosystems industries A low-cost microfluidic chip for rapid genotyping of malaria-transmitting mosquitoes A microfluidic platform to isolate avian erythrocytes infected with Plasmodium gallinaceum malaria parasites based on surface morphological changes Simultaneous detection of C-reactive protein and other cardiac markers in human plasma using micromosaic immunoassays and self-regulating microfluidic networks Microfluidic chips for immunoassays Rapid development of real-time RT-PCR assays and positive controls in response to emerging coronavirus 2012 A novel thermostable polymerase for RNA and DNA loop-mediated isothermal amplification (LAMP) keywords: amplification; blood; care; chip; detection; diagnostics; membrane; nucleic; plasma; point; reaction; sample; target; time cache: cord-002178-ggtxuulg.txt plain text: cord-002178-ggtxuulg.txt item: #3 of 85 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: 5140 flesch: 47 summary: Our shotgun metagenomic sequence data indicated that the most frequent RNA viral family in dog samples with acute diarrhoea was Astroviridae, being identified in more than half of the diarrheal samples. Other dog sample had contigs/singletons similar to a canine kobuvirus (JN387133.1), covering 2.2% of complete genome. keywords: acute; astrovirus; canine; contigs; diarrhoea; dogs; faecal; genome; samples; sequences; singletons; viruses cache: cord-002560-pue5q5wp.txt plain text: cord-002560-pue5q5wp.txt item: #4 of 85 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: 4296 flesch: 44 summary: Influenza Other Respir Viruses Study of influenza C virus infection in France Epidemiological information regarding the periodic epidemics of influenza C virus in Japan (1996-2013) and the seroprevalence of antibodies to different antigenic groups Bericht zur Epidemiologie der Influenza in Deutschland Saison on the communicable diseases and related special health issues to be covered by epidemiological surveillance as well as relevant case definitions Diagnostic approach for the differentiation of the pandemic influenza A(H1N1)v virus from recent human influenza viruses by realtime PCR Detection and quantification of influenza C virus in pediatric respiratory specimens by real-time PCR and comparison with infectious viral counts Influenza C virus hemagglutinin: comparison with influenza A and B virus hemagglutinins Age distribution of the antibody to type C influenza virus Detection of influenza C virus by a real-time RT-PCR assay. key: cord-003523-byxuruk1 authors: Fritsch, Annemarie; Schweiger, Brunhilde; Biere, Barbara 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 journal: Euro Surveill DOI: 10.2807/1560-7917.es.2019.24.10.1800174 sha: doc_id: 3523 cord_uid: byxuruk1 INTRODUCTION: keywords: children; detection; infection; influenza; patients; samples; sequences; virus; viruses cache: cord-003523-byxuruk1.txt plain text: cord-003523-byxuruk1.txt item: #5 of 85 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: 10138 flesch: 42 summary: Other important examples related to human health include, the greater differential abundance of Haemophilus influenzae in non-exposed controls (950 sequences in non-exposed control samples vs. 5 in samples from pig farmers), and the differential abundance of Klebsiella in samples from pig farmers (400 sequences in pig farmer samples vs. 3 in non-exposed controls). Other important examples related to human health include, the greater differential abundance of Haemophilus influenzae in non-exposed controls (950 sequences in non-exposed control samples vs. 5 in samples from pig farmers), and the differential abundance of Klebsiella in samples from pig farmers (400 sequences in pig farmer samples vs. 3 in non-exposed controls). keywords: abundance; air samples; bioaerosols; controls; diversity; exposure; flora; microbial; nasopharyngeal; nasopharynx samples; non; pig; pig buildings; pig farmers; samples; test; workers cache: cord-003640-psnec2qp.txt plain text: cord-003640-psnec2qp.txt item: #6 of 85 id: cord-004133-32w6g7qk author: Walker, Faye M. title: Advances in Directly Amplifying Nucleic Acids from Complex Samples date: 2019-09-30 words: 13589 flesch: 39 summary: A Useful Tool for the Surveillance of blaOXA-23-Positive Carbapenem-Resistant Acinetobacter baumannii Flinders technology associates (FTA) filter paper-based DNA extraction with polymerase chain reaction (PCR) for detection of Pneumocystis jirovecii from respiratory specimens of immunocompromised patients Operational feasibility of using loop-mediated isothermal amplification for diagnosis of pulmonary tuberculosis in microscopy centers of developing countries Successful use of saliva without DNA extraction for detection of macrolide-resistant Mycoplasma pneumoniae DNA in children using LNA probe-based real-time PCR Rapid typing of STRs in the human genome by HyBeacon melting Ultra-rapid DNA analysis using HyBeacon probes and direct PCR amplification from saliva Comparison of boiling and robotics automation method in DNA extraction for metagenomic sequencing of human oral microbes Comparison of DNA Extraction Methods in Analysis of Salivary Bacterial Communities Study of inter-and intra-individual variations in the salivary microbiota Microbiological diversity of generalized aggressive periodontitis by 16S rRNA clonal analysis A Sweet Spot for Molecular Diagnostics: Coupling Isothermal Amplification and Strand Exchange Circuits to Diagnosis of mycobacterial infections by nucleic acid amplification: 18-month prospective study Pilot study of a rapid and minimally instrumented sputum sample preparation method for molecular diagnosis of tuberculosis Efficacy of loop mediated isothermal amplification (LAMP) assay for the laboratory identification of Mycobacterium tuberculosis isolates in a resource limited setting A novel and more sensitive loop-mediated isothermal amplification assay targeting IS6110 for detection of Mycobacterium tuberculosis complex Development of an in-house loop-mediated isothermal amplification (LAMP) assay for detection of Mycobacterium tuberculosis and evaluation in sputum samples of Nepalese patients Rapid detection of Mycobacterium tuberculosis by recombinase polymerase amplification Polymerase chain reaction for diagnosis of M. tuberculosis: Comparison of simple boiling and a conventional method for DNA extraction Detection of Mycobacterium tuberculosis in sputum samples by polymerase chain reaction using a simplified procedure Detection of Mycobacterium tuberculosis in clinical samples by two-step polymerase chain reaction and nonisotopic hybridization methods Rapid, simple method for treating clinical specimens containing Mycobacterium tuberculosis to remove DNA for polymerase chain reaction An extremely rapid and simple DNA-release method for detection of M. tuberculosis from clinical specimens Evaluation of a simple loop-mediated isothermal amplification test kit for the diagnosis of tuberculosis Evaluation of the efficacy of five DNA extraction methods for the detection of Mycobacterium tuberculosis DNA in direct and processed sputum by an in-house PCR method Clinical usefulness of multiplex PCR lateral flow in MRSA detection: A novel, rapid genetic testing method Development and evaluation of a rapid multiplex-PCR based system for Mycobacterium tuberculosis diagnosis using sputum samples Polymerase chain reaction for detection of Mycobacterium tuberculosis A simple method for diagnosing M. tuberculosis infection in clinical samples using PCR Self-Collected versus Clinician-Collected Sampling for Chlamydia and Gonorrhea Screening: A Systemic Review and Meta-Analysis Validation of real-time PCR for laboratory diagnosis of Acanthamoeba keratitis Effects of topical anaesthetics and fluorescein on the real-time PCR used for the diagnosis of Herpesviruses and Acanthamoeba keratitis Inhibition of PCR by Aqueous and Vitreous Fluids Use of the polymerase chain reaction to detect Bordetella pertussis in patients with mild or atypical symptoms of infection Diagnostic accuracy of a prototype point-of-care test for ocular chlamydia trachomatis under field conditions in the Gambia and Senegal High-throughput STR analysis for DNA database using direct PCR Multicenter clinical evaluation of the novel Amongst the collection of approaches for direct PCR amplification on saliva samples, those that begin with dried saliva swabs fully circumvent DNA extraction, purification, and quantification [93] . keywords: acid; amplification; assay; blood; clinical; detection; diagnostics; dna; extraction; isothermal; lamp; loop; method; nucleic; pcr; polymerase; reaction; samples; sensitivity; serum; sputum; testing; tests cache: cord-004133-32w6g7qk.txt plain text: cord-004133-32w6g7qk.txt item: #7 of 85 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: 1254 flesch: 49 summary: A novel coronavirus from patients with pneumonia in China First cases of coronavirus disease 2019 (COVID-19) in the WHO European region Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR Quality control implementation for universal characterization of DNA and RNA viruses in clinical respiratory samples using single metagenomic next-generation sequencing workflow Amino acid analysis for the SARS-CoV-2 outbreak Letter to the Editor / Clinical Microbiology and Infection xxx (xxxx) A mean of 19 445 767 reads per sample were generated, of which a mean of 605 243 reads per sample were mapped to the SARS-CoV-2 reference genome. keywords: cov-2; deletion; sample; sars cache: cord-009295-4c0zwhdh.txt plain text: cord-009295-4c0zwhdh.txt item: #8 of 85 id: cord-010092-uftc8inx author: None title: Abstract of 29th Regional Congress of the ISBT date: 2019-06-07 words: 233543 flesch: 50 summary: One central question is the need of individual NAT screening (ID) versus minipool NAT screening (MP) approaches to identify all relevant viremias in blood donors. 3A-S02-03 Background: The screening of blood donors and returning travelers from active transmission areas have highlighted the importance of diagnosis of acute arboviral infections. keywords: abo blood; addition; aims; allele; alloimmunization; analysis; anemia; anti; antibodies; antibody; antigen; apheresis; approach; assay; available; average; background; bacterial; bleeding; blood bank; blood cells; blood center; blood chimerism; blood collection; blood components; blood count; blood culture; blood demand; blood donation; blood donors; blood establishments; blood flow; blood group; blood grouping; blood loss; blood management; blood plasma; blood platelet; blood pressure; blood processing; blood products; blood results; blood safety; blood samples; blood services; blood supply; blood system; blood test; blood transfusion; blood type; blood units; blood volume; care; cases; cause; cell donors; cell transfusion; clinical; concentrates; concentration; conclusions; confirmed; content; control; cord blood; countries; criteria; cross; current; data; day; days; deferral; detection; difference; disease; dna; donations; donor samples; effect; events; evidence; exon; expression; factors; female; ferritin; flow; following; frequency; gel; gene; genotyping; group system; groups; hbv; hcv; health; hemoglobin; hev; history; hiv; hla; hospital; hospital blood; human; identification; igg; impact; incidence; increase; individuals; infection; information; international; iron; laboratory; levels; life; low; major; mean; median; medical; methods; min; ml blood; model; molecular; months; n =; national; need; negative; new; non; number; order; overall; p =; patients; pcr; pcs; period; phenotype; plasma; plasma donors; plasma transfusion; platelet; platelet donors; platelet transfusion; population; positive; post; potential; practice; presence; present; prevalence; procedure; process; production; quality; quality blood; range; rate; rbc blood; rbc transfusion; rbcs; reactive; red; reduced; repeat donors; research; results; rhd; rhd blood; risk; routine; screening; selection; sequencing; serum; significant; specific; staff; standard; status; storage; studies; study; summary; surgery; systems; tested; testing; tests; therapy; time donors; total; transfusion medicine; transfusion reactions; transfusion safety; transfusion service; transfusion therapy; transfusions; treated; treatment; typing; use; value; variant; versus; weak; women; years cache: cord-010092-uftc8inx.txt plain text: cord-010092-uftc8inx.txt item: #9 of 85 id: cord-010119-t1x9gknd author: None title: Abstract Presentations from the AABB Annual Meeting San Diego, CA ctober 7‐10, 2017 date: 2017-09-04 words: 230433 flesch: 50 summary: Probability of occurrence of cannabis metabolites in blood donor samples is likely to be highly variable across donor centers and is largely dependent on blood donor demographics. OBRR, CBER, FDA Background/Case Studies: Extended molecular typing of a large number of blood donors can increase the likelihood of identifying donor red blood cells (RBCs) that match those of the recipient. keywords: abo; abo blood; acute; addition; alleles; alloimmunization; analysis; anemia; anti; antibodies; antibody; antigen; apheresis; approach; assay; average; background; bacterial; blood; blood bank; blood cells; blood center; blood collection; blood components; blood count; blood donation; blood donors; blood group; blood loss; blood management; blood order; blood ordering; blood products; blood safety; blood samples; blood screening; blood services; blood specimens; blood supplier; blood supply; blood system; blood testing; blood transfusion; blood type; blood units; blood volume; care; case studies; case study; cases; cd36; cell transfusion; center background; centers; change; clinical; collections; concentration; conclusion; control; cord blood; cost; count; cross; culture; current; data; days; decreased; detection; difference; disease; dna; donations; donor samples; dose; dtt; effect; emergency blood; evaluation; events; evidence; expression; factors; fda; female; ffp; finding; flow; following; frequency; fresh; gel; gene; genotyping; given; groups; hbv; hcv; health; hemoglobin; hemolysis; high; history; hiv; hla; hospital; hospital blood; hospital transfusion; hours; human; identification; igg; immucor; impact; implementation; improvement; incidence; increase; infection; information; initial; institution; inventory; iron; laboratory; levels; low; manual; mean; median; medical; method; mice; minutes; model; molecular; months; mtp; need; negative; new; non; normal; number; order; partial; pathogen; patients; pcr; performance; period; phase; phenotype; plasma; plasma samples; plasma transfusion; plasma units; platelet; platelet blood; platelet transfusion; platelet units; plt; plts; population; positive; post; post transfusion; potential; practice; pre; presence; present; prevalence; procedure; process; processing; program; protocol; quality; r blood; range; rate; rbc; rbc blood; rbc transfusion; rbc units; rbcs; reactive; reactivity; reagent; recipients; recovery; red; reduced; reduction; reference; report; response; results; review; rhd; risk; routine; screening; second; sensitivity; sequencing; serum; set; small; solution; specific; specificity; staff; standard; storage; study design; study period; survey; systems; table; technology; test results; testing; tests; therapy; time; titer; total; tpe; training; transfused; transfusion medicine; transfusion practice; transfusion protocol; transfusion reactions; transfusion results; transfusion service; transfusions; trauma; treatment; tube; typing; units; university; use; values; virus; wastage; wbc; weak; weeks; women; year; zika; zikv cache: cord-010119-t1x9gknd.txt plain text: cord-010119-t1x9gknd.txt item: #10 of 85 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: 2830 flesch: 38 summary: 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). keywords: class; laboratory; samples; session; students; teaching; undergraduate; urine cache: cord-011444-6jh3lvm3.txt plain text: cord-011444-6jh3lvm3.txt item: #11 of 85 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: 5639 flesch: 49 summary: The performance of the HIV immunoassay cassette was evaluated with HIV urine sample. Therefore, compared to traditional eye observation, the handheld optical reader is helpful to improve the detection sensitivity of HIV urine test with lateral flow strip. keywords: cassette; detection; fig; flow; hiv; module; reader; sample; strip; test; urine cache: cord-011485-15wtv6bt.txt plain text: cord-011485-15wtv6bt.txt item: #12 of 85 id: cord-015482-ovuofl9q author: Chen, Xinguang title: Probability Sampling by Connecting Space with Households Using GIS/GPS Technologies date: 2018-01-23 words: 5987 flesch: 48 summary: This method is developed by integrating various reported GIS/GPS-assisted sampling methods (Chang et al. 2009; Wampler et al. 2013; Escamilla et al. 2014; Haenssgen 2015; Pearson et al. 2015) , particularly the methods with a stratified cluster sampling approach (Cochran 1977; Groves et al. 2009 ). Applying this method to another study conducted in 2012-2014, we estimated that approximately fifty-eight thousand [95% CI: 47,000, 68,000] rural-tourban migrants in Wuhan were MSM with 3,650 [95% CI: 2,960, 4,282] being tested HIV positive (Chen et al. 2015) . keywords: area; data; et al; geounit; households; method; number; population; sample; sampling; size cache: cord-015482-ovuofl9q.txt plain text: cord-015482-ovuofl9q.txt item: #13 of 85 id: cord-017248-a37t31u1 author: None title: Alphabetic Listing of Diseases and Conditions date: 2010-05-17 words: 48773 flesch: 37 summary: Peptic ulcers may be associated with emphysema,* tuberculosis,* and other chronic pulmonary diseases. Procedures See under Alcoholism and alcohol intoxication. keywords: abnormalities; acute; air; alcohol; analysis; aorta; aortic; arteries; artery; atresia; autopsy; blood; body; bone; brain; cases; cause; cell; cerebral; changes; chapter; chronic; column; concentrations; conditions; congenital; coronary; death; defect; deficiency; diagnosis; disease; dissection; embolism; evidence; examination; findings; formalin; gas; hand; heart; histologic; histologic study; infection; lesions; liver; lung; manifestations; material; neck; note; organs; patients; photograph; pneumonia; poisoning; preparation; prepare; present; procedures; pulmonary; record; removal; renal; report; request; right; roentgenograms; samples; sections; skin; specimen; spinal; stain; study; syndrome; synonyms; terms; time; tissue; toxicologic; tumor; type; valve; ventricular; vessels; victim; water; weight cache: cord-017248-a37t31u1.txt plain text: cord-017248-a37t31u1.txt item: #14 of 85 id: cord-017543-60q9iecq author: Tian, Wei-Chang title: Microfluidic Applications in Biodefense date: 2008-08-23 words: 16571 flesch: 33 summary: DNA samples were forced onto the surface of the glass capillary using chaotrophic agents, the DNA-coated capillary was then evacuated, and 500 nL of PCR reagents re-filled the tube by capillary action. [37] as a stand-alone, autonomous aerosol detection device. keywords: agents; amplification; analysis; anthracis; applications; array; assays; bacillus; beads; biodefense; capillary; detection; device; dna; electrophoresis; field; identification; immunoassays; methods; microchip; microfluidics; nucleic; pcr; polymerase; preparation; reaction; sample; separations; sequencing; system; target; time; use cache: cord-017543-60q9iecq.txt plain text: cord-017543-60q9iecq.txt item: #15 of 85 id: cord-018761-vm86d4mj author: Bradt, David A. title: Technical Annexes date: 2017-11-08 words: 10432 flesch: 48 summary: In some countries, vaccine may also be used with close contacts of sporadic disease cases to prevent secondary cases. Classic biotype caused the 5th and 6th pandemics but little epidemic disease since the 1970s though it still causes cases in India. keywords: age; bias; cases; data; disease; e.g.; epidemic; health; malnutrition; meningitis; mortality; non; outbreak; patients; population; precision; prevalence; sample; sampling; size; study; use; water cache: cord-018761-vm86d4mj.txt plain text: cord-018761-vm86d4mj.txt item: #16 of 85 id: cord-022147-istz1iql author: None title: Procedures to Investigate Waterborne Illness date: 2016-07-13 words: 38236 flesch: 47 summary: Collecting clinical samples and water samples • Conducting an on-site investigation at the facility alleged to be responsible to determine the mode of contamination or process failure, e.g., low disinfectant level • Characterizing the etiologic agents by laboratory analysis using various typing schemes. Instruct the ill person to hold all clinical specimens and water samples until the health agency evaluates the epidemiological evidence and arranges, if necessary, to collect them. keywords: agencies; agent; cases; chlorine; coli; contact; contamination; data; disease; disinfectant; distribution; drinking water; example; exposure; health; illness; incubation; information; investigation; laboratory; non; number; outbreak; pathogens; period; persons; public; records; results; risk; samples; source; specimens; symptoms; system; table; test; time; use; value; water; water samples; water source; water supply; water treatment; waterborne; waterborne illness cache: cord-022147-istz1iql.txt plain text: cord-022147-istz1iql.txt item: #17 of 85 id: cord-022879-j6cecioe author: Fager, Edward W. title: Determination and Analysis of Recurrent Groups date: 1957-10-01 words: 6289 flesch: 50 summary: =non-affinity The species are put in order in terms of the number of other species with which they have affinity. Because the species were put Ecology, Vol. 38, No. 4 in order in terms of the number of other species with which they had affinity, the species beyond H will either have the same number of affinities as H, in which case they are also potential members of a group of 7 species, or fewer affinities than H, in which case they cannot be included in a group of 7 species satisfying requirement ( 1). keywords: affinities; affinity; group; number; recurrent; samples; species cache: cord-022879-j6cecioe.txt plain text: cord-022879-j6cecioe.txt item: #18 of 85 id: cord-023095-4dannjjm author: None title: Research Abstract Program of the 2011 ACVIM Forum Denver, Colorado, June 15–18, 2011 date: 2011-05-03 words: 134382 flesch: 49 summary: Mminimum HR, mean HR and the HRV variables (7 and 10) differing between dog groups, also consistently decreased with increasing MR, LA/Ao and the proximal isovelocity surface area in CKCS. The apparently normal levels of hexosaminidase A activity in affected dog samples may be a result of b subunit overexpression. keywords: abnormalities; acid; acth; activity; administration; adult; age; aim; analysis; animals; assay; association; available; baseline; blood; blood samples; body; breed dogs; breeds; canine; cardiac; cases; cats; cell; changes; chf; chronic; clinical; cobalamin; compare; concentrations; control dogs; controls; correlation; cortisol; creatinine; data; days; decrease; detection; diagnosis; diet; difference; disease; dna; dogs; dose; drug; duration; effects; elisa; equine; evidence; examination; expression; failure; fecal; feline; findings; foals; following; food; function; gastrointestinal; gene; glucose; group; heart; horses; hours; human; increase; infection; insulin; isolates; levels; mean; median; medical; minutes; model; months; negative; non; number; observed; outcome; p o; parameters; patients; pcr; period; plasma; platelet; post; potential; presence; present; prevalence; protein; pulmonary; purpose; range; rate; reference; resistance; response; results; risk; role; samples; serum; serum concentrations; serum samples; severity; significance; signs; species; specific; spinal; spp; standard; studies; study; survival; test; therapy; time; tissue; total; treatment; type; urinary; urine; uroliths; use; values; veterinary; weeks; weight; years cache: cord-023095-4dannjjm.txt plain text: cord-023095-4dannjjm.txt item: #19 of 85 id: cord-023442-4vzwc2d2 author: None title: Proceedings of SCANNING 94/SEEMS 94 Charleston, South Carolina, USA date: 2006-12-05 words: 55600 flesch: 45 summary: Applications include both thin-film and bulk x-ray microanalysis and examples of contrast in backscattered electron images obtained in the SEM. The effects of adjusting the Wehnelt-to-tip distance vary for different electron microscope systems. keywords: addition; analysis; associated; atomic; backscattered; carlo; cells; chemical; comparison; composition; conditions; confocal; contrast; cross; crystal; data; detection; detector; developed; development; distribution; drying; effects; electron; electron beam; electron microscopy; energy; field; fig; figure; form; formation; glass; image; imaging; laser; light; lines; material; measurement; method; microscope; milk; model; monte; new; number; particles; pattern; phase; point; preparation; probe; process; program; ray; region; resolution; results; sample; scanning; scattering; sections; sem; signal; silicon; simulation; size; specific; specimen; structures; studies; study; substrate; supplement; surface; system; techniques; temperature; time; tissue; transmission electron; type; use; vol; water; work cache: cord-023442-4vzwc2d2.txt plain text: cord-023442-4vzwc2d2.txt item: #20 of 85 id: cord-024503-f4ibgn9i author: Jawed, Shayan title: Self-supervised Learning for Semi-supervised Time Series Classification date: 2020-04-17 words: 4339 flesch: 53 summary: Multitask learning DTW-D: time series semi-supervised learning from a single example The UCR time series classification archive Unsupervised visual representation learning by context prediction Multi-task self-supervised visual learning Deep learning for time series classification: a review Unsupervised representation learning by predicting image rotations Learning time-series shapelets Lars: Invariant time-series factorization Multi-task learning using uncertainty to weigh losses for scene geometry and semantics Temporal ensembling for semi-supervised learning SUCCESS: a new approach for semi-supervised classification of time-series Shuffle and learn: unsupervised learning using temporal order verification Positive unlabeled learning for time series classification Unsupervised learning of visual representations by solving jigsaw puzzles An overview of multi-task learning in deep neural networks Time series feature learning with labeled and unlabeled data Bag-of-words representation for biomedical time series classification Time series classification from scratch with deep neural networks: a strong baseline Learning and using the arrow of time Semi-supervised time series classification Time series analysis with graph-based semi-supervised learning Colorful image colorization Semi-supervised learning using gaussian fields and harmonic functions Semi-supervised learning literature survey Acknowledgements. The idea behind semi-supervised learning is to exploit unlabeled data for training purpose in the presence of only few labeled instances. keywords: classification; forecasting; learning; model; series; task; time cache: cord-024503-f4ibgn9i.txt plain text: cord-024503-f4ibgn9i.txt item: #21 of 85 id: cord-024553-jat7pttf author: Fan, Haoyi title: Correlation-Aware Deep Generative Model for Unsupervised Anomaly Detection date: 2020-04-17 words: 3028 flesch: 43 summary: [8] conducts anomaly detection by building trees using randomly selected split values across sample features, and defining the anomaly score as the average path length from a specific sample to the root. Although the above-mentioned methods had their fair share of success in anomaly detection, most of these methods neglect the complex correlation among data samples. keywords: anomaly; correlation; data; detection; feature; samples cache: cord-024553-jat7pttf.txt plain text: cord-024553-jat7pttf.txt item: #22 of 85 id: cord-030409-bwxkxvsl author: Mamontov, Eugene title: Effect of Hydration on the Molecular Dynamics of Hydroxychloroquine Sulfate date: 2020-08-10 words: 6139 flesch: 42 summary: While free base hydroxychloroquine (C 18 For the preparation of hydrated solid HCQS samples, various approaches have been attempted. Diffusivity of HCQS in aqueous solutions; neutron diffraction patterns from the solid samples; mean-squared displacements (MSD) in the solid samples; QENS broadening in the dry and main hydrated solid samples; hydration water dynamics in the more ordered hydrated solid sample; temperature dependence of the EISF(Q) measured at BASIS for the dry and main hydrated solid samples; temperature dependence of the fraction of immobilized water molecules in the main hydrated sample (PDF) DE-AC02−05CH11231, for access to supercomputing resources. keywords: data; dry; energy; figure; hcqs; hcqs sample; hydration; hydration water; methyl; mev; sample; water cache: cord-030409-bwxkxvsl.txt plain text: cord-030409-bwxkxvsl.txt item: #23 of 85 id: cord-030725-876arxiu author: None title: September 2020 New in Review date: 2020-08-20 words: 2745 flesch: 41 summary: Clinical significance of nutritional risk screening for older adult patients with COVID-19. Lifestyle factors documented included smoking status, alcohol intake, and diet by way of a food frequency questionnaire. keywords: age; analysis; participants; risk; sample; status; study; vitamin; weight; years cache: cord-030725-876arxiu.txt plain text: cord-030725-876arxiu.txt item: #24 of 85 id: cord-031907-ilhr3iu5 author: None title: ISEV2020 Abstract Book date: 2020-07-15 words: 201435 flesch: 40 summary: Normal pancreas cells (hTERT-HPNE and HPDE-H6c7) were co-cultured with cancer cell EVs for 24-48 hours. Before EV isolation cells were kept for 24 h either under normoxia or hypoxia (1% oxygen). keywords: ability; activation; activity; ad evs; addition; aim; analysis; analysis methods; anti; approach; assay; associated; bacterial evs; biological; biomarkers; blood; blood cells; blood evs; blot; bone; brain; breast; breast cancer; cancer cells; cancer evs; cancer introduction; cancer patients; cd63; cd81; cd9; cell communication; cell culture; cell evs; cell exosomes; cell function; cell lines; cell proliferation; cell surface; cell types; cells; cells introduction; changes; characterization; chromatography; composition; concentration; conclusion; conditions; content; control; control evs; cultured; current; cytometry; data; delivery; density; detection; development; diagnosis; differential; disease; distribution; dna; drug; effect; electron; endothelial; enrichment; epithelial; ev analysis; ev cargo; ev evs; ev isolation; ev markers; ev numbers; ev preparations; ev production; ev protein; ev release; ev research; ev rna; ev samples; ev subpopulations; ev surface; ev treatment; ev uptake; evs; exclusion; exosomal; exosomes; experiments; expression; expression analysis; extracellular; factors; findings; flow; fluorescent; fluorescent evs; fold; formation; fractions; free; function; funding; gene; group; growth; host cells; human; human evs; imaging; immune; increase; inflammation; inflammatory; introduction; isolated; isolation methods; key; large; levels; lipid; lung; macrophages; mass; mechanisms; media; medium; membrane; membrane vesicles; mesenchymal; metastasis; methods; mice; microscopy; migration; milk evs; mirna; model; molecular; molecules; mouse; msc evs; mscs; nanoparticle; national; neuronal; neurons; new; non; normal; novel; nta; number; particles; pathway; patients; plasma evs; plasma samples; platelet; platform; play; positive; positive evs; post; potential; presence; present; primary; process; production; profile; profiling; progression; proliferation; properties; prostate; prostate cancer; protein; protein cargo; protein expression; protein markers; proteomic; purification; purity; range; recipient cells; research; resistance; response; results; rna; rnas; role; samples; sec; secretion; sequencing; serum; sevs; signalling; single; size; small evs; specific; specific evs; spectrometry; stem cells; stromal cells; studies; study; summary; surface; system; target cells; targets; tau; techniques; tested; therapeutic; therapy; time; tissue; total; total evs; tracking; transfer; transmission; treatment; tumour cells; ultracentrifugation; university; uptake; urinary evs; urine; usa; usa introduction; use; vesicles; vesicles introduction; vitro; vivo; work cache: cord-031907-ilhr3iu5.txt plain text: cord-031907-ilhr3iu5.txt item: #25 of 85 id: cord-032379-pelz3ygf author: None title: October 2020 New in Review date: 2020-09-21 words: 3599 flesch: 42 summary: Eligibility criteria included journal articles describing at least one tool potentially used by health care providers to promote healthy dietary intake in healthy, pregnant women; and articles published in Western countries. The investigators sought a review of tools to be integrated into antenatal care for promotion of healthy dietary behavior in healthy pregnant women. keywords: analysis; data; dietary; health; intervention; participants; randomized; researchers; review; sample; studies; study; weight cache: cord-032379-pelz3ygf.txt plain text: cord-032379-pelz3ygf.txt item: #26 of 85 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: 4456 flesch: 44 summary: Further optimization is needed to improve the sensitivity of our protocol for clinical samples with lower viral titres (Ct values >30). How to be ready for the next influenza pandemic Real-time, portable genome sequencing for Ebola surveillance Metagenomic sequencing at the epicenter of the Nigeria 2018 Lassa fever outbreak Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis Diagnostic tests for influenza infection. keywords: author; funder; influenza; license; medrxiv; perpetuity; preprint; samples; sequencing cache: cord-102471-dtukacm7.txt plain text: cord-102471-dtukacm7.txt item: #27 of 85 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: 6510 flesch: 48 summary: More than 98% of basecalled RNA reads (9,065 reads) were taxonomically classified using BLASTN against NCBI's nucleotide (nt) database. We used a chloroform/bead pre-treatment in DRS samples for enrichment of viral capsid and although it might be efficient in enriching viral reads, it could also reduce the overall amount of RNA extracted. keywords: drs; enterovirus; genome; illumina; miseq; nanopore; preprint; reads; rna; samples; sequences; sequencing cache: cord-102547-nxut8ov1.txt plain text: cord-102547-nxut8ov1.txt item: #28 of 85 id: cord-102613-hly07ne3 author: Danko, David title: Global Genetic Cartography of Urban Metagenomes and Anti-Microbial Resistance date: 2020-05-04 words: 6556 flesch: 51 summary: 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. compared to an average of 6.01M 194 reads per sample. keywords: amr; cities; city; distance; figure; genes; number; reads; samples; species; supp; taxa; taxonomic cache: cord-102613-hly07ne3.txt plain text: cord-102613-hly07ne3.txt item: #29 of 85 id: cord-103180-5hkoeca7 author: Furstenau, Tara N. title: Sample pooling methods for efficient pathogen screening: Practical implications date: 2020-07-16 words: 3802 flesch: 51 summary: 43 Group testing theory primarily focuses on minimizing the number of tests required 44 to identify positive samples and many nearly-optimal strategies for sample pooling have 45 been described. 25 Due to practical concerns, Dorfman's group testing approach was never applied to 26 syphilis screening because the large number of negative samples had a tendency to 27 dilute the antigen in positive samples below the level of detection keywords: number; pooling; positive; samples; testing; tests cache: cord-103180-5hkoeca7.txt plain text: cord-103180-5hkoeca7.txt item: #30 of 85 id: cord-103735-nil1vv6h author: Alfano, Niccolo title: Non-invasive surveys of mammalian viruses using environmental DNA date: 2020-03-29 words: 5837 flesch: 49 summary: Viral contigs were confirmed by PCR and Sanger sequencing for samples L7, L17, L25 and L37 (Suppl. Of the 11 water filtrate samples tested, two samples from Mongolia (WM3 and WM20) (18.2%) had viral contigs with 100% identity to the Equid herpesvirus 1 and 3 (EHV-1 and EHV-3). keywords: capture; contigs; dna; fig; identity; leeches; pcr; reads; rna; samples; sediment; sequences; suppl; viruses; water; wildlife cache: cord-103735-nil1vv6h.txt plain text: cord-103735-nil1vv6h.txt item: #31 of 85 id: cord-130198-pyg81vwb author: Tabak, Tom title: Temporal Mental Health Dynamics on Social Media date: 2020-08-30 words: 6289 flesch: 42 summary: Quantifiable data sources pertaining to mental health are scarce in comparison to physical health data (Coppersmith et al. 2014 ). Unlike physical health conditions that often show physical symptoms, mental health is often reflected by more subtle symptoms (Chung & Pennebaker 2007 , De Choudhury, Counts & Horvitz 2013a . keywords: classifier; dataset; depression; dynamics; health; lockdown; media; national; performance; samples; training; tweets cache: cord-130198-pyg81vwb.txt plain text: cord-130198-pyg81vwb.txt item: #32 of 85 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: 6917 flesch: 45 summary: key: cord-254596-wsmnlnlk authors: Grädel, Carole; Terrazos Miani, Miguel A.; Baumann, Christian; Barbani, Maria Teresa; Neuenschwander, Stefan; Leib, Stephen L.; Suter-Riniker, Franziska; Ramette, Alban title: Whole-Genome Sequencing of Human Enteroviruses from Clinical Samples by Nanopore Direct RNA Sequencing date: 2020-07-31 journal: Viruses DOI: 10.3390/v12080841 sha: doc_id: 254596 cord_uid: wsmnlnlk 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. More than 98% of basecalled RNA reads (9065 reads) were taxonomically classified using BLASTN against the NCBI's nucleotide (nt) database. keywords: cdna; drs; enterovirus; genome; illumina; min; nanopore; reads; rna; samples; sequences; sequencing; total cache: cord-254596-wsmnlnlk.txt plain text: cord-254596-wsmnlnlk.txt item: #33 of 85 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: 6211 flesch: 40 summary: 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. For the guano samples, these consisted of an aliquot of each of the TruSeq RNA Access libraries from the step prior to virus enrichment. keywords: detection; enrichment; genome; probes; reads; rna; samples; sequencing; target; viral; virus; viruses cache: cord-254963-cnvxlv6h.txt plain text: cord-254963-cnvxlv6h.txt item: #34 of 85 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: 6069 flesch: 42 summary: This article discloses detailed materials, methods, sample processing, and data analyses. Inject 1 µL of each sample including quality control samples in the GC-MS. keywords: analysis; cancer; data; dna; hpv; human; metabolites; metabolomics; microbiome; note; sample; solution; step; urine; vials cache: cord-258014-lzzi4rnz.txt plain text: cord-258014-lzzi4rnz.txt item: #35 of 85 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: 4292 flesch: 65 summary: While it takes 8 hours to test 1,000 samples using a roche cobas 8800 analyzer, the authors have calculated that with pool size 5 it takes a little more than 14 hours for the same samples (1 % positives), and, with recursive pool testing at size 25 and 5, the turnaround-time would go up to 17 hours. Rather than testing all samples in a positive pool, the idea is to again split this pool subset into 2 (or more) smaller subsets for pool testing, and keep splitting as long as possible. keywords: method; pool; samples; size; testing cache: cord-263831-7aj9ozpn.txt plain text: cord-263831-7aj9ozpn.txt item: #36 of 85 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: 3177 flesch: 49 summary: key: cord-273495-hruq0hdw authors: Waffo Tchounga, C.A.; Sacre, P.Y.; Ciza, P.; Ngono, R.; Ziemons, E.; Hubert, Ph.; Marini, R.D. title: Composition analysis of falsified chloroquine phosphate samples seized during the COVID-19 pandemic date: 2020-11-12 journal: J Pharm Biomed Anal DOI: 10.1016/j.jpba.2020.113761 sha: doc_id: 273495 cord_uid: hruq0hdw 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. These suspect chloroquine samples were seized by local authorities as being part of the WHO alert list. keywords: chloroquine; covid-19; imaging; medicines; paracetamol; phosphate; presence; raman; samples cache: cord-273495-hruq0hdw.txt plain text: cord-273495-hruq0hdw.txt item: #37 of 85 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: 1676 flesch: 41 summary: Herein, we propose a mass population screening approach, based on sample pooling strategy for rapid and wide-scale population screening that may be adopted by laboratories currently using RT-PCR based methods to test for SARS-CoV-2. To minimize this, use of a minimum of two identifiers and well documented workflows to ensure traceability of all pooled samples is essential. keywords: covid-19; pooling; samples; sars; testing cache: cord-275360-uphdzj5l.txt plain text: cord-275360-uphdzj5l.txt item: #38 of 85 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: 8040 flesch: 37 summary: Treatment with DNase twice yielded the best percentage recovery of However, despite very low viral titers, H1N1 influenza was still detectable by deep sequencing, with 270 and 18 reads aligning to influenza for Cal-UC12 and BC-59, respectively (Table 1) . Emergence of a novel swine-origin influenza A (H1N1) virus in humans Triplereassortant swine influenza A (H1) in humans in the United States Pandemic potential of a strain of influenza A (H1N1): early findings Rapid-test sensitivity for novel swine-origin influenza A (H1N1) virus in humans Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic Metagenomics for the discovery of novel human viruses Microarray detection of human parainfluenzavirus 4 infection associated with respiratory failure in an immunocompetent adult Microarray-based detection and genotyping of viral pathogens Characterization of a novel coronavirus associated with severe acute respiratory syndrome Viral discovery and sequence recovery using DNA microarrays Pan-viral screening of respiratory tract infections in adults with and without asthma reveals unexpected human coronavirus and human rhinovirus diversity Identification of cardioviruses related to Theiler's murine encephalomyelitis virus in human infections Achalasia and viral infection: new insights from veterinary medicine Recovery of divergent avian bornaviruses from cases of proventricular dilatation disease: identification of a candidate etiologic agent Utility of DNA microarrays for detection of viruses in acute respiratory tract infections in children Identification of a novel astrovirus (astrovirus VA1) associated with an outbreak of acute gastroenteritis The complete genome of klassevirus -a novel picornavirus in pediatric stool Metagenomic analyses of viruses in stool samples from children with acute flaccid paralysis Bat guano virome: predominance of dietary viruses from insects and plants plus novel mammalian viruses Multiple diverse circoviruses infect farm animals and are commonly found in human and chimpanzee feces Genetic detection and characterization of Lujo virus, a new hemorrhagic feverassociated arenavirus from southern Africa A new arenavirus in a cluster of fatal transplant-associated diseases Influenza vaccine-outmaneuvering antigenic shift and drift Broadspectrum respiratory tract pathogen identification using resequencing DNA microarrays Robust sequence selection method used to develop the FluChip diagnostic microarray for influenza virus Panmicrobial oligonucleotide array for diagnosis of infectious diseases Experimental evaluation of the FluChip diagnostic microarray for influenza virus surveillance Detection in 2009 of the swine origin influenza A (H1N1) virus by a subtyping microarray Large-scale evolutionary surveillance of the 2009 H1N1 influenza A virus using resequencing arrays Identifying influenza viruses with resequencing microarrays Detection of molecular markers of drug resistance in the 2009 pandemic influenza A (H1N1) viruses using pyrosequencing Direct metagenomic detection of viral pathogens in nasal and fecal specimens using an unbiased high-throughput sequencing approach Characterization of quasispecies of pandemic 2009 influenza A virus (A/H1N1/ 2009) by de novo sequencing using a next-generation DNA sequencer California Pandemic Working G (2010) Severe 2009 H1N1 influenza in pregnant and postpartum women in California E-Predict: a computational strategy for species identification based on observed DNA microarray hybridization patterns Development and quantitative analyses of a universal rRNA-subtraction protocol for microbial metatranscriptomics The NIH Human Microbiome Project Xenotropic Murine Leukemia Virus-related Gammaretrovirus in Respiratory Tract Identification of a novel Gammaretrovirus in prostate tumors of patients homozygous for R462Q RNASEL variant Detection of an infectious retrovirus, XMRV, in blood cells of patients with chronic fatigue syndrome Antiviral actions of interferons Clonal integration of a polyomavirus in human Merkel cell carcinoma Metagenomic analysis of respiratory tract DNA viral communities in cystic fibrosis and non-cystic fibrosis individuals Streptococcus pneumoniae coinfection is correlated with the severity of H1N1 pandemic influenza RNA viral community in human feces: prevalence of plant pathogenic viruses Substantial biases in ultra-short read data sets from high-throughput DNA sequencing Inefficient control of host gene expression by the 2009 pandemic H1N1 influenza A virus NS1 protein Real-time DNA sequencing from single polymerase molecules The next generation becomes the now generation The long march: a sample preparation technique that enhances contig length and coverage by high-throughput short-read sequencing Kleine-Levin syndrome: a systematic study of 108 patients PANTHER pathway: an ontology-based pathway database coupled with data analysis tools SSAHA: a fast search method for large DNA databases Multiple sequence alignment using ClustalW and ClustalX We thank Aurora París at the Ministry of Health BSL-3 state laboratory in Veracruz for providing 2009 H1N1 samples from Mexico. keywords: analysis; data; detection; genome; h1n1; human; influenza; novel; pcr; reads; samples; sequence; sequencing; virochip; virus; viruses cache: cord-280846-bbv6f5gf.txt plain text: cord-280846-bbv6f5gf.txt item: #39 of 85 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: 4127 flesch: 40 summary: The underrecognized burden of influenza in young children Viral epidemiology and severity of respiratory infections in infants in 2009: a prospective study Techniques actuelles de diagnostic des infections virales respiratoires en réanimation Cost analysis of multiplex PCR testing for diagnosing respiratory virus infections Superiority of reverse-transcription polymerase chain reaction to conventional viral culture in the diagnosis of acute respiratory tract infections in children Increased detection of respiratory syncytial virus, influenza viruses, parainfluenza viruses, and adenoviruses with real-time PCR in samples from patients with respiratory symptoms Quantitation of respiratory syncytial virus RNA in nasal aspirates of children by real-time RT-PCR assay Molecular diagnosis of respiratory viruses Comparison of multiplex PCR assays and conventional techniques for the diagnostic of respiratory virus infections in children admitted to hospital with an acute respiratory illness Comparative evaluation of six commercialized multiplex PCR kits for the diagnosis of respiratory infections Identification of respiratory viruses in adults: nasopharyngeal versus sampling Development of an efficient qRT-PCR assay for quality control and cellular quantification of respiratory samples Guideline to reference gene selection for quantitative realtime PCR Comparison of flocked and rayon swabs for collection of respiratory epithelial cells from uninfected volunteers and symptomatic patients Nasal swab samples and real-time polymerase chain reaction assays in community-based, longitudinal studies of respiratory viruses: the importance of sample integrity and quality control Swabbing for respiratory viral infections in older patients:a comparison of rayon and nylon flocked swabs Comparison among nasopharyngeal swab, nasal wash, and oropharyngeal swab for respiratory virus detection in adults with acute pharyngitis Improved detection of respiratory viruses in pediatric outpatients with acute respiratory illness by real-time PCR using nasopharyngeal flocked swabs Comparison of nasopharyngeal and oropharyngeal swabs for the diagnosis of eight respiratory viruses by real-time reverse transcription-PCR assays Evaluation of the Quidel QuickVue test for detection of influenza A and B viruses in the pediatric emergency medicine setting by use of three specimen collection methods A quantification of human cells using an ERV-3 real time PCR assay Not applicable. 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 BACKGROUND: Respiratory viral diagnosis of upper respiratory tract infections has largely developed through multiplex molecular techniques. keywords: age; cellularity; detection; diagnosis; pcr; samples; study cache: cord-281916-v6u5mr2i.txt plain text: cord-281916-v6u5mr2i.txt item: #40 of 85 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: 5128 flesch: 40 summary: Although the rate of success has been highly variable, it has become evident that a tight control of dog infections is the key element to arrest the life cycle of the parasite. However, accurate diagnosis of dog infection is complex and challenging, and other than careful necropsy of dogs, there is no perfect gold standard [6] . keywords: antigens; dogs; elisa; granulosus; hydatigena; infection; parasite; samples; test cache: cord-288202-r3r2bc7v.txt plain text: cord-288202-r3r2bc7v.txt item: #41 of 85 id: cord-290722-neqj85xf author: Lojkić, Ivana title: Faecal virome of red foxes from peri-urban areas date: 2016-01-29 words: 3232 flesch: 50 summary: In this study, 8 pooled fox faecal samples of juvenile (marked as 55588, 55591, 55594, 55596) and adult (55539, 55589, 55590, 55592) animals were used for metagenomic analysis by random cDNA synthesis followed by high-throughput sequencing. [3] other prevalent fox faecal viruses (fox hepevirus and fox astroviruses) were not discovered. keywords: adult; analysis; circovirus; foxes; picobirnavirus; reads; samples; sequence; viruses cache: cord-290722-neqj85xf.txt plain text: cord-290722-neqj85xf.txt item: #42 of 85 id: cord-291540-raksomda author: None title: July 2020 New in Review date: 2020-07-31 words: 3301 flesch: 38 summary: Are obstructive sleep apnea and sleep improved in response to multidisciplinary weight loss interventions in youth with obesity? The investigators hypothesized that multidisciplinary weight loss interventions will effectively reduce obstructive sleep apnea (OSA) indicators such as the apnea-hypopnea index, oxygen desaturation index, and obstructive apnea-hypopnea index, and in improving sleep duration and sleep architecture. keywords: analysis; authors; food; health; intervention; meta; participants; review; risk; sample; studies; weight cache: cord-291540-raksomda.txt plain text: cord-291540-raksomda.txt item: #43 of 85 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: 4514 flesch: 33 summary: Viruses were detected in 13.8% (43/312) and bacteria in 93.3% (291/312) of non-acute samples. Hi-nonB, rhinovirus, and coronavirus 229 were detected significantly less frequently in non-acute samples collected at the start of the training period than acute samples (p-values < 0.05) ( Table 1) . keywords: acute; infection; load; non; samples; specimens; tract; value cache: cord-294062-3esrg1jw.txt plain text: cord-294062-3esrg1jw.txt item: #44 of 85 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: 6503 flesch: 47 summary: For Covid-19 lung tissue, the scans were recorded at the GINIX endstation of the PETRA III storage ring (DESY,Hamburg). Based on the extracted structural parameters, the degree of inflammation and swelling of lung tissue can be evaluated. keywords: alveolar; beam; blood; covid-19; fig; license; lung; phase; preprint; sample; size; tissue; tomography cache: cord-298295-epxd03pt.txt plain text: cord-298295-epxd03pt.txt item: #45 of 85 id: cord-298697-v1qdizwx author: Chang, Jia Jin Marc title: Takeaways from Mobile DNA Barcoding with BentoLab and MinION date: 2020-09-24 words: 7224 flesch: 49 summary: We sought to investigate if the basecalling model had an impact on MinION barcodes generated from an error correction pipeline like miniBarcoder. We then performed MinION barcode calling using the miniBarcoder pipeline [35] . keywords: barcodes; barcoding; basecalling; bentolab; dataset; dna; field; flow; laboratory; minion; model; nanopore; pcr; reads; samples; sequencing; species; time cache: cord-298697-v1qdizwx.txt plain text: cord-298697-v1qdizwx.txt item: #46 of 85 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: 13021 flesch: 38 summary: Recent studies on four different commercial antigen tests demonstrated a wide range of sensitivities from 16.7 to 85% (with 100% specificity) in COVID-19 clinical samples [113] . Such methods have been extensively reviewed [44, 163, 164] and will need to be validated with COVID-19 clinical samples. keywords: amplification; antibody; antigen; assay; collection; coronavirus; cov-2; covid-19; crispr; detection; diagnostic; novel; pandemic; patients; pcr; rna; samples; sars; sensitivity; sequencing; swabs; testing; tests cache: cord-300399-21xozruq.txt plain text: cord-300399-21xozruq.txt item: #47 of 85 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: 6124 flesch: 46 summary: key: cord-301823-fbeb1nw1 authors: Sridhar, Sushmita; Forrest, Sally; Kean, Iain; Young, Jamie; Bartholdson Scott, Josefin; Maes, Mailis; Pereira-Dias, Joana; Parmar, Surendra; Routledge, Matthew; Sparkes, Dominic; Rivett, Lucy; Dougan, Gordon; Weekes, Michael; Curran, Martin; Goodfellow, Ian; Baker, Stephen 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 journal: Eurosurveillance Editorial Team: Updated rapid risk assessment from ECDC on the novel coronavirus disease 2019 (COVID-19) pandemic: increased transmission in the EU/EEA and the UK Challenges for NHS hospitals during covid-19 epidemic COVID-19: towards controlling of a pandemic PubMed Abstract | Publisher Full Text | Free Full Text The Laboratory Diagnosis of COVID-19: Current Issues and Challenges Virological assessment of hospitalized patients with COVID-2019 RT-qPCR detection of SARS-COV-2 RNA from patient nasopharyngeal swab using qiagen rneasy kits or directly via omission of an rna extraction step Rapid and simple method for purification of nucleic acids The use of control charts in the clinical laboratory Performance characteristics of rules for internal quality control: probabilities for false rejection and error detection countries: COVID-19 and risks to the supply and quality of tests, drugs, and vaccines PubMed Abstract | Publisher Full Text | Free Full Text A blueprint for the implementation of a validated approach for the detection of SARS-Cov2 in clinical samples in academic facilities: extended data We wish to acknowledge all involved from the onset in giving their time, effort, and knowledge in getting this going. keywords: assay; cov2; covid-19; data; hospital; laboratory; pcr; plate; samples; sars; staff cache: cord-301823-fbeb1nw1.txt plain text: cord-301823-fbeb1nw1.txt item: #48 of 85 id: cord-301991-n87le8ix author: Saxena, Abhishek title: Diatoms recovery from wastewater: Overview from an ecological and economic perspective date: 2020-10-16 words: 9973 flesch: 36 summary: It is ideal to note the microhabitat of diatoms species [35] . Low dense cells, for example, microscopic organisms and others present in the supernatant, are emptied while diatoms species stay at the base as a pellet. keywords: bodies; cell; conditions; culture; diatoms; environment; freshwater; growth; isolation; marine; media; metal; method; microalgae; organisms; quality; sample; silica; species; target; techniques; water cache: cord-301991-n87le8ix.txt plain text: cord-301991-n87le8ix.txt item: #49 of 85 id: cord-303647-c4umbcvn author: Reed, Patricia E. title: A New Approach for Monitoring Ebolavirus in Wild Great Apes date: 2014-09-18 words: 5645 flesch: 40 summary: This study represents the first time that ebolavirus antibodies have been detected in wild great ape fecal samples, and carries important implications for the future management and survival of these primates. We also tested ape fecal samples obtained from the outbreakfree (NRO) region to explore whether NP antibody detection can be used as a potential surveillance tool. keywords: animal; antibodies; ape; apes; detection; ebolavirus; ebov; feces; gorilla; human; samples; wild; wildlife; zone cache: cord-303647-c4umbcvn.txt plain text: cord-303647-c4umbcvn.txt item: #50 of 85 id: cord-305282-x2zzzw43 author: SUEN, C. Y. title: Feasibility of Reusing Surgical Mask Under Different Disinfection Treatments date: 2020-05-20 words: 2696 flesch: 49 summary: Surgical mask decontamination methods have been reported from various media. 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. keywords: disinfection; efficiency; filtration; mask; methods; minutes; samples; treatment cache: cord-305282-x2zzzw43.txt plain text: cord-305282-x2zzzw43.txt item: #51 of 85 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: 6718 flesch: 45 summary: By using a short LC gradient focusing on the region of interest identified in our previous study, we tested the detection of the virus in samples containing different quantities of viral peptides, as well as COVID-19 clinical samples, paving the way for the development of time-efficient viral diagnostic tests based on an alternative platform. This was repeated several times to obtain a one-third dilution cascade of viral peptides. keywords: cov-2; covid-19; detection; mass; min; peptides; proteins; samples; sars; spectrometry; swabs; virus cache: cord-305755-6jup93v4.txt plain text: cord-305755-6jup93v4.txt item: #52 of 85 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: 4054 flesch: 43 summary: Instrumentation for the FilmArray process was provided by Idaho Technology, Inc. Development of three multiplex RT-PCR assays for the detection of 12 respiratory RNA viruses Multiplex real-time PCR assay for detection of influenza and human respiratory syncytial viruses Use of a multiplex real-time PCR to study the incidence of human metapneumovirus and human respiratory syncytial virus infections during two winter seasons in a Belgian paediatric hospital Multiplex real-time PCR for detection of respiratory tract infections Evaluation of the Prodesse Hexaplex multiplex PCR assay for direct detection of seven respiratory viruses in clinical specimens Evaluation of the Hexaplex assay for detection of respiratory viruses in children Rapid and sensitive method using multiplex real-time PCR for diagnosis of infections by influenza a and influenza B viruses, respiratory syncytial virus, and parainfluenza viruses 1, 2, 3, and 4 Development of a respiratory virus panel test for detection of twenty human respiratory viruses by use of multiplex PCR and a fluid microbead-based assay MultiCode-PLx system for multiplexed detection of seventeen respiratory viruses Multiplex PCR and emerging technologies for the detection of respiratory pathogens Detection of respiratory viruses by molecular methods Nucleic acid amplification-based diagnosis of respiratory virus infections Cloning of a human parvovirus by molecular screening of respiratory tract samples Human metapneumovirus infections in young and elderly adults Metapneumovirus and acute wheezing in children Human metapneumovirus: a newly emerging respiratory pathogen A newly discovered human pneumovirus isolated from young children with respiratory tract disease Identification of a new human coronavirus Characterization and complete genome sequence of a novel coronavirus, coronavirus HKU1, from patients with pneumonia A novel multiplex real-time RT-PCR assay with FRET hybridization probes for the detection and quantitation of 13 respiratory viruses Evaluation of commercial ResPlex II v2.0, MultiCode-PLx, and xTAG respiratory viral panels for the diagnosis of respiratory viral infections in adults Immunofluorescence versus xTAG multiplex PCR for the detection of respiratory picornavirus infections in children Viral and atypical bacterial detection in acute respiratory infection in children under five years Comparison of the Eragen multi-code respiratory virus panel with conventional viral testing and real-time multiplex PCR assays for detection of respiratory viruses Clinical evaluation of multiplex real-time PCR panels for rapid detection of respiratory viral infections Rhinovirus and acute respiratory infections in hospitalized children retrospective study Multiple simultaneous viral infections in infants with acute respiratory tract infections in Spain Dual infection of infants by human metapneumovirus and human respiratory syncytial virus is strongly associated with severe bronchiolitis Comparison of two multiplex methods for detection of respiratory viruses: FilmArray RP and xTAG keywords: detection; filmarray; pcr; respiratory; resplex; samples; time; viral; viruses cache: cord-307261-0a3iztns.txt plain text: cord-307261-0a3iztns.txt item: #53 of 85 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: 7063 flesch: 37 summary: Mosby International Limited Rapid identification of mycoplasma bovis from bovine bronchoalveolar lavage fluid with MALDI-TOF MS after enrichment procedure Matrix-assisted laser desorption ionizationtime of flight mass spectrometry is a superior diagnostic tool for the identification and differentiation of Mycoplasmas isolated from animals Rapid identification of respiratory bacterial pathogens from bronchoalveolar lavage fluid in cattle by MALDI-TOF MS Rapid detection of tetracycline resistance in bovine Pasteurella multocida isolates by MALDI Biotyper antibiotic susceptibility test rapid assay Analysis of culture-dependent versus culture-independent techniques for identification of bacteria in clinically obtained bronchoalveolar lavage fluid Patterns of detection of respiratory viruses in nasal swabs from calves in Ireland: a retrospective study Pathogen-specific risk factors in acute outbreaks of respiratory disease in calves Bayesian estimation of pneumonia etiology: epidemiologic considerations and applications to the pneumonia etiology research for child health study Metagenomic characterization of the virome associated with bovine respiratory disease in feedlot cattle identified novel viruses and suggests an etiologic role for influenza D virus Respiratory viruses identified in western Canadian beef cattle by metagenomic sequencing and their association with bovine respiratory disease Modular approach to customise sample preparation procedures for viral metagenomics: a reproducible protocol for virome analysis Respiratory bacterial microbiota in cattle: from development to modulation to enhance respiratory health Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples Nanopore sequencing as a revolutionary diagnostic tool for porcine viral enteric disease complexes identifies porcine kobuvirus as an important enteric Nanopore metagenomics enables rapid clinical diagnosis of bacterial lower respiratory infection Mycoplasma bovis infections in cattle Transmission dynamics of Mycoplasma bovis in newly received beef bulls at fattening operations Detection by real-time RT-PCR of a bovine respiratory syncytial virus vaccine in calves vaccinated intranasally Characterization of Mannheimia haemolytica isolated from feedlot cattle that were healthy or treated for bovine respiratory disease Colonization and infection Variability in acquired resistance of Pasteurella and Mannheimia isolates from the nasopharynx of calves, with particular reference to different herd types Bacterial pathogens of the bovine respiratory disease complex Bioaerosols play a major role in the nasopharyngeal microbiota content in agricultural environment Effects of transportation to and co-mingling at an auction market on nasopharyngeal and tracheal bacterial communities of recently weaned beef cattle Quantitative bacterial cultures and cytological examination of bronchoalveolar lavage specimens in dogs Differential expression of sheep betadefensin-1 and -2 and interleukin 8 during acute Mannheimia haemolytica pneumonia Comparison of bronchoalveolar lavage fluid bacteriology and cytology in calves classified based on combined clinical scoring and lung ultrasonography Clinicopathological features of 11 suspected outbreaks of bovine adenovirus infection and development of a real-time quantitative PCR to detect bovine adenovirus type 10 Prevalence of respiratory pathogens in diseased, non-vaccinated, routinely medicated veal calves Bovine adenovirus type 3 pneumonia in dexamethasone-treated calves Apoptosis in calf pneumonia induced by endobronchial inoculation with bovine adenovirus type 3 (BAV-3) Structured literature review of responses of cattle to viral and bacterial pathogens causing bovine respiratory disease complex What is the evidence that bovine coronavirus is a biologically significant respiratory pathogen in cattle? A deep nasopharyngeal swab versus nonendoscopic bronchoalveolar lavage for isolation of bacterial pathogens from preweaned calves with respiratory disease Transmission dynamics of Mannheimia haemolytica in newly-received beef bulls at fattening operations A sequential broncho-alveolar washing in non-anaesthetized normal bovines: method and preliminary results Comparison of the nasopharyngeal bacterial microbiota of beef calves raised without the use of antimicrobials between healthy calves and those diagnosed with bovine respiratory disease Distinct bacterial metacommunities inhabit the upper and lower respiratory tracts of healthy feedlot cattle and those diagnosed with bronchopneumonia Use of deep nasopharyngeal swabs as a predictive diagnostic method for natural respiratory infections in calves The microbial flora of the respiratory tract in feedlot calves: associations between nasopharyngeal and bronchoalveolar lavage cultures Agreement among 4 sampling methods to identify respiratory pathogens in dairy calves with acute bovine respiratory disease Sample collection for diagnostics of bovine respiratory diseases Respiratory disease in calves: microbiological investigations on trans-tracheally aspirated bronchoalveolar fluid and acute phase protein response Collection and interpretation of tracheal wash and bronchoalveolar lavage for diagnosis of infectious and non-infectious lower airway disorders Factors associated with lung cytology as obtained by non-endoscopic broncho-alveolar lavage in grouphoused calves Effect of sedation on the intrapulmonary position of a bronchoalveolar lavage catheter in calves Influence of tilmicosin on quantified pulmonary concentrations of three bacterial pathogens in calves with naturallyoccurring bovine respiratory disease Mini-BAL, Blinded Bronchial Sampling, Blinded Protected Specimen Brush] to investigate for pulmonary infections, inflammation, and cellular and molecular markers: a narrative review Comparison of deep nasopharyngeal swab, bronchoalveolar lavage and transtracheal wash for the diagnosis of infectious bronchopneumonia in calves: which one is most animal friendly? keywords: animals; bovine; calves; cattle; culture; disease; pathogens; primary; results; sample; sampling; test; tract; use cache: cord-307874-0obomty2.txt plain text: cord-307874-0obomty2.txt item: #54 of 85 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: 6490 flesch: 35 summary: 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. (12)-(14) provides a useful starting point, illustrating how eDNA concentrations, and thus per sample detection www.nature.com/scientificreports www.nature.com/scientificreports/ probabilities, vary with volume, time, and rates of shedding and degradation (Fig. 3) . keywords: animals; batrachochytrium; detection; edna; individual; pathogen; probability; samples; sensitivity; trade; water cache: cord-308687-wrzzb9cy.txt plain text: cord-308687-wrzzb9cy.txt item: #55 of 85 id: cord-310061-nro623aa author: Valitutto, Marc T. title: Detection of novel coronaviruses in bats in Myanmar date: 2020-04-09 words: 3682 flesch: 42 summary: Supporting information S1 Fauci AS The challenge of emerging and reemerging infectious diseases Factors in the emergence of infectious diseases Host range and emerging and reemerging pathogens Global trends in emerging infectious diseases Risk factors for human disease emergence Human ecology in pathogenic landscapes: two hypotheses on how land use change drives viral emergence Ecology of zoonoses; natural and unnatural histories Impacts of biodiversity on the emergence and transmission of infectious diseases Diseases of humans and their domestic mammals: pathogen characteristics, host range and the risk of emergence Bat origin of human coronaviruses Bats: Important reservoir hosts of emerging viruses Host and viral traits predict zoonotic spillover from mammals Bats as reservoirs of severe emerging infectious diseases Isolation and characterization of a bat SARS-like coronavirus that uses the ACE2 receptor Bats are natural reservoirs of SARS-like coronaviruses Severe acute respiratory syndrome coronavirus-like virus in Chinese horseshoe bats Middle East respiratory syndrome coronavirus in bats, Saudi Arabia Further evidence for bats as the evolutionary source of Middle East respiratory syndrome coronavirus A pneumonia outbreak associated with a new coronavirus of probable bat origin Global epidemiology of bat coronaviruses Bats and coronaviruses Discovery of seven novel mammalian and avian coronaviruses in the genus Deltacoronavirus supports bat coronaviruses as the gene source of Alphacoronavirus and Betacoronavirus and avian coronaviruses as the gene source of Gammacoronavirus and Deltacoronavirus Fatal swine acute diarrhea syndrome caused by an HKU2-related coronavirus of bat origin A new bat-HKU2-like coronavirus in swine Prevalence and genetic diversity of coronaviruses in bats from China Bat coronavirus in Brazil related to Appalachian Ridge and porcine epidemic diarrhea viruses Ecosystem services provided by bats Global patterns in coronavirus diversity Optimizing viral discovery in bats Global hotspots and correlates of emerging zoonotic diseases Emerging infectious diseases in southeast Asia: regional challenges to control Zoonoses in South-East Asia: a regional burden, a global threat Bat coronaviruses and experimental infection of bats, the Philippines Identification of a severe acute respiratory syndrome coronavirus-like virus in a leaf-nosed bat in Nigeria Identification of mosquito bloodmeals using mitochondrial cytochrome oxidase subunit I and cytochrome b gene sequences PREDICT 1 & 2 Test Data HealthMap Database Group C betacoronavirus in bat guano fertilizer Coronaviruses in guano from Pteropus medius bats in Peradeniya Diversity of coronavirus in bats from Eastern Thailand Virome profiling of bats from Myanmar by metagenomic analysis of tissue samples reveals more novel mammalian viruses Circulation of Alphacoronavirus, Betacoronavirus and Paramyxovirus in Hipposideros bat species in Zimbabwe Recombination, reservoirs, and the modular spike: mechanisms of coronavirus cross-species transmission Bats, coronaviruses, and deforestation: Toward the emergence of novel infectious diseases? 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 The recent emergence of bat-borne zoonotic viruses warrants vigilant surveillance in their natural hosts. keywords: bats; coronaviruses; guano; health; host; human; myanmar; samples; sars; species cache: cord-310061-nro623aa.txt plain text: cord-310061-nro623aa.txt item: #56 of 85 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: 2891 flesch: 45 summary: In a recent study Hogan and co-workers made a similar observation while assessing the utility of pooled sample testing strategy to detect community transmission of SARS-CoV-2 in San Francisco Bay Area, CA, USA. At the reported point prevalence of 4.8% among the individuals tested in this study, the NPV of pooled sample strategy was around 96%; thereby suggesting the possibility of missing infected cases and risking community transmission from undiagnosed individuals. keywords: covid-19; pcr; pools; samples; strategy; study; testing cache: cord-313107-6cfenpxm.txt plain text: cord-313107-6cfenpxm.txt item: #57 of 85 id: cord-313670-tbah33ro author: Cannovo, Nunzia title: Regulation of Biobanks in Italy date: 2020-09-02 words: 3402 flesch: 30 summary: 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) . In Italy, biobanks are defined as service units, without direct profit-making purposes, for the collection and conservation of human biological material used for diagnostic purposes, for studies of biodiversity and for research (52) . keywords: biobank; cells; data; distribution; information; material; research; samples; tissues cache: cord-313670-tbah33ro.txt plain text: cord-313670-tbah33ro.txt item: #58 of 85 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: 7455 flesch: 48 summary: There was virtually no mask wearing reported by farmworker family respondents, and only some use of masks reported by nonfarmworker respondents. In all cases, we will compare farmworker families and families with no worker engaged in farm work. keywords: behaviors; covid-19; families; farmworker; health; knowledge; masks; nonfarmworker; respondents; sample; study; workers cache: cord-313887-8sabsrgy.txt plain text: cord-313887-8sabsrgy.txt item: #59 of 85 id: cord-314503-u1y1bznk author: Jaluria, Pratik title: A perspective on microarrays: current applications, pitfalls, and potential uses date: 2007-01-25 words: 7765 flesch: 37 summary: Microcirculation The use and analysis of microarray data Microarray expression profiling: capturing a genome-wide portrait of the transcriptome Microarray expression profiling: analysis and applications From patterns to pathways: gene expression data analysis comes of age Bioinformatics in microbial biotechnology -a mini review Computational analysis of microarray data Differential gene expression in recombinant Pichia pastoris analysed by heterologous DNA microarray hybridization An analysis of the use of genomic DNA as a universal reference in two channel DNA microarrays A framework to analyze multiple time series data: a case study with Streptomyces coelicolor Design of studies using DNA microarrays Applications of microarrays in the pharmaceutical industry Methods and approaches in the analysis of gene expression data Uncovering evolutionary patterns of gene expression using microarrays Microarray analysis of gene expression during the cell cycle Biological methods for cell-cycle synchronization of mammalian cells TM4: a free, open-source system for microarray data management and analysis Comparisons and validation of statistical clustering techniques for microarray gene expression data Cluster analysis and display of genome-wide expression patterns Systematic determination of genetic network architecture Fundamentals of Biostatistics Environmental genomics: exploring the unmined richness of microbes to degrade xenobiotics Transcriptional response of Candida albicans to nitric oxide and the role of the YHB1 gene in nitrosative stress and virulence High-resolution mutation mapping reveals parallel experimental evolution in Without these considerations, it can be exceedingly difficult to ascertain valuable information from microarray data. keywords: analysis; arrays; control; data; dna; experiments; expression; genes; methods; microarray; number; researchers; samples; technology cache: cord-314503-u1y1bznk.txt plain text: cord-314503-u1y1bznk.txt item: #60 of 85 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: 6344 flesch: 38 summary: 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 RNA viruses cause significant human pathology and are responsible for the majority of emerging zoonoses. 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. keywords: genome; hcv; hiv; human; mapping; panel; plasma; reads; rna; rrna; samples; sequences; virus; viruses cache: cord-314753-xflhxb13.txt plain text: cord-314753-xflhxb13.txt item: #61 of 85 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: 4466 flesch: 37 summary: Extra care during tissue handling was needed to avoid tissue damage, and to retain whole-organ tissue architecture for handling, collection, and processing prior to fixation. Extra care during tissue handling and collection was required to avoid tissue damage and loss of tissue architecture prior to fixation. keywords: analysis; carcasses; et al; handling; omics; rna; samples; space; thawing; tissue cache: cord-315054-kji2kfek.txt plain text: cord-315054-kji2kfek.txt item: #62 of 85 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: 11582 flesch: 39 summary: Apart from the aforementioned strengths of this system, it did exhibit certain limitations (Zhu et al., 2014) . More recently, Zhu et al. developed an immunoassay based on similar concepts, but with certain alterations to expunge the existing drawbacks (Zhu et al., 2014) . keywords: acid; amplification; antibodies; assay; aunps; detection; diagnosis; dna; ecm; et al; gold; hiv; lod; magnetic; nps; nucleic; poc; range; sample; sensitivity; size; system; time; virus cache: cord-317213-vhprfb1o.txt plain text: cord-317213-vhprfb1o.txt item: #63 of 85 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: 5692 flesch: 52 summary: Overall, a leucine codon was found in the majority (39/43; 91%) of FIP tissue samples, but a significant number had a methionine codon (4/43; 9%). Second, a significant number (9%) of FIP tissue samples had a methionine codon at this position. keywords: cats; codon; faecal; fcov; feline; fip; pcr; position; protein; samples; tissue cache: cord-319685-dw0qsl4s.txt plain text: cord-319685-dw0qsl4s.txt item: #64 of 85 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: 3461 flesch: 47 summary: Pathophysiology, transmission, diagnosis, and treatment of coronavirus disease 2019 (COVID-19): a review Diagnostic accuracy of canine scent detection in early-and late-stage lung and breast cancers Trained dogs identify people with malaria parasites by their odour Using dog scent detection as a point-of-care tool to identify toxigenic clostridium difficile in stool Canine detection of the volatilome: a review of implications for pathogen and disease detection Realtime detection of a virus using detection dogs Biomedical scent detection dogs: would they pass as a health technology? Furthermore, detection dogs were provided both negative control samples with and without previous BPL treatment to exclude hydrolysed BPL as a potential distracting reagent. keywords: cov-2; covid-19; detection; dogs; individuals; samples; sars; study; training cache: cord-321549-r7bmtloy.txt plain text: cord-321549-r7bmtloy.txt item: #65 of 85 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: 9786 flesch: 42 summary: This is an old technique that was used in the early days of PCR systems, with three baths with different temperatures and a laboratory technician or robot to move a basket with samples from bath to bath. There was another push to release PCR systems for POC applications and this has contributed to disease diagnosis during pandemics such as the 2014 Ebola outbreak. keywords: amplification; analysis; cartridge; chamber; chip; detection; dna; nucleic; pcr; poc; polymerase; preparation; reaction; rna; sample; system; temperature; test; time; viral; virus cache: cord-323973-wszo9s3d.txt plain text: cord-323973-wszo9s3d.txt item: #66 of 85 id: cord-324944-ixh3ykrc author: Mitsakakis, Konstantinos title: Diagnostic tools for tackling febrile illness and enhancing patient management date: 2018-12-05 words: 20813 flesch: 41 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. Nucleic acid amplification technologies (NAATs) are based on sequence-specific recognition and amplification of unique target regions in the genome of pathogens to be detected. keywords: acid; amplification; assay; blood; care; cartridge; detection; diagnosis; diseases; dna; e.g.; febrile; fever; fig; health; infections; malaria; management; nucleic; patients; pcr; platform; point; process; reaction; reagents; sample; specific; system; target; technologies; technology; test; time; tools; use; virus cache: cord-324944-ixh3ykrc.txt plain text: cord-324944-ixh3ykrc.txt item: #67 of 85 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: 6114 flesch: 31 summary: Although these small differences in protein extraction results seen using MPLEx should be considered in proteomics studies employing absolute quantification, they likely do not introduce artifacts in the results, as these studies typically have very small (up to 15%) errors when stable isotope-labeled peptides are used as internal standards (28) and up to 2-fold to 3-fold variations in label-free analyses (29, 30) . We then calculated the variance of protein measurements by comparing different extraction protocols. keywords: analysis; data; extraction; fig; measurements; metabolites; mplex; protein; proteomics; protocol; results; samples cache: cord-326133-d46wbfrx.txt plain text: cord-326133-d46wbfrx.txt item: #68 of 85 id: cord-326380-9ecsp66y author: Griesemer, Sara B title: Assessment of sample pooling for clinical SARS-CoV-2 testing date: 2020-05-27 words: 2239 flesch: 43 summary: To investigate this possibility, detection rates in pooled samples were evaluated, with extensive assessment of pools containing weak positive specimens. Methods for pooling vary widely and testing large numbers of pooled samples is not possible without an inherent loss of sensitivity. keywords: detection; pooling; pools; samples; specimens; testing cache: cord-326380-9ecsp66y.txt plain text: cord-326380-9ecsp66y.txt item: #69 of 85 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: 4840 flesch: 44 summary: The software BLAST was then employed to first compare the representative sequences (RS) against virus-only nucleotide and protein databases that were collected by selection of virus sequences from GenBank NT and GenBank NR databases, respectively, to identify viral nucleotide candidate RS (nRS) and protein candidate RS (pRS) with E-value cutoffs of 10 -5 and 10 -3 , respectively. We also observed a considerable number of viral reads corresponding to various genera in some samples (B27, B46, B49, B58, B66, and B69), despite the absence of specific primers in the panel for their enrichment. keywords: detection; enrichment; genus; number; panel; pcr; primer; reads; samples; sequences; sequencing; viruses cache: cord-329162-6w8qcv1c.txt plain text: cord-329162-6w8qcv1c.txt item: #70 of 85 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 flesch: 47 summary: Based on these findings, our study focused on pheasant chicks up to eleven weeks of age. Previous studies on pheasants indicated that the most sensitive age class for infectious diseases was pheasant chicks, possibly due to a higher susceptibility keywords: ac1; ac2; ac3; age; animals; birds; chicks; germany; inflammation; mycoplasma; pcr; pheasant; population; samples; virus cache: cord-333413-8buawes0.txt plain text: cord-333413-8buawes0.txt item: #71 of 85 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: 6079 flesch: 49 summary: [38] We found no reports in which such oral streptococci were evaluated as indicators of oral contamination of dental equipment surfaces. This article addresses the difficult task of infection control assessment and monitoring for oral contamination on dental operatory surfaces handled during dental treatment. keywords: ahs; contamination; control; dental; infection; operatory; patients; percent; saliva; samples; sampling; surfaces cache: cord-335372-tncjfdtp.txt plain text: cord-335372-tncjfdtp.txt item: #72 of 85 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: 2194 flesch: 46 summary: Summary of probable SARS cases with onset of illness from 1 Laboratory-acquired severe acute respiratory syndrome Severe acute respiratory syndrome (SARS) in Taiwan, China Update 4: review of probable and laboratory-confirmed SARS cases in southern China Investigation into China's recent SARS outbreak yields important lessons for global public health Changes in antibody avidity after virus infections: detection by an immunosorbent assay in which a mild protein-denaturing agent is employed Avidity of IgG in serodiagnosis of infectious diseases Comparative evaluation of the use of immunoblots and of IgG avidity assays as confirmatory tests for the diagnosis of acute EBV infections Differential maturation of avidity of IgG antibodies to gp41, p24 and p17 following infection with HIV-1 Measurement of antibody avidity can be used to differentiate primary infection from reexposure and to assess humoral responses to candidate vaccines 2003 and January 2004) keywords: antibody; avidity; infection; samples; sars cache: cord-335375-n6q70o35.txt plain text: cord-335375-n6q70o35.txt item: #73 of 85 id: cord-336103-ufvq0ngl author: Sharma, R. title: Optimal sample pooling: an efficient tool against SARS-CoV-2 date: 2020-07-04 words: 1565 flesch: 55 summary: The determination of sample pool size for each lab using its prevalence rate would yield desired efficiency and be easy to implement. Hence, sample pool size should be decided individually for a testing facility using the prevalence rates recorded by the same lab. keywords: pooling; sample; size; testing cache: cord-336103-ufvq0ngl.txt plain text: cord-336103-ufvq0ngl.txt item: #74 of 85 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: 5039 flesch: 42 summary: Here we have used two of the most common NGS technologies (Nanopore and Illumina) to study the diversity of SARS-CoV-2 found in sewage samples, from the Netherlands and Belgium, and compared these results with the virus diversity found in sequenced clinical samples. Given the high chemical and biological complexity of wastewater samples, virus concentration and RNA extraction methods are crucial parts of the process to reach enough is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted September 22, 2020. . keywords: consensus; cov-2; license; medrxiv; mutations; preprint; samples; sars; sequencing; sewage cache: cord-342538-5bwsm290.txt plain text: cord-342538-5bwsm290.txt item: #75 of 85 id: cord-344131-e7phs0jd author: Ford, Richard B. title: Section 4 Diagnostic and Therapeutic Procedures date: 2012-12-31 words: 40231 flesch: 50 summary: Doing so can enhance significantly the patient's tolerance for the displacement of skin during the period of administration and, in small patients, prevent hypothermia. Additional training and/or experience is recommended for performing tracheoscopy in small patients. keywords: administration; animal; aspiration; biopsy; biopsy needle; bladder; blood; bone; catheter; cats; cells; collection; contrast; culture; disease; dogs; end; examination; figure; fluid; hair; hours; marrow; material; nasal; needle; patient; place; pressure; procedure; sample; site; skin; slide; syringe; technique; tissue; tract; tube; urinary; urine; use cache: cord-344131-e7phs0jd.txt plain text: cord-344131-e7phs0jd.txt item: #76 of 85 id: cord-344627-w2efsshj author: Han, Tae-Hee title: Human Bocavirus 2 in Children, South Korea date: 2009-10-17 words: 1441 flesch: 41 summary: A small number of pulmonary M. haemophilum infections associated with AIDS or solid organ or bone marrow transplantation have been described (1) . We report pulmonary M. haemophilum infection in a woman who had been immunosuppressed by tumor necrosis factor-α antagonist (TNF-αA) (adalimumab) treatment for rheumatoid arthritis. keywords: children; hbov-2; samples; virus cache: cord-344627-w2efsshj.txt plain text: cord-344627-w2efsshj.txt item: #77 of 85 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: 7910 flesch: 44 summary: Different strategies of electrochemical sensing have been used for DNA electrochemical detection: (1) direct DNA electrochemistry, (2) indirect DNA electrochemistry, (3) DNA-specific redox indicator detection, (4) DNA-mediated charge transport, and (5) nanoparticle-based electrochemistry amplification. To our knowledge there is no evidence in the literature of analysis of fungi via electrochemical detection of DNA or RNA. keywords: ache; assay; biosensor; detection; dichlorvos; dna; durum; extraction; food; method; samples; screen; use; wheat cache: cord-345144-zvu22n8f.txt plain text: cord-345144-zvu22n8f.txt item: #78 of 85 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: 7875 flesch: 29 summary: The present study detected two viral contigs exhibiting similarity (96-99% nucleotide identity) to the Gyrovirus genus in only one RSS-affected sample, VF14-92 A1, which specifically showed similarity to chicken anaemia virus (CAV, genus: Gyrovirus) while the unaffected samples displayed no Circoviridae contigs. Infections Caliciviruses: an overview A very small porcine virus with circular singlestranded DNA Development and application of an RT-PCR test for detecting avian nephritis virus Capsid protein sequence diversity of avian nephritis virus Genome sequence determinations and analyses of novel circoviruses from goose and pigeon Genetic characterization of chicken anaemia virus from commercial broiler chickens in Alabama Conservative fragments in bacterial 16S rRNA genes and primer design for 16S ribosomal DNA amplicons in metagenomic studies Coronavirus pathogenesis Coronavirus pathogenesis and the emerging pathogen severe acute respiratory syndrome coronavirus The complete sequence of a human astrovirus Genetic characterization of a novel calicivirus from a chicken Molecular detection of norovirus in sheep and pigs in New Zealand farms Characterization of a picornavirus isolated from broiler chicks Isolation and some characteristics of an agent inducing anaemia in chicks Velvet: algorithms for de novo short read assembly using de Bruijn graphs Identification and genome characterization of the first sicinivirus isolate from chickens in mainland China by using viral metagenomics Chicken parvovirusinduced runting-stunting syndrome in young broilers The authors would like to acknowledge the Department of Agriculture, Environment, and Rural Affairs (DAERA) for funding this study. keywords: avian; birds; broiler; chicken; contigs; enteric; et al; family; rna; rss; samples; sequencing; study; vf14; viruses cache: cord-345302-wbkfjz8r.txt plain text: cord-345302-wbkfjz8r.txt item: #79 of 85 id: cord-345992-3ij1vbqp author: Drosten, Christian title: SARS Molecular Detection External Quality Assurance date: 2004-12-17 words: 1746 flesch: 38 summary: New case of laboratory-confirmed SARS in Guangdong, China-update 5 Identification of a novel coronavirus in patients with severe acute respiratory syndrome A novel coronavirus associated with severe acute respiratory syndrome Coronavirus as a possible cause of severe acute respiratory syndrome Koch's postulates fulfilled for SARS virus Evaluation of advanced reverse transcription-PCR assays and an alternative PCR target region for detection of severe acute respiratory syndrome-associated coronavirus Quantitative analysis and prognostic implication of SARS coronavirus RNA in the plasma and serum of patients with severe acute respiratory syndrome World Health Organization. WHO SARS International Reference and Verification Laboratory Network: Policy and procedures in the interepidemic period Real-time reverse transcription-polymerase chain reaction assay for SARS-associated coronavirus Real-time polymerase chain reaction for detecting SARS coronavirus Detection of SARS coronavirus in patients with severe acute respiratory syndrome by conventional and real-time quantitative reverse transcription-PCR assays World Health Organization. keywords: laboratories; samples; sars; virus cache: cord-345992-3ij1vbqp.txt plain text: cord-345992-3ij1vbqp.txt item: #80 of 85 id: cord-346906-1wmp43ti author: Lewandowski, Kuiama title: Metagenomic Nanopore Sequencing of Influenza Virus Direct from Clinical Respiratory Samples date: 2019-12-23 words: 6771 flesch: 36 summary: To our knowledge, this is the first report of successfully applying metagenomic Nanopore sequencing directly to respiratory samples to detect influenza virus and generate influenza virus sequences. Having demonstrated our ability to retrieve influenza virus sequences from pooled influenza virus-positive material diluted with negative samples, we next applied our methods to individual anonymized clinical samples, with 40 samples testing influenza virus positive and 10 samples testing influenza virus negative in the clinical diagnostic laboratory. keywords: copies; data; fig; genome; influenza; min; nanopore; reads; rna; samples; sensitivity; sequence; sequencing; time; virus cache: cord-346906-1wmp43ti.txt plain text: cord-346906-1wmp43ti.txt item: #81 of 85 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: 3463 flesch: 47 summary: The fear of COVID-19 scale: development and initial validation Psychometric evaluation of the Arabic version of the fear of COVID-19 scale Coughing while asian': living in fear as racism feeds off coronavirus panic. stuff.co.nz Fear of COVID-19 scale: psychometric characteristics, reliability and validity in the israeli population New Zealand should consider quitting lockdown early, David Seymour says Why are conservatives less concerned about the coronavirus (COVID-19) than liberals? keywords: covid-19; fcv-19s; fear; participants; sample; scale cache: cord-348464-1c08mb2k.txt plain text: cord-348464-1c08mb2k.txt item: #82 of 85 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: 2482 flesch: 39 summary: However, it is unlikely that Asian dust has an important role in epidemics caused by respiratory viral pathogens, because HRV was more frequently detected in non-Asian dust samples than in Asian dust samples. 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. keywords: air; ambient; dust; period; samples cache: cord-353394-lq1f53qv.txt plain text: cord-353394-lq1f53qv.txt item: #83 of 85 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: 5697 flesch: 46 summary: Immunohistochemistry, like biomolecular investigations performed on autopsy tissue samples, allows also to detect the presence of the SARS-CoV-2 in the body, detailing its distribution in single cell types ( fig. In addition, immunohistochemical tests on autopsy samples taken within 1-2 hours from death are more reliable, which is particularly important when these tests are used to describe a new pathologic entity such as COVID-19 ( fig. 3) . keywords: autopsies; autopsy; blood; body; cov-2; death; evisceration; examination; patients; room; samples; sars cache: cord-354372-vfvnjmv1.txt plain text: cord-354372-vfvnjmv1.txt item: #84 of 85 id: cord-355351-seqwx9x1 author: Battey, CJ title: Predicting geographic location from genetic variation with deep neural networks date: 2020-06-08 words: 8745 flesch: 37 summary: 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. The most common approaches to estimating sample locations are based on unsupervised genotype clustering or dimensionality reduction techniques. keywords: data; error; et al; figure; genome; individual; location; locator; model; population; predictions; samples; set; snps; training cache: cord-355351-seqwx9x1.txt plain text: cord-355351-seqwx9x1.txt item: #85 of 85 id: cord-355743-vjiecd4k author: Ghosh, Sabyasachi title: Tapestry: A Single-Round Smart Pooling Technique for COVID-19 Testing date: 2020-04-29 words: 4834 flesch: 58 summary: Sample pools containing one or more positive samples were emulated by spiking with appropriate amounts of RNA fragments to simulate the viral load after pooling. While these strategies can augment testing capacities, they do not substantially improve throughput, since two rounds of testing are still needed to identify positive samples. keywords: license; pooling; positives; preprint; rna; samples; testing; tests; threshold cache: cord-355743-vjiecd4k.txt plain text: cord-355743-vjiecd4k.txt