item: #1 of 61
          id: cord-001387-2g9dc5z4
      author: McIntyre, K. Marie
       title: A Quantitative Prioritisation of Human and Domestic Animal Pathogens in Europe
        date: 2014-08-19
       words: 4582
      flesch: 33
     summary: Finally, the acceptability of the H-index proxy for animal pathogen impact was examined by comparison with other measures. There were statistically significant differences between H-indices for host types (humans, animal, zoonotic), and there was limited evidence that H-indices are a reasonable proxy for animal pathogen impact.
    keywords: animal; animal pathogens; approaches; burden; data; database; differences; different; discontools; disease; domestic; domestic animal; eid2; estimates; european; evidence; fet; fungi; gbd; global; health; higher; host; human; human pathogens; impact; index; indices; infectious; information; list; literature; mcintyre; measures; method; non; oie; pathogens; previous; prioritisation; priority; proxy; quantitative; research; results; risk; scientific; searches; significant; species; status; study; surveillance; table; unpublished; virus; viruses; work; years; zoonoses; zoonotic
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        item: #2 of 61
          id: cord-004914-cnz61qjy
      author: Pedersen, Amy B.
       title: Cross-Species Pathogen Transmission and Disease Emergence in Primates
        date: 2010-03-16
       words: 7177
      flesch: 38
     summary: We expand on our previous analysis to explore the potential for future pathogen host shifts and disease emergence within and between wild primates and humans. Primates with higher phylogenetic risk had a significantly lower proportion of host specific pathogens (all pathogens combined), consistent with an increased frequency of host shifts in species with lots of closely related neighbors, but this was found only in the weighted GLM (P value <0.05, Z = -2.13, df = 103; P = 0.29 for the unweighted GLM).
    keywords: africa; areas; cell; centers; central; close; communities; community; contact; cross; data; davies; density; disease; distribution; ecological; emergence; establishment; et al; evolutionary; factors; fig; frequency; frequent; future; geographic; glm; global; growth; high; hiv-1; host; host shifts; host species; humans; infectious; likely; map; model; neighbors; new; number; opportunity; overlap; pathogen; pathogen species; pedersen; phylogenetic; phylogenetic risk; population; potential; prhs; primate species; primates; proportion; range; rates; regions; related; relatedness; relationship; relatives; richness; risk; sharing; shifts; similarity; size; species; specific; successful; transmission; viruses; wild; wild primates; wildlife
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        item: #3 of 61
          id: cord-009394-3jeexu27
      author: Amalaradjou, Mary Anne Roshni
       title: Modern Approaches in Probiotics Research to Control Foodborne Pathogens
        date: 2012-09-30
       words: 15049
      flesch: 21
     summary: PET helps in the controlled and continuous delivery of probiotic cells in the gut. Probiotic bacteria also affect the composition and function of intestinal microbial population (O'Toole & Cooney, 2008) .
    keywords: ability; able; acid; acidophilus; action; activation; activity; addition; adherence; adhesion; administration; agents; animal; antibiotic; antibody; antimicrobial; application; approaches; associated; attachment; bacteria; bacteriocins; bacteriophages; barrier; beneficial; benefits; bifidobacterium; binding; broiler; campylobacter; casei; cells; challenges; changes; chickens; chitosan; clinical; cocktail; coli; colonization; complex; components; conditions; contamination; control; culture; cytokines; defense; defensins; delbrueckii; delivery; development; diarrhea; different; disease; dna; effect; effective; efficacy; ehec; enhanced; enhancement; enteric; enterococcus; epithelial; epithelial cells; escherichia; escherichia coli; essential; et al; evaluation; expression; factors; faecium; fao; fecal; feed; fermented; food; foodborne; foodborne pathogens; function; gastric; gastrointestinal; gel; gill; gram; growth; gut; health; help; high; host; human; illness; immune; immunity; impact; increase; induced; infection; inflammation; inhibit; inhibition; innate; interaction; intervention; intestinal; invasion; jejuni; junctions; lactic; lactobacillus; listeria; major; matrix; mechanisms; metabolic; mice; microbiota; microflora; microorganisms; milk; model; molecular; molecules; monocytogenes; monolayers; mucosal; mucus; natural; neonatal; nissle; nonpathogenic; o157; organic; pathogens; peptides; permeability; physical; plantarum; population; positive; potential; poultry; poults; prevention; probiotic bacteria; probiotic strains; probiotics; production; products; properties; protective; proteins; rats; receptor; recombinant; reduced; release; research; resident; resistance; responses; review; rhamnosus; role; saccharomyces; safety; salmonella; secretion; serovar; shedding; sherman; shirota; similar; simulated; species; specific; strains; strategies; stress; studies; study; subjects; system; t84; target; tight; toxin; tract; treatment; type; typhimurium; use; viability; virulence; vitro; vivo; wall
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        item: #4 of 61
          id: cord-015484-t1zbpyin
      author: None
       title: Emerging Pathogens: What Are the Sources and How Can They Be Spotted Quickly?
        date: 2003-05-01
       words: 2174
      flesch: 45
     summary: The new tools for identifying new viruses and bacteria have shortened the time needed for identification and genome sequencing. Other tools make it possible to develop medications that may ease the problems with new pathogens.
    keywords: action; cases; cause; cdc; days; disease; drug; fluoroquinolones; genome; health; human; illness; india; infections; multi; national; new; nihniaid; number; organisms; outbreak; pathogens; patient; plan; problems; public; research; resistance; respiratory; salmonella; sars; seeds; sequence; sequencing; sprouts; test; time; understanding; virus; í í
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        item: #5 of 61
          id: cord-016588-f8uvhstb
      author: Sintchenko, Vitali
       title: Informatics for Infectious Disease Research and Control
        date: 2009-10-03
       words: 8187
      flesch: 25
     summary: These tools use either a statistical approach, in which the inferred model and prediction are 1 Informatics for Infectious Disease Research and Control treated as regression problems, or machine learning algorithms, in which the model is addressed as a classification problem (Sintchenko et al. 2008a) . ualberta.ca/basys/cgi/submit.pl) also support comparative analysis and the automated annotation of bacterial genomic (chromosomal and plasmid) sequences (Van Domselaar et al. 2005) .
    keywords: algorithms; analysis; annotation; antibiotic; antimicrobial; approach; assembly; bacterial; barcode; bioinformatics; biological; biomedical; clinical; coding; community; comparative; comparison; computational; control; data; databases; decision; detection; development; diagnostic; different; discovery; disease; diversity; dna; drug; dynamic; et al; example; experimental; factors; field; functional; gene; genetic; genome; genomic; global; health; high; host; human; identification; infectious; infectious disease; informatics; institute; integration; interactions; knowledge; large; learning; length; level; life; lisacek; machine; management; metabolic; methods; microbial; microorganisms; mining; models; molecular; multiple; networks; new; nucleotide; number; open; order; outcomes; particular; pathogen; pathways; patient; phenotypic; post; potential; prediction; prescribing; present; profiles; project; protein; public; quality; range; rapid; recent; reference; related; research; resistance; resources; scale; science; sequence; sequencing; set; sets; silico; single; software; solutions; species; specific; strains; studies; support; surveillance; systems; targets; task; technologies; technology; therapy; time; tools; traditional; treatment; tuberculosis; understanding; unique; use; variation; view; viral; virulence; virus; way; web; wide; world
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        item: #6 of 61
          id: cord-016717-2twm4hmc
      author: Vourc’h, Gwenaël
       title: How Does Biodiversity Influence the Ecology of Infectious Disease?
        date: 2011-06-28
       words: 7767
      flesch: 35
     summary: We highlight that the number of pathogen species is not well known but that new findings are facilitated by the rapid expansion of molecular techniques. For these reasons, combined with the limited knowledge available of the systematics of many pathogens (Brooks and Hoberg 2001) , it is difficult to accurately estimate the number of pathogen species.
    keywords: abundance; addition; amplification; analysis; animals; bacteria; begon; biodiversity; biology; case; change; communities; community; competent; competition; consequences; different; difficult; dilution; disease; distribution; disturbance; diversity; dynamics; ecology; ecosystem; effect; emergence; equator; et al; evolutionary; example; exposure; falciparum; forests; genes; genetic; global; habitat; high; higher; host; host species; human; hypothesis; immune; impact; important; increase; individuals; infectious; infectious diseases; instance; interactions; investigations; knowledge; level; link; loss; low; lyme; major; mhc; molecular; mortality; multi; natural; new; number; organisms; parasite; pathogen species; pathogens; plant; population; question; rate; reservoir; resistance; response; results; richness; risk; role; selective; small; species; species richness; studies; susceptibility; systems; temperate; theoretical; ticks; time; transmission; tropics; vaccines; variability; vector; viral; virulence; viruses; work; years
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        item: #7 of 61
          id: cord-018101-zd4v222b
      author: Kawashima, Kent
       title: Disease Outbreaks: Critical Biological Factors and Control Strategies
        date: 2016-05-31
       words: 13132
      flesch: 39
     summary: One reason of this apparent inconsistency might be the assumption of a fixed mean R. Under this assumption, increased variance in the R distribution increases both the numbers of individuals with extremely high R and low R. Individuals with low R are essentially dead ends in disease infection and high numbers of such individuals will decrease outbreak risk. The SARS example illustrates the need for extensive interdisciplinary efforts, combining expertise from physics (fluid mechanics), biology (especially understanding mechanisms of disease transmission), and building design for resilience to future outbreaks.
    keywords: ace2; acute; affected; airborne; animal; bat; bats; biological; boots; cases; cause; cell; chance; changes; china; civets; close; connections; contact; contagious; contaminated; control; coronavirus; countries; cov; critical; cross; different; difficult; direct; disease; distance; distribution; droplets; dynamics; ebola; effect; emergence; epidemic; et al; events; evolution; example; exposure; factors; future; general; global; health; high; higher; hiv; hong; hospital; host; hotel; human; immune; impact; important; increases; index; individuals; infected; infection; infectious disease; infectiousness; infectivity; influenza; interferon; isolation; key; kong; large; like; likely; lipsitch; lipsitch et; long; low; major; measures; mechanisms; medical; mers; models; mutation; network; new; novel; number; occurs; outbreak; palm; pandemic; pathogen; patients; people; period; plague; population; potential; prevention; probability; protein; public; quarantine; range; rapid; rates; receptor; regions; respiratory; response; risk; rna; role; sars; severe; short; similar; single; society; species; spike; spread; structure; studies; superspreaders; superspreading; susceptible; symptomatic; symptoms; syndrome; theoretical; time; transmission; urban; vector; viral; virulence; virus; viruses; water; world
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        item: #8 of 61
          id: cord-021966-5m21bsrw
      author: Shaw, Alan R.
       title: Vaccines
        date: 2009-05-15
       words: 21179
      flesch: 27
     summary: 67 n NeW ANTIGeN dISCOVeRy MeThOdS n Historically, vaccine antigens were not discovered in the literal sense. The history of vaccine development is rich with immunologic insights that emerged from careful observations of how diseases spread in populations and how such spread differs in disease-naïve and experienced populations, as well as of how innovative experimental approaches revealed fundamental aspects of immune system function.
    keywords: ability; active; adaptive; addition; adenovirus; adjuvant; administration; adults; advances; adverse; age; agents; alum; animal; antibodies; antibody; antibody responses; antigens; apcs; approaches; associated; attenuated; available; bacterial; bcg; benefits; biology; bovine; canarypox; candidate; care; cases; cause; cd4; cd8; cell; cell responses; cellular; certain; challenges; chapter; childhood; children; clear; clinical; cmv; combination; common; concerns; correlate; countries; course; cpg; culture; current; delivery; development; different; diphtheria; discovery; disease; distinct; diverse; dna; dna vaccines; early; effective; effects; efficacy; efforts; end; evaluation; evidence; example; experimental; expressed; expression; fever; fig; form; function; future; gene; general; generation; genetic; genome; global; group; health; hepatitis; herpes; high; hiv; host; host immune; hpv; human; humoral; immune; immune protection; immune responses; immune system; immunity; immunization; immunized; immunogenicity; immunogens; immunologic; impact; important; inactivated; individuals; induction; infected; infection; influenza; initial; innate; instances; interest; large; level; licensed; likely; limited; live; major; malaria; measles; mechanisms; memory; methods; molecular; morbidity; multiple; mva; natural; necessary; need; neutralizing; new; new vaccine; novel; number; particles; passive; pathogen; pathways; pertussis; phase; placebo; polio; polysaccharide; population; potential; poxvirus; preclinical; pregnant; present; presentation; prevention; prior; process; products; programs; protection; protein; public; purified; range; recent; recombinant; recombinant vaccine; relative; replication; respiratory; responses; result; risk; rna; rotavirus; rsv; safety; second; severe; significant; size; smallpox; specific; specific immune; spread; strain; strategies; studies; study; subunit; successful; sufficient; surface; system; target; time; tlrs; transmission; trials; tuberculosis; type; use; vaccination; vaccine; vaccine development; vaccine safety; vaccine vectors; vaccinia; variants; varicella; vectors; viral; virus; virus vaccine; viruses; vivo; vlps; way; women; years
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        item: #9 of 61
          id: cord-023830-w218ogsk
      author: Perlin, David
       title: Rapid Detection of Bioterrorism Pathogens
        date: 2008-09-10
       words: 6051
      flesch: 35
     summary: The problem is not limited to a bioterrorism outbreak as hospital and public health laboratories, confounded by inadequate and slow methodology for pathogen detection, often have difficulty identifying pathogens. This technique allows for continuous, automated operation over an extended time with an assay time is less than 30 min for pathogen detection.
    keywords: acid; acute; agents; amplification; analysis; anthrax; antibodies; antibody; antigen; approach; assays; automated; bacteria; beacons; biological; bioterrorism; blood; cause; clinical; coronavirus; critical; detection; development; diagnostic; different; disease; dna; early; environmental; extraction; false; fidelity; fluorescence; fungi; genes; genetic; genomic; health; high; human; hybridization; identification; infectious; interactions; laboratories; large; levels; like; mass; methods; microarray; molecular; multiplex; new; novel; nucleic; nucleotide; organisms; outbreak; pathogens; pcr; polymerase; positive; possible; presence; primers; probes; public; range; rapid; reaction; real; regions; respiratory; response; ribosomal; rna; samples; sars; sensitive; sensitivity; sequences; single; species; specific; specificity; specimens; suitable; system; taqman; target; techniques; technology; testing; throughput; time; toxin; unknown; viruses; wide
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        item: #10 of 61
          id: cord-024652-4i6kktl0
      author: Santra, Hiran Kanti
       title: Natural Products as Fungicide and Their Role in Crop Protection
        date: 2020-05-12
       words: 20776
      flesch: 25
     summary: to echinocandin LY303366, itraconazole and amphotericin B Biochemical defense mechanisms in cotton plants against Ramularia leaf spot mediated by silicon In vitro antifungal activity of 2-(3,4-dimethyl-2,5-dihydro-1H-pyrrol-2-yl)-1-methylethyl pentanoate, a dihydro -pyrrole derivative Phytoalexin accumulation in tissues of Brassica napus inoculated with Leptosphaeria maculans Naphthalene, an insect repellent, is produced by Muscodor vitigenus, a novel endophytic fungus Activities of essential oils from Asarum heterotropoides var. mandshuricum against five phytopathogens Antagonist actinomycetes metabolites against plant pathogens fungi of agricultural importance Induction of phytoalexins and proteins related to pathogenesis in plants treated with extracts of cutaneous secretions of southern Amazonian Bufonidae amphibians Natural products in crop protection Bioassay-guided isolation of allelochemicals from Avena sativa L.: allelopathic potential of flavone C-glycosides Antifungal activity of crude extracts from brown and red seaweeds by a supercritical carbon dioxide technique against fruit postharvest fungal diseases Rhizospheric streptomycetes as potential biocontrol agents of Fusarium and Armillaria pine rot and as PGPR for Pinus taeda Geldanamycin, a new antibiotic Induction of Fusarium solani mutants insensitive to tomatine, their pathogenicity and aggressiveness to tomato fruits and pea plants Molecular engineering of resveratrol in plants Antifungal properties of surangin B, a coumarin from Mammea longifolia Phytochemical analysis and antifungal activity of moss Bryum cellulare against some phytopathological fungi Studies on antifungal potential of Bryum cellulare against spore germination of fungus Curvularia lunata In vitro antifungal activity of Plagiochasma appendiculatum against Alternaria solani Evaluation of bryophyte for green fungicides as alternative treatment to control plant pathogen Oxidative ring contraction of the phytoalexin cyclobrassinin: a way to brassilexin Brassilexin, a novel sulphur-containing phytoalexin from Brassica juncea L., (cruciferae) Nees against sporulation and growth of postharvest phytopathogenic fungi Evaluation of Streptomyces griseorubens E44G for the biocontrol of Fusarium oxysporum f. sp. lycopersici: ultrastructural and cytochemical investigations Interactions between a root-knot nematode (Meloidogyne exigua) and arbuscular mycorrhizae in coffee plant development (Coffea arabica) Foliar epicuticular wax of Arrabidaea brachypoda: flavonoids and antifungal activity Metabolites of Helminthosporium monoceras: structures of monocerin and related benzopyrans Trans-trans-3, 11-tridecadiene5, 7, 9-triyne-1,2-diol, an antifungal polyacetylene from diseased safflower (Carthamus tinctorius) Mycofumigation by the volatile organic compound-producing fungus Muscodor albus induces bacterial cell death through DNA damage Mycorrhizal fungi and Trichoderma harzianum as biocontrol agents for suppression of Rhizoctonia solani damping off disease of tomato Effect of volatile metabolites of Trichoderma species against seven fungal plant pathogens in vitro Production of gliotoxin on natural substrates by Trichoderma virens Studies on antagonistic effect against plant pathogenic fungi from endophytic fungi isolated from Houttuynia cordata Thunb.
    keywords: ability; abiotic; accumulation; acetate; acid; actinobacteria; actinomycetes; action; activities; activity; agar; agent; agricultural; albus; alcohols; algae; alkaloids; alternaria; analysis; antagonistic; antibacterial; antibiotics; antifungal; antifungal activity; antifungal compounds; antimicrobial; antimicrobial activity; antioxidant; apples; application; arbuscular; area; aromatic; aspergillus; associated; association; attack; bacillus; bacterial; banerjee; bean; bioactive; bioactive compounds; bioactivity; biochemical; biocontrol; biological; biosynthesis; blight; botrytis; brassica; broad; brown; bryophytes; butanoic; butanol; carbon; causal; cause; cell; cellular; cereals; change; characterization; chemical; chinese; chitinases; cinerea; cinnamomum; cladosporium; colletotrichum; colonization; commercial; common; components; compounds; concentration; conditions; contamination; control; crop; cucumber; culture; cymbopogon; date; day; death; defense; derivatives; development; different; digitatum; direct; disease; diverse; diversity; ecosystem; effect; effective; effectivity; efficacy; elicitors; endophytic; endophytic actinomycetes; endophytic fungi; endophytic streptomyces; environmental; enzymes; essential; ester; et al; ether; evaluation; example; existence; expression; extracts; family; field; fig; flavus; flora; food; france; free; fruits; fungal cell; fungal pathogens; fungal plant; fungi; fungi antifungal; fungicides; fungistatic; fungitoxic; fungus; fusarium; germination; gloeosporioides; glyceolin; graminis; green; group; growth; health; higher; host; host plant; huge; human; identification; importance; increase; india; induced; induction; infected; infection; inhibited; inhibition; inhibitory; interactions; isocoumarins; isoflavonoid; isolated; isolation; jeandet; jeandet et; kingdom; known; laminarin; large; leaf; leaves; life; like; liquid; loss; low; maize; major; management; marine; mechanisms; media; medicinal; medicinal plant; members; membrane; metabolites; method; methyl; methyl-1; microorganisms; mildew; mixture; mode; mold; molecular; molecules; monocerin; morphology; muscodor; mycelial; mycofumigation; mycorrhizal; mycorrhizal fungi; natural; nature; new; new endophytic; nodulisporium; non; novel; number; nutrient; occurrence; oils; organic; organic compounds; origin; oryzae; oxysporum; parts; pathogenesis; pathogenic fungi; pathogens; pathway; penicillium; phenolics; phenols; phoma; physiological; phytoalexins; phytopathogenic; phytophthora; plant; plant extracts; plant growth; plant pathogens; poaceae; polysaccharides; popular; postharvest; potato; potential; present; prime; problem; producers; production; products; properties; property; proteins; pythium; range; reports; resistance; response; result; resveratrol; review; rhizoctonia; rhizospheric; rice; role; root; rot; salicylic; saponins; scab; sclerotinia; screening; search; seaweed; secondary; seedlings; seeds; selection; selective; significant; smith; soil; soilborne; solani; solvents; sorghum; source; southern; soybean; species; spectrum; spore; spot; spp; storage; strain; strawberry; streptomyces; stress; strong; structures; studies; study; suppression; surface; survival; sustainability; symptoms; synthesis; synthetic; system; table; tangerine; techniques; terms; terpenes; terpenoids; tissue; tobacco; tomato; total; treatment; tree; trichoderma; tritici; type; unique; uptake; use; useful; var; variety; vitro; vivo; vocs; volatile; volatile organic; wall; water; weapon; wheat; wilt; world; xylaria; year
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        item: #11 of 61
          id: cord-031017-xjnbmah5
      author: Van Goethem, N.
       title: Perceived utility and feasibility of pathogen genomics for public health practice: a survey among public health professionals working in the field of infectious diseases, Belgium, 2019
        date: 2020-08-31
       words: 8494
      flesch: 27
     summary: Previous surveys in the field of public health genomics focused on: human genomics Whole genome sequencing in clinical and public health microbiology High throughput genomic and proteomic technologies in the fight against infectious diseases The potential of whole genome NGS for infectious disease diagnosis Rapid, comprehensive, and affordable mycobacterial diagnosis with wholegenome sequencing: a prospective study Transforming clinical microbiology with bacterial genome sequencing Routine Whole-Genome Sequencing for Outbreak Investigations of Staphylococcus aureus in a Utility of Whole-Genome Sequencing of Escherichia coli O157 for Outbreak Detection and Epidemiological Surveillance The challenges of implementing an integrated One Health surveillance system in Australia The One Health Approach-Why Is It So Important Needs Assessment for Research Use of High-Throughput Sequencing at a Large Academic Medical Center Knowledge, attitudes, and values among physicians working with clinical genomics: a survey of medical oncologists European survey on knowledge and attitudes of public health professionals on public health genomics: Pilot Study Evidence-based design and evaluation of a whole genome sequencing clinical report for the reference microbiology laboratory How ownership rights over microorganisms affect infectious disease control and innovation: A root-cause analysis of barriers to data sharing as experienced by key stakeholders Survey on the Use of Whole-Genome Sequencing for Infectious Diseases Surveillance: Rapid Expansion of European National Capacities Outcome of EC/EFSA questionnaire (2016) on use of Whole Genome Sequencing (WGS) for food-and waterborne pathogens isolated from animals, food, feed and related environmental samples in EU/EFTA countries LimeSurvey: An Open Source survey tool.
    keywords: activities; additional; analysis; attitude; belgian; belgium; bioinformaticians; clinical; clinicians; concerns; context; control; cost; current; data; diagnostic; different; diseases; e.g.; end; epidemiologists; european; expertise; experts; familiar; feasibility; field; fig; file; food; genome; genomics; health; health professionals; high; hospital; human; implementation; important; infectious; infectious diseases; information; investigations; involved; key; laboratories; laboratory; lack; level; local; main; management; methods; microbiologists; microbiology; molecular; monitoring; national; ngs; outbreak; participants; pathogen; pathogen genomics; population; practice; practitioners; prevention; professionals; providers; public; public health; questionnaire; questions; reference; related; resistance; respondents; responses; results; routine; safety; sequence; sequencing; sharing; study; surveillance; survey; table; technologies; time; training; use; users; utility; value; wgs; working
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        item: #12 of 61
          id: cord-211735-qqm4fbor
      author: Gulec, Fatih
       title: Mobile Human Ad Hoc Networks: A Communication Engineering Viewpoint on Interhuman Airborne Pathogen Transmission
        date: 2020-11-02
       words: 4642
      flesch: 44
     summary: To this end, we propose a communication engineering approach that melts different disciplines such as epidemiology, biology, medicine, and fluid dynamics in the same pot to model airborne pathogen transmission among humans. The aim of this article is to present a unified framework using communication engineering, and to highlight future research directions for modeling the spread of infectious diseases among humans through airborne pathogen transmission.
    keywords: airborne; airborne pathogen; approach; architecture; article; body; breathing; channel; communication; coughing; different; disciplines; diseases; droplets; dynamics; emitted; engineering; environments; epidemic; experimental; fig; human; indoor; infected; infectious; initial; issues; laden; large; layer; literature; mechanisms; mobile; model; modeling; mohanet; molecular; networks; nodes; pathogen; pathogen transmission; reception; relative; research; respiratory; risk; spread; survival; susceptible; transmission; ventilation
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        item: #13 of 61
          id: cord-255230-i6q73bhs
      author: Makhanova, Anastasia
       title: Capturing Fluctuations in Pathogen Avoidance: the Situational Pathogen Avoidance Scale
        date: 2020-08-13
       words: 12476
      flesch: 47
     summary: Future research can benefit from using the SPA scale alongside existing pathogen avoidance scales to further examine parallel and divergent effects associated with chronic versus situational sources of pathogen avoidance. Although the present research validated the scale's function by assessing how experimental manipulations of pathogen threat increase SPA scores, pathogen avoidance is also affected by other situations such as being rejected (Sacco et al. 2014) or imagining oneself in a crowded place (Brown and Sacco 2020) .
    keywords: age; analyses; article; association; aversion; aversive; avoidance; b =; behavioral; biases; chronic; condition; contagion; control; current; differences; disease; disgust; effect; et al; ethnocentrism; experimental; factor; fit; fluctuations; germ; group; higher; human; illness; immune; important; individual; infectability; items; levels; likely; literature; m =; makhanova; manipulation; measure; model; moment; moral; motives; non; obese; order; p =; participants; pathogen; pathogen avoidance; pathogen disgust; pathogen threat; people; perceptions; prejudice; processes; psychological; pvd; questionnaire; reactions; research; responses; sample; scale; scores; self; sexual; significant; situational; situational pathogen; size; social; spa; spa scale; spa scores; state; studies; study; target; test; threat; trait; tybur; validity; white; wipe
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        item: #14 of 61
          id: cord-255351-vp19ydce
      author: Lanata, Claudio F.
       title: Global Causes of Diarrheal Disease Mortality in Children <5 Years of Age: A Systematic Review
        date: 2013-09-04
       words: 5453
      flesch: 43
     summary: We stratified studies by the number of pathogens sought and calculated the unadjusted and age-adjusted medians, as described above, separately for single pathogen studies and for studies that sought 5 to 13 pathogens. GBD used rates reported in diarrhea studies published between 1975 and 2010 done in outpatients, casecontrol, and community-based studies as a reference category to adjust the proportions seen in inpatient studies.
    keywords: age; articles; burden; calicivirus; cases; cause; cherg; children; coli; countries; data; deaths; diarrhea; different; disease; enteropathogenic; epec; estimates; gbd; giardia; global; group; illness; infections; inpatient; isolation; lamblia; median; methods; mixed; months; mortality; norovirus; number; pathogens; prevalence; problem; proportions; review; rotavirus; salmonella; severe; shigella; single; spp; stool; studies; study; surveillance; systematic; table; total; unknowns; vaccine; world; years
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        item: #15 of 61
          id: cord-256543-7kfi2yvu
      author: de Graaf, Miranda
       title: Sustained fecal-oral human-to-human transmission following a zoonotic event
        date: 2016-11-23
       words: 3323
      flesch: 28
     summary: The potential for respiratory droplet-transmissible A/ H5N1 influenza virus to evolve in a mammalian host Year in review 2015: extracorporeal membrane oxygenation Noroviruses as a cause of diarrhea in immunocompromised pediatric hematopoietic stem cell and solid organ transplant recipients High prevalence of prolonged norovirus shedding and illness among hospitalized patients: a model for in vivo molecular evolution Persistent spiking fever in a child with acute myeloid leukemia and disseminated infection with enterovirus Infectious complications and vaccinations in the posttransplant population Prolonged influenza virus shedding and emergence of antiviral resistance in immunocompromised patients and ferrets Twentyeight years of poliovirus replication in an immunodeficient individual: impact on the Global Polio Eradication Initiative Host transmission of Salmonella enterica serovar Typhimurium is controlled by virulence factors and indigenous intestinal microbiota This study showed that NTS strains of persistently infected humans acquired antimicrobial resistance and virulence genes Inoculum size in shigellosis and implications for expected mode of transmission Norwalk virus shedding after experimental human infection An outbreak of gastroenteritis and fever due to Listeria monocytogenes in milk Cell attachment protein VP8* of a human rotavirus specifically interacts with A-type histoblood group antigen Noroviruses and histoblood groups: the impact of common host genetic polymorphisms on virus transmission and evolution Hepatitis E: an emerging awareness of an old disease Molecular biology and replication of hepatitis E virus Hepatitis E virus genotype 1 infection of swine kidney cells in vitro is inhibited at multiple levels Human cryptosporidiosis in Europe Effect of sanitation and water treatment on intestinal protozoa infection: a systematic review and meta-analysis This systemic review and meta-analysis shows how lack of clean water is associated with increased risk of intestinal protozoa infection Pig Ascaris: an important source of human ascariasis in China Assessing the zoonotic potential of Ascaris suum and Trichuris suis: looking to the future from an analysis of the past From the twig tips to the deeper branches: new insights into evolutionary history and phylogeography of Ascaris Prophylactic treatment with the nucleoside analogue 2 0 -C-methylcytidine completely prevents transmission of norovirus Here, we present a framework of human-to-human transmission of zoonotic pathogens that considers the factors relevant for fecal-oral human-to-human transmission route at the levels of host, pathogen, and environment.
    keywords: adaptation; addition; amplifiers; bacteria; clinical; conditions; contact; contaminated; disease; emergence; enteric; environment; event; example; factors; fecal; food; genes; health; hepatitis; high; host; human; human transmission; immune; impact; important; infection; influenza; intestinal; key; likelihood; multiple; oral; oral route; oral transmission; outbreak; parasites; pathogens; patients; population; research; risk; route; salmonella; shedding; species; specific; sustained; transmissible; transmission; transmit; typhimurium; virus; viruses; water; zoonotic
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        item: #16 of 61
          id: cord-256615-gvq8uyfk
      author: Rosenberg, Ronald
       title: Detecting the emergence of novel, zoonotic viruses pathogenic to humans
        date: 2014-11-22
       words: 6694
      flesch: 42
     summary: Understanding how such adaptability works could focus our attention on those virus families or species with the greatest chance of infecting humans but how this knowledge could be used more specifically to identify potential threats to humans among animal viruses, as has recently been proposed Because all scientists worked in a single unit connections between human virus isolates and those from animals or vectors were readily made.
    keywords: ability; acute; admission; africa; animal; arboviruses; areas; arthropods; attention; cases; cause; cells; chikungunya; common; contact; countries; data; days; discovery; disease; diversity; east; emergence; endemic; epidemic; evidence; example; families; febrile; fever; fig; genomes; geographic; global; health; heartland; high; hospital; host; human; illness; increase; infectious; influenza; known; laboratory; limited; long; lujo; malaria; mammal; men; mers; methods; modeling; new; non; novel; number; pathogens; populations; potential; public; range; rate; recent; replication; research; respiratory; richness; risk; rna; single; sites; species; strategy; support; surveillance; symptoms; tier; time; transmission; tropical; tropics; unknown; vector; vertebrate; viral; viruses; west; wild; world; year; zoonoses; zoonotic
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        item: #17 of 61
          id: cord-257802-vgizgq2y
      author: Uttamchandani, Mahesh
       title: Applications of microarrays in pathogen detection and biodefence
        date: 2008-11-12
       words: 6576
      flesch: 32
     summary: [48] also developed protein microarrays for simultaneous diagnostics using parasitic and viral antigens. [49] monitored the antibody profiles of SARS patients using protein microarrays containing 82 purified coronavirus proteins.
    keywords: ability; able; accuracy; agents; analysis; antibodies; antibody; antigens; applications; biodefence; biological; capabilities; category; causes; cdc; clinical; colleagues; coronavirus; days; detection; development; diagnostics; disease; dna; environmental; example; figure; future; genetic; genome; greater; health; high; host; human; hybridization; identification; immobilized; impact; infection; influenza; laboratory; low; major; microarrays; molecular; multiplexed; non; novel; oligonucleotide; organisms; pathogen; pcr; peptide; pestis; platforms; potential; presence; present; probes; profiling; protein; proteome; public; rapid; related; research; resequencing; respiratory; response; result; samples; sars; screening; sensitivity; sequence; sera; small; species; specific; specificity; strains; systems; target; technology; threat; throughput; tiling; time; tularensis; unique; use; vaccine; vaccinia; viral; virulence; virus; viruses; wide; yersinia
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        item: #18 of 61
          id: cord-258139-x4js9vqe
      author: Callan, Robert J
       title: Biosecurity and bovine respiratory disease
        date: 2005-03-04
       words: 7692
      flesch: 34
     summary: This problem has an infectious origin, and it is by far the most frequently occurring form of cattle respiratory disease. In general, nasal shedding of viral respiratory pathogens is significantly reduced by 14 days after infection but may persist longer in individual animals, which suggests that quarantine for approximately 14 to 21 days should significantly reduce the exposure and transmission of these pathogens within an operation.
    keywords: adult; agents; airborne; ambient; animal; areas; authors; bacterial; beef; biosecurity; bovine; bovine respiratory; brdc; bvdv; calf; calves; cattle; common; contact; cow; dairy; decrease; density; development; diarrhea; disease; dust; effect; effective; environmental; epidemiology; exposure; factors; fans; feedlot; general; health; herd; high; housing; humidity; immune; important; improved; increase; individual; infected; infection; levels; livestock; management; means; milk; multiple; mycoplasma; occurrence; particles; pathogens; pneumonia; population; potential; practical; practices; prevalence; prevention; primary; problems; production; programs; rate; relative; resistance; respiratory; respiratory disease; respiratory pathogens; risk; role; shedding; significant; single; spp; spread; stocking; stress; survival; systems; temperature; time; tract; transmission; vaccination; vaccine; ventilation; viral; virus
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        item: #19 of 61
          id: cord-260420-4s7akmdp
      author: Mubareka, Samira
       title: Bioaerosols and Transmission, a Diverse and Growing Community of Practice
        date: 2019-02-21
       words: 4022
      flesch: 17
     summary: Ongoing research has also facilitated the development and dissemination of procedures and protocols for experimental work, including artificial aerosols, as well as animal models of transmission including the ferret model for influenza virus transmission and macaque model for Ebola virus transmission (34, 35) . The effect of environmental parameters on the survival of airborne infectious agents Exposure to influenza virus aerosols during routine patient care Influenza aerosols in UK hospitals during the H1N1 (2009) pandemicthe risk of aerosol generation during medical procedures Human viral pathogens are pervasive in wastewater treatment center aerosols Respiratory performance offered by N95 respirators and surgical masks: human subject evaluation with NaCl aerosol representing bacterial and viral particle size range Comparison of aerosol and bioaerosol collection on air filters Water and air ozone treatment as an alternative sanitizing technology Effect of different disinfectants on bacterial aerosol diversity in poultry houses Drivers of airborne human-to-human pathogen transmission Challenge of liquid stressed protective materials and environmental persistence of ebola virus.
    keywords: acute; advances; aerobiology; african; agents; agricultural; air; airborne; animal; animal health; approach; assessment; bioaerosols; content; control; coronavirus; cov; data; detection; development; different; dispersion; effects; efforts; engineering; environmental; experimental; exposure; fever; field; gaps; health; healthcare; human; industrial; infectious; influenza; knowledge; limited; major; mers; metagenomics; models; network; new; novel; occupational; outbreak; pathogens; potential; prevention; progress; public; research; respiratory; risk; samples; sampling; sars; settings; significant; strategies; studies; study; support; surveillance; swine; syndrome; transmission; treatment; understanding; use; viral; virus
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        item: #20 of 61
          id: cord-260679-tm1s6wvj
      author: Lim, Wei Shen
       title: Pneumonia—Overview
        date: 2020-05-20
       words: 6882
      flesch: 35
     summary: A systematic review Peto TE, and Infections in Oxfordshire Research Database (IORD) (2016) Increasing burden of community-acquired pneumonia leading to hospitalisation Corticosteroids in sepsis: An updated systematic review and meta-analysis Mortality reduction among pneumonia patients still substantial despite the impact of coding changes Host-response biomarkers for the diagnosis of bacterial respiratory tract infections Procalcitonin to initiate or discontinue antibiotics in acute respiratory tract infections HIV-1 and bacterial pneumonia in the era of antiretroviral therapy Diagnosis of pneumonia in the ED has poor accuracy despite diagnostic uncertainty Alcohol and the risk of pneumonia: Pneumococcal pneumonia caused 55% of LRI deaths in all ages (1.5 million deaths).
    keywords: acute; admission; adults; agents; analysis; antibiotics; antimicrobial; aspiration; associated; available; bacterial; biomarkers; burden; cap; care; cases; cause; clinical; common; community; countries; data; days; deaths; development; diagnosis; disease; drug; et al; exposure; factors; hap; high; higher; hiv; hospital; host; icu; illness; immune; immunocompromised; important; incidence; increase; infection; influenza; leading; levels; likely; lower; lrti; lung; management; meta; microbiological; mortality; non; pathogens; patients; persons; pneumococcal; pneumonia; present; radiological; range; rates; reduction; resistant; respiratory; response; results; review; rise; risk; serotypes; severe; severity; specific; studies; symptoms; systematic; table; term; therapy; time; tract; treatment; vaccines; vap; ventilator; viral; years
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        item: #21 of 61
          id: cord-263484-afcgqjwq
      author: Ladner, Jason T.
       title: Precision epidemiology for infectious disease control
        date: 2019-02-06
       words: 3991
      flesch: 15
     summary: During infectious disease outbreaks, however, genomic sequence information from the pathogen is arguably more important than an individual's genomic data for designing appropriate treatment and intervention strategies 16 . Pathogen genomes can also be used to inform population-level intervention strategies for infectious disease outbreaks.
    keywords: advances; africa; agencies; analysis; approach; care; cases; characterization; clinical; control; critical; data; design; detection; development; disease; drug; ebola; efforts; epidemic; epidemiology; evolution; example; fever; generation; genetic; genome; genomic; health; hiv; human; individual; infected; infectious; influenza; information; international; interventions; level; medicine; metagenomic; molecular; novel; outbreak; pathogen; patients; point; population; potential; precision; public; rapid; real; recent; research; researchers; response; samples; scale; seasonal; sequence; sequencing; spread; strategies; surveillance; technologies; time; transmission; treatment; use; viral; virus; zika
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        item: #22 of 61
          id: cord-269124-oreg7rnj
      author: Spyrou, Maria A.
       title: Ancient pathogen genomics as an emerging tool for infectious disease research
        date: 2019-04-05
       words: 11937
      flesch: 32
     summary: In this Review, we discuss methodological advancements, persistent challenges and novel revelations gained through the study of ancient pathogen genomes. In the absence of ancient pathogen genomes, the tim ings of infectious disease emergence and early spread are inferred mainly through comparative genomics of modern pathogen diversity 92, 93 , palaeopathological eval uation of ancient skeletal remains 94 or analysis of his torical records 95, 96 .
    keywords: 18th; active; addition; adna; age; agent; analysis; ancient; ancient dna; ancient human; ancient pathogen; approaches; archaeological; assessment; authentication; authenticity; bacterial; bacterium; bayesian; best; black; bone; branch; bronze; bubonic; capture; cases; causative; century; certain; challenges; clock; common; comparative; complete; data; database; date; dating; day; death; detection; determined; different; direct; disease; divergence; diversity; dna; early; emergence; enrichment; environmental; epidemic; eurasia; europe; european; evaluation; events; evidence; evolutionary; example; fast; fig; flea; foci; frequency; genes; genome; genomic; hbv; health; high; historical; history; hosts; human; identification; important; infectious; inference; information; initial; insights; large; leprae; leprosy; likely; limited; lineages; long; low; mapping; medieval; metagenomic; methods; microbial; model; modern; molecular; neolithic; ngs; nucleotide; number; old; organism; pallidum; pandemic; past; pathogen; pathogen dna; pathogen genomes; patterns; pcr; period; pestis; phylogenetic; phylogeny; plague; population; possible; potential; presence; present; program; pseudotuberculosis; rate; reads; recent; recombination; recovery; reference; region; relationships; remains; research; result; retrieval; robust; rodent; sample; sampling; screening; second; sequence; sequencing; set; sets; shotgun; single; size; skeletal; snp; source; species; specific; specimens; spread; strains; studies; study; subsp; target; targeted; techniques; teeth; temporal; term; time; today; tool; transmission; tree; tuberculosis; unique; use; virulence; virus; wide; world; y. pestis; years; yersinia; yersinia pestis
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        item: #23 of 61
          id: cord-269607-xh1hu3k4
      author: Dhir, Bhupinder
       title: Effective control of waterborne pathogens by aquatic plants
        date: 2020-02-14
       words: 7255
      flesch: 33
     summary: Role of Aquatic Plants in Environmental Clean-Up Potential of aquatic macrophytes for removing contaminants from the environment Efficacy of constructed wetlands for removal of bacterial contamination from agriculture return flows Understanding wastewater treatment mechanisms: a review on detection, removal, and purification efficiencies of faecal bacteria indicators across constructed wetlands Potential uses of aquatic plants for wastewater treatment Giardia and Cryptosporidium removal from waste-water by duckweed (Lemna gibba L.) covered pond Rotifers ingest oocysts of Cryptosporidium parvum Role of hydraulic retention time and granular medium in microbial removal in tertiary treatment reed beds Effect of plants and the combination of wetland treatment type systems on pathogen removal in tropical climate conditions Assessment of enteric pathogen shedding during recreational activity and its impact on water quality Pathogen removal in constructed wetlands Ozone and photocatalytic processes for pathogens removal from water: a review Removal of bacteria in subsurface flow wetlands Removal of plant pathogens from recycled greenhouse wastewater using constructed wetlands Removal of pathogens by membrane bioreactors: a review of the mechanisms, influencing factors and reduction in chemical disinfectant dosing Removal of ammonia-N from landfill leachate by vertical flow wetland: a pilot study Nutrient processing capacity of a constructed wetland in western Ireland Fate of physical, chemical and microbial contaminants in domestic wastewater following treatment by small constructed wetlands Removal of Salmonella and microbial indicators in constructed wetlands treating swine wastewater Hydrologic and vegetative removal of Cryptosporidium parvum, Giardia lamblia, and Toxoplasma gondiisurrogate microspheres in coastal wetlands Unit process wetlands for removal of trace organic contaminants and pathogens from municipal wastewater effluents Helminth ova removal from wastewater for agriculture and aquaculture reuse Effects of plant species in a horizontal subsurface flow constructed wetland ephytoremediation of treated urban wastewater with Cyperus alternifolius L. and Typha latifolia L Role of Phytoremediation in reducing cadmium toxicity in soil and water Constructed wetlands Wastewater treatment by stabilization ponds with and without macrophytes under arid climate Wastewater treatment by reed beds an experimental approach Assessment of pathogen removal potential of root zone technology from domestic wastewater Efficiency of a Spanish wastewater treatment plant for removal potentially pathogens: characterization of bacteria and protozoa along water and sludge treatment lines Removal of bacterial pathogen from domestic wastewater in a tropical subsurface horizontal flow constructed wetland Conceptual model and experimental framework to determine the contributions of direct and indirect photoreactions to the solar disinfection of MS2, phiX174, and adenovirus How to increase microbial degradation in constructed wetlands: influencing factors and improvement measures Participation of oxygen and role of exogenous and endogenous sensitizers in the photoinactivation of Escherichia coli by photosynthetically radiation Constructed wetland for wastewater treatment and reuse: a case study of developing country Bioactive chemicals and biologicalbiochemical activities and their functions in rhizospheres of wetland plants Helsinge sludge reed bed system: reduction of pathogenic microorganisms Sunlight inactivation of fecal indicator bacteria in open-water unit process treatment wetlands: modeling endogenous and exogenous inactivation rates Microbial water quality improvement by small scale on-site subsurface wetland treatment Pollution indicators and pathogenic microorganisms in wastewater treatment: implication on receiving water bodies Using Wetlands to Remove Microbial Pollutants from Farm Discharge Water Microbial characteristics of constructed wetlands Harmful cyanobacterial toxic blooms in waste stabilization ponds Contamination of water resources by pathogenic bacteria Removal of enteric bacteria in a surface flow constructed wetland in Yorkshire, England Rhizosphere treatment technology for community wastewater treatment Seasonal pathogen removal by alternative on-site wastewater systems Removal of pathogenic and indicator microorganisms by a constructed wetland receiving untreated domestic wastewater Removal of Pathogenic Bacteria in Algal Turf Scrubbers (Thesis Pathogen removal by aquatic plants mainly occurs because of toxicity exerted by exudates produced by them or attachment of pathogens to plant roots followed by filtration.
    keywords: adsorption; algae; aquatic; attachment; bacteria; biofilms; biological; capacity; chemical; coliforms; concentration; contaminants; contaminated; cryptosporidium; cysts; damage; different; domestic; effective; efficiency; eggs; et al; exposure; fecal; filter; filtration; flow; free; giardia; helminth; high; horizontal; inactivation; increases; indicator; levels; log; macrophytes; mechanisms; media; membrane; microbes; microbial; microorganisms; municipal; organic; oxygen; pathogen removal; pathogens; physical; phytoremediation; plants; ponds; potential; predation; presence; processes; protozoa; quality; rate; reduction; removal; review; rhizosphere; role; roots; salmonella; scale; sedimentation; sharma; significant; species; studies; substances; subsurface; sunlight; systems; technologies; temperature; time; total; toxic; treatment; vegetation; vertical; viruses; vymazal; wastewater; wastewater treatment; waterborne; wetlands; zone
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        item: #24 of 61
          id: cord-276966-wmelyonk
      author: Roe, Kevin
       title: A proposed treatment for pathogenic enveloped viruses having high rates of mutation or replication
        date: 2020-07-08
       words: 5244
      flesch: 33
     summary: All rights reserved 11 Viral mutation rates Accelerated viral dynamics in bat cell lines, with implications for zoonotic emergence Appendix -Structure, genome organization, and infectious cycles Viral escape from endosomes and host detection at a glance AVPdb: a database of experimentally validated antiviral peptides targeting medically important viruses The gamma interferon(IFN-gamma) mimetic peptide IFNgamma (95-133) prevents encephalomyocarditis virus infection both in tissue culture and in mice HIPdb: a database of experimentally validated HIV inhibiting peptides AVPpred: collection and prediction of highly effective antiviral peptides Pentraxins in the activation and regulation of innate immunity Protective immunity against Hepatitis C: many shades of gray Human Vδ2 versus non-Vδ2 γδ T cells in antitumor immunity Tissue adaptations of memory and tissue-resident gamma delta T cells Cytomegalovirus and tumor stress surveillance by binding of a human γδ T cell antigen receptor to endothelial protein C receptor Endothelial cell protein C receptor-dependent signaling Six-of-the-best: unique contributions of γδ T cells to immunology IgE repertoire and immunological memory: compartmental regulation and antibody function Disabling of lymphocyte immune response by Ebola virus Recent mass spectrometry-based techniques and considerations for disulfide bond characterization in proteins Antigen recognition by B-cell and T-cell receptors T cell receptor signaling for γδ T cell development Gamma-delta γδ T cells: friend or foe in cancer development Harnessing microglia and macrophages for the treatment of glioblastoma Innate immunity: the induced response to infection Role of hepatitis C virus envelope glycoprotein E1 in virus entry and assembly Identification of novel functions for hepatitis C virus envelope glycoprotein E1 in virus entry and assembly Conformational states of a soluble, uncleaved HIV-1 envelope trimer Measles virus fusion protein: structure, function, and inhibition Cryo-EM structures of eastern equine encephalitis virus reveal mechanisms of virus disassembly and antibody neutralization Protective antibodies against eastern equine encephalitis virus bind to epitopes 2 in domains A and B of the E2 glycoprotein Antigen-antibody interactions: principles and applications The humoral immune response Stopping untreatable pathogen infections using peptide ligands to sabotage pathogenic cell surface proteins Dual-peptide ligand masks: a proposed treatment approach to stop prion disease dementias Penetration of drugs through the blood-cerebrospinal fluid/bloodbrain barrier for treatment of central nervous system infections Accepted Article 20 In targeting specific viral pathogens, dual-protein ligand masks (for brevity, henceforth called dualprotein ligands) should be able to create a quick and powerful immune memory response with existing memory immune cells against some viral pathogens or virus infected cells, without some of the practical limitations of vaccines.
    keywords: acid; amino; antibody; antigen; antigenic; antiviral; applicable; article; blood; bond; bonding; brain; cells; change; copyright; database; defenses; dual; effective; encephalitis; enveloped; example; genetic; high; host; human; immune; immune cells; infected; infections; innate; ligand; macrophages; mammalian; memory; mhc; mutation; pathogen; peptides; phenotype; protein; protein ligand; rates; receptor; recombination; replication; reserved; response; rights; second; specific; strain; surface; surface protein; system; t cells; targeted; term; treatment; vaccines; viral; viral pathogens; virus; viruses
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        item: #25 of 61
          id: cord-279376-0x4zrfw3
      author: Cherrie, Mark P. C.
       title: Pathogen seasonality and links with weather in England and Wales: a big data time series analysis
        date: 2018-08-28
       words: 5401
      flesch: 39
     summary: The detection of seasonality in pathogen time series data and the identification of relevant weather predictors can improve forecasting and public health planning. key: cord-279376-0x4zrfw3 authors: Cherrie, Mark P. C.; Nichols, Gordon; Iacono, Gianni Lo; Sarran, Christophe; Hajat, Shakoor; Fleming, Lora E. title: Pathogen seasonality and links with weather in England and Wales: a big data time series analysis date: 2018-08-28 journal: BMC Public Health DOI: 10.1186/s12889-018-5931-6 sha: doc_id: 279376 cord_uid: 0x4zrfw3 BACKGROUND: Many infectious diseases of public health importance display annual seasonal patterns in their incidence.
    keywords: additional; aic; air; analysis; associated; associations; cases; climate; coefficients; correlation; current; data; database; days; different; disease; e.g.; effects; england; factors; fig; file; frost; future; group; health; higher; highest; human; humidity; incidence; infectious; influenza; information; level; mean; medmi; meteorological; methods; model; monthly; months; national; non; number; organisms; parameters; pathogens; patterns; period; pressure; prevalence; public; rain; respiratory; results; salmonella; seasonality; series; serotypes; strong; study; summer; sunshine; surveillance; temperature; time; transmission; vapour; variables; virus; wales; weather
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        item: #26 of 61
          id: cord-280107-tulne0v3
      author: Rabaa, Maia A.
       title: The Vietnam Initiative on Zoonotic Infections (VIZIONS): A Strategic Approach to Studying Emerging Zoonotic Infectious Diseases
        date: 2015-09-24
       words: 4420
      flesch: 22
     summary: Specifically, we predict that exotic food production systems with mixed species and limited biosecurity, abattoirs and wet markets operating with minimal basic hygiene, poor cold chains for meat distribution, limited meat inspections in the market sector, and consumption of raw/undercooked blood, meat, organ tissues, and wild animal products promote the risk of zoonotic pathogen transmission. VIZIONS, initiated in March 2012, is now an established platform for one-health research in Vietnam. With VIZIONS, we are aiming to integrate traditional clinical, epidemiological, and medical anthropological methods with new approaches for pathogen detection and discovery, including novel sequencing approaches combined with phylogenetic analysis to characterize pathogen populations.
    keywords: address; aim; animal; animal populations; approach; behavioral; burden; cases; clinical; cohort; component; consumption; cross; data; detection; diagnostic; disease; diversity; duos; emergence; established; et al; events; exposure; factors; farming; figure; governmental; health; high; hospital; human; individuals; infections; infrastructure; international; investigations; key; large; livestock; local; major; methods; novel; origin; outbreaks; pathogens; patients; populations; potential; project; relevant; research; reservoirs; resource; risk; samples; scale; sequencing; species; study; surveillance; syndromes; transmission; understanding; van; vietnam; viral; virus; vizions; wildlife; workers; zoonotic; zoonotic infections
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        item: #27 of 61
          id: cord-282610-zim7nond
      author: Proal, Amy
       title: Myalgic Encephalomyelitis/Chronic Fatigue Syndrome in the Era of the Human Microbiome: Persistent Pathogens Drive Chronic Symptoms by Interfering With Host Metabolism, Gene Expression, and Immunity
        date: 2018-12-04
       words: 12434
      flesch: 33
     summary: Pathogens that persist inside human immune cells and associated tunneling nanotubuoles have been particularly hard to detect. Expanding research on the human microbiome now allows ME/CFS-associated pathogens to be studied as interacting members of human microbiome communities.
    keywords: ability; activation; activity; acute; agents; alzheimer; amyloid; analysis; archaea; associated; aureus; autoimmunity; bacterial; bacteriophage; beta; better; biofilms; blood; body; brain; breast; cancer; capable; cause; cells; central; certain; cfs; changes; characterized; chronic; chronic fatigue; clinical; common; communities; community; composition; conditions; contribute; control; cytokine; damage; different; disease; diversity; dna; dysbiosis; dysfunction; dysregulate; early; ebola; ecosystems; effect; encephalomyelitis; environmental; et al; example; exposure; expression; factors; fatigue; findings; forms; functional; fungi; gene; genome; growth; gut; gut microbiome; healthy; history; hiv; holobiont; host; host immune; human; human microbiome; identification; illness; imbalance; immune; immune response; immune system; immunity; immunopathology; individuals; infected; infection; inflammation; inflammatory; initial; innate; intestinal; intracellular; large; like; likely; manner; measles; mechanisms; metabolism; metabolites; metabolome; mice; microbes; microbial; microbiome; microbiome dysbiosis; mimicry; molecular; myalgic; nervous; novel; number; organisms; pathobionts; pathogens; pathways; patients; persistent; placenta; post; processes; proteins; range; receptor; related; research; response; rna; samples; severe; signaling; similar; single; sites; species; specific; state; studies; study; subjects; successive; survival; symptoms; syndrome; system; target; teams; time; tissue; transcription; treatment; unique; vdr; viral; virome; virulence; viruses; years
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        item: #28 of 61
          id: cord-282628-6uoberfu
      author: Tiwari, Bhagyashree
       title: Future impacts and trends in treatment of hospital wastewater
        date: 2020-05-01
       words: 5921
      flesch: 31
     summary: For instance, the outbreak of Nipah virus diseases was occurred due Anaplasma phagocytophilum [7] Buruli ulcers Mycobacterium ulcerans [8] to the extensive deforestation of a forest of Southeast Asia [24] . These fruit bats are natural reservoir (host) of Nipah virus and their migration to cultivable land lead to transmission of Nipah virus disease in farm animals and subsequently in humans [24] .
    keywords: action; agents; alternative; amr; animals; antibiotics; antimicrobial; approach; aquatic; arboviruses; associated; bacteria; borne; cause; change; class; climate; coli; colistin; community; compounds; concentration; control; cov; deforestation; development; disease; drivers; drug; effects; emergence; environment; estrogen; evolution; example; exposure; factors; food; formation; frequent; gene; global; group; health; help; high; host; human; increase; infected; infection; instance; known; lead; low; lysins; medicines; microbial; model; mosquito; new; novel; organisms; pathogens; persisters; phage; pharmaceuticals; population; potential; presence; prevalence; public; rate; receptor; research; researchers; resistant; results; risk; salmonella; sfts; species; specific; spread; studies; superbugs; surveillance; term; therapy; ticks; toxic; transmission; treatment; ulcerans; vector; viral; virus; viruses; wastewater; water; wildlife; world; zoonotic
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        item: #29 of 61
          id: cord-285778-80baxwgc
      author: None
       title: Introduction to the Immune Response
        date: 2014-10-10
       words: 7980
      flesch: 43
     summary: If a pathogen replicates rapidly, large amounts of DAMPs and PAMPs are present that immediately activate innate leukocytes, including the APCs needed to initiate T cell responses. Innate immune responses are triggered by disruptions to homeostasis caused by either non-infectious or infectious means.
    keywords: activation; adaptive; adaptive immune; adaptive response; antigen; attack; b cells; barriers; blood; body; cancer; cells; chapter; clearance; complex; cytokines; damage; defense; disease; effector; elements; entities; fig; healthy; homeostasis; host; humoral; immune; immune response; immune system; immunity; individual; infection; inflammation; innate; innate immune; innate leukocytes; innate response; intracellular; large; leukocytes; lymphocytes; mechanisms; memory; mhc; molecular; molecules; normal; pamps; particular; pathogen; phagocytosis; present; prms; proteins; receptors; recognition; response; result; self; specific; surface; system; t cells; threat; time; tissues; tolerance; types; unique; vaccination; way
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        item: #30 of 61
          id: cord-288170-i01pdngb
      author: Böhm, R.
       title: Chapter 9 Pathogenic agents
        date: 2007-12-31
       words: 6086
      flesch: 39
     summary: The data in the table show that pathogens for humans and animals are not always limited to materials from warm-blooded individuals, but that they can originate from plant materials as well. Moreover, concerning plant pathogens and seeds, this strategy is ineffective if the products are to be used in agriculture.
    keywords: animals; bacteria; böhm; certain; compost; conditions; contaminated; der; different; easy; eggs; enterococci; environment; epidemiological; exposure; fecal; fig; final; framework; fungi; health; humans; hygienic; importance; inactivation; indicator; indirect; industrial; introduction; involved; isolation; large; limited; materials; means; microbiological; necessary; occupational; order; organic; organisms; origin; parameters; parasites; pathogens; plants; point; presence; present; process; processes; processing; product; properties; raw; recycling; related; relevant; representative; risks; safety; salmonella; sample; sewage; sludge; soil; species; table; technical; temperature; test; time; transmission; treatment; type; und; validated; validation; view; viruses; von; wastes; wastewater
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        item: #31 of 61
          id: cord-289443-46w52de3
      author: Sironi, Manuela
       title: Evolutionary insights into host–pathogen interactions from mammalian sequence data
        date: 2015-03-18
       words: 9373
      flesch: 31
     summary: PLoS Pathog MHC class I antigen presentation: learning from viral evasion strategies An evolutionary analysis of antigen processing and presentation across different timescales reveals pervasive selection A 175 million year history of T cell regulatory molecules reveals widespread selection, with adaptive evolution of disease alleles The intertransmembrane region of Kaposi's sarcoma-associated herpesvirus modulator of immune recognition 2 contributes to B7-2 downregulation The Nef protein of HIV-1 induces loss of cell surface costimulatory molecules CD80 and CD86 in APCs Members of adenovirus species B utilize CD80 and CD86 as cellular attachment receptors Structural basis for langerin recognition of diverse pathogen and mammalian glycans through a single binding site Hiding lipid presentation: viral interference with CD1d-restricted invariant natural killer T (iNKT) cell activation A threonine-based targeting signal in the human CD1d cytoplasmic tail controls its functional expression Evolutionary history of copynumber-variable locus for the low-affinity Fcγ receptor: mutation rate, autoimmune disease, and the legacy of helminth infection One of the few studies of helminth-driven selective pressure in mammals that also integrates evolutionary analysis with epidemiological information Thrombosis as an intravascular effector of innate immunity Dual host-virus arms races shape an essential housekeeping protein An extremely interesting study extending the arms race scenario to a housekeeping protein, the transferrin receptor Evolutionary reconstructions of the transferrin receptor of caniforms supports canine parvovirus being a re-emerged and not a novel pathogen in dogs Escape from bacterial iron piracy through rapid evolution of transferrin Mammalian NPC1 genes may undergo positive selection and human polymorphisms associate with type 2 diabetes Niemann-Pick C1 (NPC1)/ NPC1-like1 chimeras define sequences critical for NPC1's function as a flovirus entry receptor Cell entry by a novel European filovirus requires host endosomal cysteine proteases and Niemann-Pick C1 Multiple cationic amphiphiles induce a Niemann-Pick C phenotype and inhibit Ebola virus entry and infection Inhibition of ebola virus infection: identification of Niemann-Pick C1 as the target by optimization of a chemical probe Small molecule inhibitors reveal Niemann-Pick C1 is essential for Ebola virus infection Evolutionary analysis of the contact system indicates that kininogen evolved adaptively in mammals and in human populations Positive selection during the evolution of the blood coagulation factors in the context of their disease-causing mutations Induction of vascular leakage through release of bradykinin and a novel kinin by cysteine proteinases from Staphylococcus aureus Viral immune modulators perturb the human molecular network by common and unique strategies Genome-wide RNAi screen identifies human host factors crucial for influenza virus replication A novel test for selection on cis-regulatory elements reveals positive and negative selection acting on mammalian transcriptional enhancers PAML 4: phylogenetic analysis by maximum likelihood Accuracy and power of Bayes prediction of amino acid sites under positive selection Bayes empirical Bayes inference of amino acid sites under positive selection Detecting individual sites subject to episodic diversifying selection High sensitivity to aligner and high rate of false positives in the estimates of positive selection in the 12 Drosophila genomes Class of multiple sequence alignment algorithm affects genomic analysis Estimates of positive Darwinian selection are inflated by errors in sequencing, annotation, and alignment The effects of alignment error and alignment filtering on the sitewise detection of positive selection Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level The effect of insertions, deletions, and alignment errors on the branch-site test of positive selection Multiple hypothesis testing to detect lineages under positive selection that affects only a few sites A random effects branchsite model for detecting episodic diversifying selection Modeling the site-specific variation of selection patterns along lineages Performance of standard and stochastic branch-site models for detecting positive selection among coding sequences Statistical properties of the branch-site test of positive selection Towards a systems understanding of MHC class I and MHC class II antigen presentation CD1 antigen presentation: how it works The authors declare no competing interests. In this case the branch of the phylogeny leading to these species may show significant evidence of positive selection .
    keywords: ace2; acid; adaptive; agents; alignment; amino; analysis; antigen; antiviral; approaches; arms; authors; bacterial; basis; bat; bats; binding; branch; branches; case; cd86; cell; cellular; changes; class; common; complement; conflicts; coronavirus; cov; data; determinants; differences; different; disease; diversity; domain; events; evidence; evolution; evolutionary; example; factors; fig; figure; fv1; genes; genetic; genome; high; hiv-1; host; human; hypothesis; immune; immunity; infection; information; interactions; like; likelihood; likely; lipid; loop; major; mammalian; mammals; mers; model; molecular; molecules; mouse; multiple; mx1; natural; niemann; non; npc1; number; observed; pathogen; phylogenetic; pick; positive; positive selection; presentation; pressure; primates; protein; queen; race; rate; recent; receptor; recognition; red; ref; regions; related; residues; restriction; results; retrovirus; review; rodents; sars; selection; selective; sequence; signatures; sites; species; specific; specificity; studies; study; surface; susceptibility; synonymous; system; tlr4; transferrin; trim5; viral; virus; viruses
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        item: #32 of 61
          id: cord-292031-weiwksh6
      author: Ramírez-Castillo, Flor Yazmín
       title: Waterborne Pathogens: Detection Methods and Challenges
        date: 2015-05-21
       words: 7362
      flesch: 27
     summary: Even though culture dependent methods are extensively used for pathogens detection in water, these methods are limited by their low sensitivity and the excessive time needed to obtain reliable results. The Microbiology of the Water Distribution System A Report on an American Academy of Microbiology Colloquium Recommended advanced techniques for waterborne pathogen detection in developing countries Dei-Cas, E. Microbial agents associated with waterborne diseases Global Water, Sanitation, and Hygiene (WASH) Progress on Sanitation and Drinking-Water Contamination of water resources by pathogenic bacteria Millennium Development Goals: Progress towards the Health-Related Millennium Development Goals Waterborne outbreaks reported in the United States Causes of outbreaks associated with drinking water in the United States from A fatal waterborne disease epidemic in Walkerton, Ontario: Comparison with other waterborne outbreaks in the developed world Surveillance for waterborne disease outbreaks associated with drinking water and other nonrecreational water-United States Epidemiology of cholera in the Philippines The 2010 cholera outbreak in Haiti: How science solved a controversy Lessons learned during public health response to cholera epidemic in Haiti and the Dominican Republic Shiga toxin-producing Escherichia coli O104:H4: A new challenge for microbiology Annual Epidemiological Report Food-and Waterborne Diseases and Zoonoses Self-reported diarrhea in a control group: A strong association with reporting of low-pressure events in tap water Global Drinking Water Management and Conservation Optimal Decision-Making Surveillance for waterborne-disease outbreaks associated with drinking water--United States Emerging waterborne pathogens: Can we kill them all? Where do emerging pathogens come from?
    keywords: analysis; approach; assay; assessment; authors; bacteria; biofilms; biosensors; cells; characterization; coli; communities; concentration; conditions; contamination; cost; cryptosporidium; culturable; culture; data; detection; development; different; disease; distribution; dna; dose; drinking; drinking water; environmental; escherichia; example; exposure; false; fish; fluorescence; food; gene; health; high; host; human; hybridization; identification; information; large; low; management; methods; microarray; microbial; microorganisms; molecular; monitoring; multiple; need; new; non; o157; oligonucleotide; optical; order; outbreaks; pathogens; pcr; presence; present; probes; protozoa; public; pyrosequencing; qmra; qpcr; quality; quantification; quantitative; rapid; reaction; real; recent; resistance; response; results; risk; safety; sample; sensitive; sensitivity; single; situ; source; species; specific; spp; state; surface; systems; target; techniques; technologies; technology; time; tool; tracking; treatment; vbnc; viable; viruses; wastewater; water; waterborne; waterborne pathogens; workers
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        item: #33 of 61
          id: cord-294585-dl5v9p50
      author: Klein, H. G.
       title: Pathogen‐reduction methods: advantages and limits
        date: 2009-02-13
       words: 4522
      flesch: 36
     summary: Pathogen-inactivation of components containing red blood cells presents a particularly challenging dilemma. S303 (Helinx), a small molecule designed for pathogeninactivation treatment of red blood cells, is an alkylating agent derived from a quinacrine mustard that belongs to a class of 'frangible anchor linker effectors' (FRALE) compounds.
    keywords: acids; activity; additional; agents; amotosalen; bacteria; bag; blood; cells; clinical; coagulation; components; cross; detergent; disease; dna; donor; enveloped; factors; ffp; filter; fractionation; heat; hepatitis; hiv; human; illumination; inactivation; infected; infectious; infectivity; light; new; non; nucleic; pathogen; patients; pct; photochemical; plasma; platelet; post; potential; process; products; protein; protozoa; psoralen; red; reduction; result; riboflavin; risk; s-303; safety; single; solvent; storage; studies; supply; system; technologies; testing; therapeutic; transfusion; transmission; treatment; trials; ultraviolet; units; viral; viruses; world
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        item: #34 of 61
          id: cord-295469-5an7836u
      author: Ijaz, M. Khalid
       title: Generic aspects of the airborne spread of human pathogens indoors and emerging air decontamination technologies
        date: 2016-09-02
       words: 5752
      flesch: 30
     summary: An overview of methods for experimentally generating and recovering airborne human pathogens is included, along with a discussion of factors that influence microbial survival in indoor air. An overview of methods for experimentally generating and recovering airborne human pathogens is included, along with a discussion of factors that influence microbial survival in indoor air.
    keywords: aerobiology; aerosolization; aerosolized; aerosols; agents; air; air decontamination; airborne; aureus; available; bacteria; cfu; chamber; conditions; contamination; control; device; difficile; disease; droplet; ebola; effect; environmental; experimental; factors; field; fungal; fungi; health; high; human; humidity; indoor; indoor air; infectious; influenza; methods; microbes; microbial; minutes; particles; pathogens; plates; potential; quality; relevant; respiratory; review; rhinovirus; risk; role; rotavirus; samples; sampling; secondary; settings; size; sources; spread; studies; study; surfaces; survival; susceptible; table; technologies; test; testing; transmission; types; variety; vegetative; vehicles; ventilation; viable; virus; viruses
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        item: #35 of 61
          id: cord-297203-f3f31h4r
      author: Afrough, B.
       title: Emerging viruses and current strategies for vaccine intervention
        date: 2019-04-16
       words: 5915
      flesch: 30
     summary: The ease of direct manipulation of viral genomes together with a growing understanding of their biology has led to the development of attenuated virus vaccines with increased safety and immunogenicity. For live attenuated RNA virus vaccines which incorporate error-prone polymerases, reversion to virulence is a distinct possibility after multiple rounds of replication.
    keywords: 17d; ability; advantages; africa; animal; antigen; approach; attenuated; basic; candidates; cases; cells; clinical; control; delivery; development; disease; dna; ebola; effective; efficacy; emergence; expression; fever; gene; global; glycoprotein; health; heterologous; high; host; human; humoral; immune; immunity; immunogenicity; infectious; interest; international; intervention; key; lassa; lasv; live; long; major; model; multiple; mva; new; non; novel; particles; pathogens; platform; populations; potential; protective; public; range; recent; recombinant; replication; replicon; research; responses; result; rna; rvfv; safety; self; similar; single; species; strategies; successful; target; technology; threat; transmission; understanding; vaccination; vaccines; vaccinia; vectors; viral; virulence; virus; viruses; vsv; west; wildlife; work; years; yellow; zoonoses; zoonotic
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        item: #36 of 61
          id: cord-297440-uw263cfc
      author: Peacock, Sharon J
       title: Microbial sequencing to improve individual and population health
        date: 2014-11-19
       words: 1282
      flesch: 32
     summary: Capillary sequencing of the human immunodeficiency virus (HIV) is already used to guide the treatment of patients who are HIV positive, but newer sequencing technologies will bring the added benefit of detecting resistant variants present as a minority of the HIV population in a given individual. Personalized anti-infective therapies and surveillance of emergent pathogen outbreaks are just two examples of the potential benefits of merging the fields of genomics and infectious diseases.
    keywords: antimicrobial; clinical; control; data; diagnostic; diseases; drug; early; emergence; genome; health; hiv; human; individual; infectious; new; outbreak; pathogens; population; resistance; sample; sequence; sequencing; technologies; transmission; tuberculosis; use
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        item: #37 of 61
          id: cord-297621-xunyqlr5
      author: None
       title: Pathogen-Inaktivierungssysteme für Thrombozytenkonzentrate: Stellungnahme
        date: 2018-06-21
       words: 5517
      flesch: 32
     summary: Die Wirkung von THERAFLEX auf Protozoen wurde Die Anwendung von Inaktivierungsmethoden könnte die Sicherheit von Blutkomponenten hinsichtlich dieser Risiken verbessern.
    keywords: abbauprodukte; aber; additive; additivlösung; alle; als; amotosalen; analyse; analysis; anderen; anstieg; anwendung; apheresis; auch; auf; aufgrund; aus; autoren; bacteria; bakterien; behandelten; behandlung; bei; beobachtet; bereits; bildung; bis; blood; blutkomponenten; blutungen; buffy; bzw; cells; clinical; coat; components; concentrates; contamination; cruzi; daher; das; dass; daten; der; des; deutschland; die; dieser; dna; donor; dosis; drei; durch; effect; effekte; efficacy; eine; einfluss; einführung; entwicklung; erhöhte; erreger; evaluation; falciparum; fanden; function; für; gefunden; haben; hcl; hinsichtlich; human; inactivation; inaktiviert; inaktivierung; infectivity; intercept; irradiation; ist; jedoch; kann; klinischen; konnten; können; leishmania; light; lrf; mehr; methoden; mirasol; mit; model; mrna; mögliche; nach; neo; nicht; noch; nukleinsäuren; nur; oder; pathogen; pathogen inactivation; pathogen reduction; pathogeninaktivierung; patienten; photochemical; plasma; plasmodium; platelet; products; protozoen; prt; psoralen; quality; reaktionen; reduction; reviews; riboflavin; risiko; schwerwiegenden; sich; sie; signifikant; sind; solution; sowie; sowohl; storage; streptococcus; studien; system; tab; technology; theraflex; thrombozyten; thrombozytenkonzentrate; transfusion; treatment; trial; trypanosoma; ultraviolet; ultraviolet light; und; unerwünschte; unterschiede; untersucht; untersuchungen; uvc; verfahren; verglichen; verwendet; veränderungen; viren; virus; viruses; vom; von; vor; werden; white; wie; wird; wirksamkeit; wurde; zeigte; zur
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        item: #38 of 61
          id: cord-299790-vciposnk
      author: Ho, Zheng Jie Marc
       title: Clinical differences between respiratory viral and bacterial mono- and dual pathogen detected among Singapore military servicemen with febrile respiratory illness
        date: 2015-06-09
       words: 4075
      flesch: 36
     summary: Such information is of particular importance to countries within the tropical belt where there is a predilection towards multiple pathogens due to the year-round circulation of respiratory pathogens. Finally, diversity in the impact of dual pathogens on clinical manifestations, as seen through the results of other symptoms, is likely indicative of complex and diverse microbial interactions between respiratory pathogens in the upper respiratory tract.
    keywords: 0.001; adenovirus; analysis; associated; bacterial; children; clinical; common; community; controls; cough; differences; different; disease; dual; enterovirus; fri; higher; illness; impact; infections; influenza; interactions; levels; mean; military; mono; monopathogen; multiple; nasal; number; observations; pairs; pathogens; patients; pneumoniae; proportions; research; respective; respiratory; samples; similar; singapore; studies; study; symptoms; table; tract; viral; virus
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        item: #39 of 61
          id: cord-301767-1jv20em8
      author: Alegbeleye, Oluwadara Oluwaseun
       title: Sources and contamination routes of microbial pathogens to fresh produce during field cultivation: A review
        date: 2018-02-03
       words: 18362
      flesch: 30
     summary: The most commonly implicated etiological agents in fresh produce borne illnesses (Brackett, 1994; Buck et al., 2003; Heaton and Jones, 2008; Jung et al., 2014; Callej on et al., 2015) . In recent time, seeds have been recognized as a significant source of inoculum for foodborne illnesses associated with sprout consumption (Mahon et al., 1997; National Advisory Committee on Microbiological Criteria for Foods, 1999; Buck et al., 2003; Yang et al., 2013) .
    keywords: ability; access; acid; activity; agents; agricultural; animals; application; areas; associated; attachment; available; bacteria; bacterial pathogens; beuchat; biofilms; buck et; campylobacter; capable; cases; cattle; certain; characteristics; chemical; clay; coli; coli o157; colonization; compost; conditions; consumption; contaminated; contamination; content; control; crops; cultivation; data; days; defense; detection; development; different; direct; disease; distribution; e. coli; ecology; edible; effect; effective; enteric; enteric pathogens; environmental; epidemiological; erickson et; escherichia; escherichia coli; essential; et al; evidence; example; experimental; factors; farm; fate; fecal; field; flies; foodborne; foodborne pathogens; fresh; fresh produce; fruits; gastroenteritis; greens; groundwater; growing; growth; harris et; harvest; hazards; health; heaton; higher; host; human; human pathogens; illness; immunity; implicated; implications; important; inactivation; incidence; influence; insects; instance; interactions; internalization; investigations; irrigation; irrigation water; islam et; james; jones; jung et; laboratory; land; leafy; leaves; lettuce; levels; likely; lim et; listeria; livestock; long; low; lynch et; management; manure; mechanisms; methods; microbial; microbiological; microorganisms; moisture; monocytogenes; necessary; need; new; newell et; non; numerous; nutrients; o157; occurrence; occurring; odumeru; organic; outbreaks; pachepsky; parasites; particles; pathogens; persistence; phyllosphere; plant; plant pathogens; play; poliovirus; portions; possible; potential; practices; pre; presence; processes; processing; produce; produce contamination; production; properties; proteins; public; quality; rainfall; rates; raw; recent; regions; relevant; research; response; retention; review; risk; rodents; roles; roots; routes; roy et; safety; salmonella; sandy; seeds; serovar; sewage; significant; slurry; soil; sources; species; specific; spinach; spp; sprouts; standards; steele; stomata; storage; strain; strategies; studies; study; surface; surveillance; survival; systems; temperature; time; tissues; tomatoes; transfer; transmission; transport; treatment; type; typhimurium; uptake; use; uyttendaele et; variations; variety; vegetables; viruses; warriner et; wastewater; water; wild; world
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        item: #40 of 61
          id: cord-307803-rlvk6bcx
      author: Balloux, Francois
       title: Q&A: What are pathogens, and what have they done to and for us?
        date: 2017-10-19
       words: 3850
      flesch: 42
     summary: The main arguments for an origin of human pathogens linked to agriculture are based on the proximity between traditional farmers with their livestock and the emergence of higher human population densities in stable settlements enabled by agricultural subsistence. There is also no obvious pattern pointing to the Neolithic revolution as a strong driver for the emergence of human pathogens.
    keywords: ability; africa; age; ancient; authors; bacteria; cause; cells; century; current; cycle; diseases; earth; emergence; environment; epidemic; evolution; evolutionary; example; facultative; genes; genetic; genome; health; hepatitis; high; history; host; human; human pathogens; immune; immunity; infected; infectious; influenza; intracellular; leprosy; life; major; malaria; mycobacterium; new; number; obligate; obvious; origin; pathogenicity; pathogens; pattern; pestis; plague; population; protective; range; recent; reduction; resistance; selective; species; symptoms; transmission; tuberculosis; variants; vast; virulence; viruses; yersinia
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        item: #41 of 61
          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: airway; analysis; animals; antimicrobial; authors; available; bacterial; bal; beef; bovine; bovine respiratory; bovis; brd; bronchoalveolar; calves; catheter; cattle; clinical; contamination; culture; current; detection; diagnosis; different; disease; dns; evidence; feedlot; field; fluid; group; guidelines; haemolytica; healthy; human; identification; important; infection; inflammation; interpretation; issue; knowledge; large; lavage; likely; limited; lower; lung; maldi; mannheimia; medicine; multiple; multocida; nasal; nasopharyngeal; nbal; opportunistic; pasteurella; pasteurellaceae; pathogens; pcr; pneumonia; positive; possible; presence; present; primary; quantitative; rapid; resistance; respiratory; respiratory disease; respiratory tract; results; risk; sample; sampling; secondary; sensitivity; sequencing; single; site; species; specific; studies; swabs; technique; test; testing; therapy; time; tof; tract; ttw; use; viral; viruses; volume
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        item: #42 of 61
          id: cord-308089-q2w9fb0i
      author: Ewald, Paul W.
       title: Evolution of virulence
        date: 2005-03-01
       words: 5407
      flesch: 37
     summary: Though this idea has not been tested directly, geographic variations in virulence and the demonstrated effect of vector proofing of houses on disease transmission suggests that it will work [17] . Theory about the evolution of virulence is fundamentally different for chronic infectious diseases than for acute infectious diseases.
    keywords: acute; agents; allele; antigen; benign; cancer; case; causation; causes; century; chlamydia; chronic; chronic diseases; common; contact; control; diphtheria; diseases; effects; evolutionary; exploitation; framework; frequency; genetic; greater; harmful; high; historical; history; hospital; host; human; increase; individuals; infected; infectious; infectious diseases; level; long; low; management; mild; natural; new; pathogens; people; pneumoniae; populations; potential; run; schizophrenia; selection; senegal; severe; sexual; sexual transmission; strains; term; theory; time; toxin; transmission; type; understanding; vaccination; vaccine; variants; vector; virulence; virulent; virus; water
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        item: #43 of 61
          id: cord-310439-z0bxsjug
      author: Martin, R. R.
       title: Pathogen-Tested Planting Material
        date: 2014-12-31
       words: 7706
      flesch: 42
     summary: However, work with grapevines has shown that many of the viruses were related to mycoviruses rather than plant viruses (Al Rwahnih et al., 2011; Coetzee et al., 2010) . Role of international organizations Plant Diseases: Their Biology and Social Impact De novo reconstruction of consensus master genomes of plant RNA and DNA viruses from siRNAs Control of viruses affecting potatoes through seed potato certification programs Plant disease: A threat to global food security Application of high-throughput DNA sequencing in Phytopathology Molecular characterization and population structure of Blackberry vein banding associated virus, a new ampelovirus associated with blackberry yellow vein disease Certified − Feasibility of Audit-Based Certification to Prevent Invasive Plant Pests in the Horticultural Industry Profiling viral infections in grapevine using a randomly primed reverse transcription-polymerase chain reaction/macroarray multiplex platform The control of African cassava mosaic virus disease: Phytosanitation and/or resistance? Understanding and exploiting late blight resistance in the age of effectors Microarray-based detection and genotyping of viral pathogens Viral discovery and sequence recovery using DNA microarrays Certification for plant viruses
    keywords: agriculture; anonymous; biological; block; bmps; cases; certification; certification programs; certified; conditions; control; countries; country; crops; culture; cycles; detection; disease; effective; et al; example; food; free; fruit; genetic; germplasm; grapevines; health; heat; impact; important; international; introduction; ippc; laboratory; level; major; material; measures; meristem; mosaic; movement; multiple; new; nursery; pathogens; pests; phytosanitary; plant pathogens; plants; potato; potatoes; present; process; production; programs; propagation; purity; quarantine; range; region; requirements; risk; scheme; seed; sequencing; single; spread; standards; states; system; targeted; testing; therapy; time; tip; tissue; trade; transmission; treatments; type; united; vegetative; viruses; years
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        item: #44 of 61
          id: cord-312161-egwo19oc
      author: Aw, Tiong Gim
       title: Detection of pathogens in water: from phylochips to qPCR to pyrosequencing
        date: 2011-12-05
       words: 4554
      flesch: 22
     summary: It is clear that the field of environmental pathogen detection is and will remain highly dynamic with tremendous potential for development of new tools and continuous improvement of existing concepts. High-density microarrays, quantitative real-time PCR (qPCR) and pyrosequencing which are considered to be breakthrough technologies borne out of the ‘molecular revolution’ are at present emerging rapidly as tools of pathogen detection and discovery.
    keywords: amplification; analysis; approach; assay; authors; bacterial; cells; challenges; clinical; coli; community; concentration; control; culture; data; density; detection; development; direct; diseases; diversity; dna; drinking; environmental; health; high; higher; human; internal; levels; metagenomic; methods; microarrays; microbial; molecular; monitoring; novel; outbreaks; pathogens; pcr; platforms; potential; public; pyrosequencing; qpcr; quality; quantification; quantitative; rapid; real; recent; rna; rrna; samples; sensitive; sensitivity; sequences; sequencing; significant; single; specific; study; target; techniques; technology; throughput; time; tools; treatment; unbiased; urban; viral; viruses; wastewater; water; waterborne; waterborne pathogens
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        item: #45 of 61
          id: cord-316999-712rit8h
      author: Chinchio, Eleonora
       title: Invasive alien species and disease risk: An open challenge in public and animal health
        date: 2020-10-22
       words: 2168
      flesch: 25
     summary: Introduced species may disrupt local infection dynamics also indirectly, i.e., nonacting as pathogen hosts but through competitive and trophic interactions with native species or modification of local habitats, thus altering the abundance and/or contact rates among local host species, parasite infective stages, or vectors. However, the identification of the contexts in which a dilution effect may occur is still highly debated in ecology, as it strongly depends on local host species diversity and on the interactions occurring between the species involved in the transmission cycle [30] .
    keywords: actions; alien; animal; area; assessment; biological; case; conservation; disease; dynamics; effects; emergence; europe; example; factors; fields; gray; health; host; human; ias; infectious; initiatives; introduction; invasion; invasive; local; native; new; parasites; pathogens; people; populations; potential; public; release; risk; species; squirrel; threats; transmission; tuberculosis; wildlife
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        item: #46 of 61
          id: cord-320295-k2i52wgs
      author: Woolhouse, Mark E.J.
       title: Host Range and Emerging and Reemerging Pathogens
        date: 2005-12-17
       words: 3403
      flesch: 39
     summary: General definitions The global distribution and population at risk of malaria: past, present and future The growing burden of tuberculosis: global trends and interactions with the HIV epidemic Evolvability of emerging viruses Emerging pathogens: the epidemiology and evolution of species jumps Population biology of emerging and re-emerging pathogens Emerging infectious pathogens of wildlife We thank Louise Taylor and Sophie Latham for their work on the original database and Ben Evans for his contribution to the updated database. RNA viruses are also prominent among the subset of emerging pathogens that have apparently entered the human population only in the past few decades, such as HIV or the SARS coronavirus (21, 22) .
    keywords: association; bacteria; capable; categories; changes; differences; disease; drivers; emergence; families; figure; fraction; fungi; groups; health; helminths; host; human; infectious; international; likely; major; nonhuman; number; online; overall; pathogen species; pathogens; population; protozoa; range; reemerging; rna; small; source; species; transmissible; types; viruses; zoonotic
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        item: #47 of 61
          id: cord-322120-wtu04r2j
      author: Goddard, Frederick G. B.
       title: Measuring Environmental Exposure to Enteric Pathogens in Low-Income Settings: Review and Recommendations of an Interdisciplinary Working Group
        date: 2020-08-19
       words: 13384
      flesch: 20
     summary: Systematic reviews of water, sanitation, and hygiene (WaSH) evaluations, conducted to identify the health effects of interventions designed to reduce enteric pathogen exposure, have generally found improved WaSH to be protective against diarrhea, 24 soil-transmitted helminthiasis, 25 and malnutrition. With this as background, an interdisciplinary group of environmental health researchers convened at Emory University in Atlanta, Georgia (U.S.A.) in September 2019 for a workshop aimed at identifying priorities for improved approaches to measuring enteric pathogen exposure.
    keywords: air; analysis; animal; applications; approaches; areas; assessments; association; bacteria; bangladesh; behaviors; benefits; better; burden; chemical; children; cluster; coli; coliform; collection; combined; community; concentrations; contamination; cost; countries; current; data; detection; development; diarrhea; different; disease; diversity; drinking; drinking water; effectiveness; effects; enteric; enteric pathogens; environmental; environmental health; epidemiology; error; estimate; evaluation; evidence; example; exposure; exposure assessments; external; external exposure; factors; fecal; fecal contamination; fecal exposure; fecal−oral; feces; field; food; global; group; growth; hands; handwashing; health; helminth; high; host; household; human; hygiene; impact; important; improved; income; indicators; individual; infection; information; ingestion; interaction; internal; interventions; laboratory; level; limited; low; matter; measurement; measures; media; metagenomics; methods; microbial; modeling; models; molecular; monitoring; multiple; need; new; number; nutritional; observations; outcomes; past; pathogen exposure; pathogens; pathways; personal; pollution; population; potential; presence; proxies; proxy; public; quality; quantitative; randomized; range; recent; relationship; reported; research; resistance; resource; results; review; risk; rural; samples; sampling; sanitation; science; self; sequencing; settings; soil; source; specific; specific pathogens; stool; strategies; studies; study; surveillance; surveys; systematic; time; tools; total; tracking; transmission; transport; treatment; trial; urban; use; variability; wash; wastewater; water; water quality; young
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        item: #48 of 61
          id: cord-325052-7vlxa0i7
      author: Williamson, E. D.
       title: Vaccines for emerging pathogens: prospects for licensure
        date: 2019-04-11
       words: 6218
      flesch: 37
     summary: An alternative is to develop such vaccines to request US Emergency Use Authorization (EUA), or equivalent status in the United States, Canada and the European Union, making use of a considerable number of regulatory mechanisms that are available prior to licensing. An alternative is to develop such vaccines to request US Emergency Use Authorization (EUA), or an alternative status in the United States, Canada and European Union (EU) making use of a considerable number of alternative regulatory mechanisms that are available prior to licensing, so that the products are deployable at the first indications of a disease outbreak.
    keywords: access; adverse; africa; alternative; animal; antibody; approval; authorization; available; bacterial; bats; canada; candidate; cause; cell; chikungunya; clinical; conditions; coronaviruses; countries; data; development; disease; drug; e.g.; effects; efficacy; endemic; eua; european; exposure; fda; fever; future; global; health; human; iii; immunogenicity; level; licensed; life; list; marketing; medical; medicines; model; national; need; new; non; number; outbreak; pathogens; pestis; phase; plague; pneumonic; potential; prevalent; priority; product; programmes; protection; regions; regulatory; research; reservoirs; respiratory; response; review; risk; safety; sars; severe; species; specific; states; syndrome; testing; trial; union; united; use; vaccination; vaccine; viral; virus; volunteers; widespread; world; yersinia; zika; zoonotic
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        item: #49 of 61
          id: cord-329149-1giy1fow
      author: Martinez-Martin, Nadia
       title: Technologies for Proteome-Wide Discovery of Extracellular Host-Pathogen Interactions
        date: 2017-02-22
       words: 11184
      flesch: 20
     summary: Interestingly, this study highlighted a small set of extracellular host proteins recurrently targeted by several of the viral and bacterial pathogens analyzed, including cell surface receptors such as VEGFR2/KDR and collagen, possibly indicating previously unrecognized roles in the immune response against pathogens. In addition, interactions between cell surface proteins are often characterized by fast dissociation rates and therefore weak binding affinities, and in consequence well-established PPI methods such as yeast-two-hybrid or affinity purification-mass spectrometry (AP/MS) largely fail to detect these interactions.
    keywords: adenovirus; affinity; analysis; antibodies; antibody; antigen; approach; authors; available; avexis; bacterial; bait; binding; biochemical; biological; biology; biophysical; candidate; cas9; cdna; cell; cell surface; characterization; colleagues; common; complex; complexes; comprehensive; crispr; cytomegalovirus; detection; development; different; discovery; domain; ebola; elucidation; entry; environment; eppis; essential; evolution; example; expression; extracellular; extracellular host; extracellular protein; factors; falciparum; findings; functions; fundamental; future; generation; genes; genetic; genome; genomic; global; glycoprotein; haploid; hepatitis; high; hiv; host; host interactions; human; identification; immune; immunology; immunomodulatory; important; infection; inhibitory; initial; insights; interactions; invasion; journal; large; lassa; libraries; library; ligand; low; major; membrane; methods; microarrays; molecular; molecules; monoclonal; mpa; multiple; nappa; networks; new; niemann; novel; number; partners; pathogen; pathogen interactions; pick; plasma; platform; positive; potential; present; principles; processes; prominent; protein; protein interactions; proteome; proteomics; recent; receptor; recognition; recombinant; relevant; research; responses; review; scale; screening; screens; selection; significant; strategies; strategy; studies; study; surface; surface receptor; system; targeting; targets; techniques; technologies; technology; therapeutic; throughput; tigit; transmembrane; tropism; type; unbiased; understanding; unique; viral; virus; viruses; wide
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        item: #50 of 61
          id: cord-330463-j4cf7vzs
      author: Sattar, Syed A.
       title: Indoor air as a vehicle for human pathogens: Introduction, objectives, and expectation of outcome
        date: 2016-09-02
       words: 2721
      flesch: 33
     summary: key: cord-330463-j4cf7vzs authors: Sattar, Syed A. title: Indoor air as a vehicle for human pathogens: Introduction, objectives, and expectation of outcome date: 2016-09-02 journal: Am J Infect Control DOI: 10.1016/j.ajic.2016.06.010 sha: doc_id: 330463 cord_uid: j4cf7vzs Airborne spread of pathogens can be rapid, widespread, and difficult to prevent. In this international workshop, a panel of 6 experts will expound on the following: (1) the potential for indoor air to spread a wide range of human pathogens, plus engineering controls to reduce the risk for exposure to airborne infectious agents; (2) the behavior of aerosolized infectious agents indoors and the use of emerging air decontamination technologies; (3) a survey of quantitative methods to recover infectious agents and their surrogates from indoor air with regard to survival and inactivation of airborne pathogens; (4) mathematical models to predict the movement of pathogens indoors and the use of such information to optimize the benefits of air decontamination technologies; and (5) synergy between different infectious agents, such as legionellae and fungi, in the built environment predisposing to possible transmission-related health impacts of aerosolized biofilm-based opportunistic pathogens.
    keywords: aerobiology; agents; air; airborne; astm; available; breathing; chamber; chemical; control; data; decontamination; environmental; exposure; focus; general; health; host; human; inactivation; indoor; indoor air; infectious; international; means; microbes; microbial; mix; movement; opportunistic; particles; pathogens; potential; proceedings; quality; respiratory; setting; spread; study; survival; technologies; use; vehicle; workshop
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        item: #51 of 61
          id: cord-337219-d81v8b4j
      author: Cheong, Chang Heon
       title: Case Study of Airborne Pathogen Dispersion Patterns in Emergency Departments with Different Ventilation and Partition Conditions
        date: 2018-03-13
       words: 7199
      flesch: 48
     summary: Airborne pathogen concentration of each monitoring point is used to calculate airborne infection risk of neighboring non-infected patient. Airborne pathogen concentration at X3-Y1 is used to evaluate companions' airborne infection risk.
    keywords: ach; adjacent; adjacent beds; airborne infection; airborne pathogen; airflow; analysis; area; average; beds; cases; concentrations; conditions; control; effect; figure; hallway; hospitals; increase; infection; infection risk; inlet; installation; locations; model; number; outlet; partitions; pathogen concentration; pathogen control; pathogen dispersion; pathogen source; pathogens; patient; patterns; periphery; plan; region; research; respiratory; results; risk; simulation; study; supply; system; ventilation; ventilation condition; ventilation inlet; ventilation rate; ventilation system
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        item: #52 of 61
          id: cord-339886-th1da1bb
      author: Gardy, Jennifer L.
       title: Towards a genomics-informed, real-time, global pathogen surveillance system
        date: 2017-11-13
       words: 8778
      flesch: 23
     summary: As genomics has moved into the domain of clinical and public health practice, the notion of free and im mediate access to genomic surveillance data has encountered several barriers: the siloing of critical metadata across multiple public health databases with no interoperability; balancing openness and transparency with patient privacy and safety; variable data quality, particularly in resource-limited settings; concerns over data reuse by third parties; a lack of standards and ontologies to capture metadata; and career advancement disincentives to releasing data [107] EIDs are driven by multiple factors, many of which have digital outputs and represent novel sources of surveillance data 91 .
    keywords: access; analysis; animal; approach; assay; bacterial; bench; benefit; capacity; cases; challenges; change; clinical; common; community; control; cost; data; databases; detection; diagnostic; digital; disease; diversity; dna; dynamics; early; ebola; efforts; emergence; environmental; epidemic; epidemiological; epidemiology; ethical; events; evidence; evolutionary; example; expansion; factors; fig; framework; genetic; genome; genomic; geographic; global; global health; health; health surveillance; high; human; important; individual; infectious; information; informed; international; internet; investigations; laboratories; laboratory; level; local; media; metagenomics; microbial; minion; mobile; molecular; multiple; nanopore; need; new; non; novel; nucleic; number; open; outbreak; pandemic; pathogen; pathogen surveillance; person; phylodynamic; platforms; population; portable; potential; predict; public; public health; range; rapid; real; recent; ref; regions; report; research; response; results; review; risk; role; routine; sample; scale; sequences; sequencing; settings; sharing; signals; single; social; species; specific; spillover; spread; streams; studies; surveillance; syndromic; systems; technology; time; tools; transmission; united; use; validation; viral; virus; viruses; west; wildlife; zika; zoonotic
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        item: #53 of 61
          id: cord-341672-k5pa3n2l
      author: Barros‐Rodríguez, Adoración
       title: Units for vigilance of emerging diseases based on wastewater treatment plants (WWTP‐UVED)
        date: 2020-07-27
       words: 1319
      flesch: 34
     summary: key: cord-341672-k5pa3n2l authors: Barros‐Rodríguez, Adoración; Manzanera, Maximino title: Units for vigilance of emerging diseases based on wastewater treatment plants (WWTP‐UVED) date: 2020-07-27 journal: Microb Biotechnol DOI: 10.1111/1751-7915.13635 sha: doc_id: 341672 cord_uid: k5pa3n2l Pandemics deeply affect the health and economy of the world population. Here, we propose the development of Units for Vigilance of Emerging Diseases based on the screening of pathogens released to wastewater treatment plants to follow the spread of the infectious agent to determine the location of infected people.
    keywords: acid; affected; analysis; communities; covid-19; different; disease; extraction; health; measures; nucleic; number; pathogens; people; research; rna; samples; sars; spread; treatment; units; vigilance; wastewater; wwtps
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        item: #54 of 61
          id: cord-345583-3auz7gi6
      author: Aliakbar Ahovan, Zahra
       title: Bacteriophage Based Biosensors: Trends, Outcomes and Challenges
        date: 2020-03-11
       words: 6737
      flesch: 39
     summary: Foodborne pathogens in milk and the dairy farm environment: Food safety and public health implications Estimating health care-associated infections and deaths in US hospitals Chemically immobilized T4-bacteriophage for specific Escherichia coli detection using surface plasmon resonance Climate change and food safety: A review Detection and enumeration of microorganisms in ready-to-eat foods, ready-to-cook foods and fresh-cut produce in Korea Recent advances in bacteriophage based biosensors for food-borne pathogen detection Methods for rapid detection of foodborne pathogens: An overview Nanomaterials 2020 Advances in rapid detection methods for foodborne pathogens ADP-ribosylation of p21ras and related proteins by Pseudomonas aeruginosa exoenzyme S AdeABC multidrug efflux pump is associated with decreased susceptibility to tigecycline in Acinetobacter calcoaceticus-Acinetobacter baumannii complex Introduction to biosensors An overview of foodborne pathogen detection: In the perspective of biosensors Bacteriophage based probes for pathogen detection A review of phage therapy against bacterial pathogens of aquatic and terrestrial organisms Bioengineering bacteriophages to enhance the sensitivity of phage amplification-based paper fluidic detection of bacteria Genetically modified bacteriophages in applied microbiology Phage-based electrochemical sensors: A review Phage immobilized magnetoelastic sensor for the detection of Salmonella typhimurium Detection of Salmonella typhimurium in fat free milk using a phage immobilized magnetoelastic sensor Immobilization of bacteriophages on gold surfaces for the specific capture of pathogens Immobilization of biotinylated bacteriophages on biosensor surfaces Progress toward the development of a lytic bacteriophages-based impedance microbiology for agro-food application Interaction between bacteriophage Sf6 and Shigella flexner Bacteriophage tailspike proteins as molecular probes for sensitive and selective bacterial detection Rapid detection of Escherichia coli in beverages using genetically engineered bacteriophage T7 φ2GFP10: A high-intensity fluorophage enables detection and rapid drug susceptibility testing of Mycobacterium tuberculosis directly from sputum samples The use of a novel NanoLuc-based reporter phage for the detection of Escherichia coli O157: H7 Classification of virulent and temperate bacteriophages of Listeria spp. With novel advances in the field of genetic engineering, new phage probes have been designed to increase the capability or to overcome the limits of the wild-type phages.
    keywords: ability; able; advances; advantages; affinity; assay; bacteria; bacteriophage; binding; biological; biosensors; cell; cfu; characteristics; coli; conditions; contamination; cycle; detection; development; diagnosis; different; direct; display; dna; electrochemical; element; escherichia; figure; food; foodborne; gold; high; host; identification; immobilized; impedance; important; infection; lysogenic; lytic; main; major; method; microorganisms; milk; molecular; new; novel; o157; optical; organic; pathogens; peptides; phage; plasmon; probes; produce; properties; proteins; range; rapid; recent; receptor; reporter; resonance; results; review; salmonella; samples; sensitive; sensitivity; signal; simple; specific; specificity; spr; substrate; surface; system; target; technique; time; transduction; type; typhimurium; viruses; water; waveguide
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        item: #55 of 61
          id: cord-345799-i0j6tctr
      author: Koon, Kassi
       title: Co-detection of Pandemic (H1N1) 2009 Virus and Other Respiratory Pathogens
        date: 2010-12-17
       words: 959
      flesch: 32
     summary: Bacterial coinfections in lung tissue specimens from fatal cases of 2009 pandemic infl uenza A (H1N1)-United States Direct screening of clinical specimens for multiple respiratory pathogens using the Genaco respiratory panels 1 and 2 Simultaneous detection and high-throughput identifi cation of a panel of RNA viruses causing respiratory tract infections Human infl uenza A virus (H5N1) detection by a novel multiplex PCR typing method Development and evaluation of a novel multiplex PCR technology for molecular differential detection of bacterial respiratory disease pathogens Evidence from multiplex molecular assays for complex multipathogen interactions in acute respiratory infections High prevalence of human bocavirus detected in young children with severe acute lower respiratory tract disease by use of a standard PCR protocol and a novel real-time PCR protocol Clinical disease in children associated with newly described coronavirus subtypes A review of strategies for enhancing the completeness of notifi able disease reporting Mrs Koon is pursuing a doctorate degree in public health at Walden University, Minneapolis, MN, USA. Our fi ndings suggest that multiplex screening for respiratory pathogens is useful for providing rapid surveillance information to inform physicians who would otherwise base decisions on clinical signs and symptoms alone.
    keywords: bacterial; centers; clinical; data; detection; disease; h1n1; infection; infl; multiplex; pandemic; pathogens; pcr; positive; respiratory; samples; screening; states; study; uenza; usa; virus
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        item: #56 of 61
          id: cord-346053-mk1mzc5z
      author: Morris, Cindy E.
       title: Expanding the Paradigms of Plant Pathogen Life History and Evolution of Parasitic Fitness beyond Agricultural Boundaries
        date: 2009-12-24
       words: 4760
      flesch: 32
     summary: In contrast, the evolution of virulence in plant pathogens has been investigated from a predominantly agro-centric perspective, and has focused overwhelmingly on evolutionary forces related to interactions with the primary plant host. Here, we argue that current concepts from the field of medical epidemiology regarding mechanisms that lead to acquisition of novel virulence, biocide resistance, and enhanced pathogenic fitness can serve as an important foundation for novel hypotheses about the evolution of plant pathogens.
    keywords: abiotic; acquisition; activity; adaptation; agricultural; antimicrobials; association; bacteria; broad; capacity; diseases; dual; ecology; efflux; elements; emergence; environmental; enzymes; erwinia; essential; evolution; evolutionary; example; factors; fitness; forces; formation; fungal; fungi; fungus; fusarium; general; genome; grisea; habitats; history; host; human; human pathogens; hypotheses; interactions; key; life; mechanisms; microbial; microorganisms; multidrug; natural; novel; parasitic; particular; pathogenicity; pathogens; pathways; plant; plant pathogens; production; pseudomonas; pumps; range; recent; reservoirs; resistance; rhizosphere; role; siderophores; soil; species; spectrum; spp; strains; streptomyces; stress; stresses; survival; syringae; systems; toxins; traits; transport; understanding; use; virulence; virulence factors; water
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        item: #57 of 61
          id: cord-347946-i6kx3n6m
      author: Raison, Charles L
       title: Pathogen–Host Defense in the Evolution of Depression: Insights into Epidemiology, Genetics, Bioregional Differences and Female Preponderance
        date: 2016-09-15
       words: 18716
      flesch: 13
     summary: Prather et al, 2009; Raison et al, 2009 Raison et al, , 2010a Raison et al, , 2010b Raison et al, , 2010d Eisenberger et al, 2010a, b; Franzen et al, 2010; Felger et al, 2011 Felger et al, , 2012 . This has been shown in studies examining the acute behavioral and CNS responses to a single exposure to endotoxin or typhoid vaccine and even more convincingly by the many studies examining the biological and behavioral effects of chronic immune activation secondary to treatment with the cytokine IFN-α for either cancer or hepatitis C virus infection (Capuron et al, 2002 (Capuron et al, , 2003a (Capuron et al, , 2003b (Capuron et al, , 2005 (Capuron et al, , 2007 (Capuron et al, , 2009 Wichers and Maes, 2004; Wichers et al, 2005b Wichers et al, , 2006 Wichers et al, , 2007 Majer et al, 2008; Harrison et al, 2009a Harrison et al, , 2009b Lotrich, 2009; Lotrich et al, 2009;
    keywords: activation; activity; acute; adaptive; addition; adults; age; alleles; alpha; analysis; ancestral; ancient; anti; anxiety; apr; associated; association; available; bacterial; behavior; benefits; biomarkers; blood; body; brain; case; cell; certain; changes; chronic; clear; cns; common; concentrations; conditions; conservation; consistent; context; costs; crp; cytokine; data; death; defeat; defense; depressed; depression; depression risk; depressive symptoms; development; differences; different; direct; disease; disorder; early; eea; effects; elevated; endotoxin; energy; enhanced; environmental; et al; evidence; evolutionary; evolved; example; explanations; exposure; factor; fatigue; features; females; fever; findings; function; genes; genetic; genome; group; hand; healthy; hepatitis; high; higher; host; host defense; human; hyperphagia; hypothesis; ifn; il-1; il-6; illness; immune; immune activation; immune response; immune system; immunity; impact; increases; individuals; infant; infection; inflammation; inflammatory; inflammatory response; influenza; innate; interactions; interferon; known; large; leptin; levels; life; likely; link; loss; low; macrophages; major; major depression; maternal; mdd; mechanisms; meta; metabolic; microbial; miller; modern; mood; mortality; multiple; natural; necrosis; non; obesity; organisms; pathogen; pathogen defense; pathos; pathways; patients; people; peripheral; perspective; phase; plasma; population; positive; possibility; potential; ppd; primary; production; protein; psychological; psychomotor; psychosocial; question; raison; rats; reactive; recent; receptor; reduced; relationships; relevant; reproductive; resistance; respiratory; response; result; review; risk; role; selection; severity; sex; sexual; sickness; signaling; significant; sirt1; sirtuin; sleep; slowing; social; societies; specific; stimulation; stress; stressors; studies; study; support; survival; symptoms; system; terms; theory; time; tnf; treatment; tuberculosis; types; viral; virus; wide; withdrawal; women; world; wounding; years
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        item: #58 of 61
          id: cord-348819-gq7lp931
      author: Becker, Daniel J.
       title: Dynamic and integrative approaches to understanding pathogen spillover
        date: 2019-08-12
       words: 4642
      flesch: 31
     summary: [34] describe how the dose -response relationship, which quantifies the probability of successful infection in the recipient host as a function of challenge dose, can act as a filter on the aforementioned upstream dynamics to shape pathogen spillover risk. Research on pathogen spillover is often focused on a single component of this process through the lens of a particular discipline.
    keywords: animal; approaches; authors; barriers; bats; boundaries; case; cross; data; detection; disease; dose; dynamics; early; ebola; ecological; ecology; ecosystem; emergence; environment; epidemics; epidemiological; et al; events; exposure; factors; fever; host; human; infection; influenza; interface; interventions; issue; key; likely; management; manuscripts; mechanistic; modelling; models; novel; onward; particular; pathogen; phil; populations; potential; present; rates; recipient; research; reservoir; risk; role; sampling; spatial; spatio; species; spillover; statistical; study; surveillance; temporal; theme; theory; time; transmission; understanding; vaccination; viral; virus; viruses; wildlife; zoonotic
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        item: #59 of 61
          id: cord-348841-qxkmngyk
      author: Kozakiewicz, Christopher P.
       title: Pathogens in space: Advancing understanding of pathogen dynamics and disease ecology through landscape genetics
        date: 2018-07-28
       words: 7501
      flesch: 20
     summary: However, host landscape genetic studies can provide indications of the potential risk of spread of infectious agents, and the understanding gained about host movements can inform subsequent studies of pathogen dynamics. Our review emphasizes the expanding utility of landscape genetic methods available for elucidating key pathogen dynamics (particularly transmission and spread) and also how landscape genetic studies of pathogens can provide insight into host population dynamics.
    keywords: addition; agents; analysis; applications; approaches; barriers; biek; changes; connectivity; contact; craft; data; difficult; disease; dispersal; distance; distribution; dyer; dynamics; ecological; ecology; environmental; epidemiology; et al; factors; features; field; flow; framework; future; genes; genetic; genetic data; genetic structure; genetic studies; genome; genomic; habitat; heterogeneity; host; human; important; individuals; infectious; influence; information; insights; key; landguth; landscape; landscape genetics; loci; management; methods; modelling; models; molecular; movement; network; new; number; parasite; particular; pathogen; pathogen genetic; patterns; phylogenetic; phylogeographic; population; potential; prevalence; processes; publications; questions; rabies; rapid; real; recent; research; resistance; response; review; risk; sampling; selection; sequencing; simulation; spatial; spatial genetic; species; spread; structure; studies; study; surfaces; systems; techniques; temporal; transmission; understanding; use; utility; variables; variation; vector; virus; viruses; wildlife
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        item: #60 of 61
          id: cord-354254-89vjfkfd
      author: Peng, Shanbi
       title: The role of computational fluid dynamics tools on investigation of pathogen transmission: Prevention and control
        date: 2020-08-31
       words: 7521
      flesch: 36
     summary: A Multi-zone Indoor Air Quality and Ventilation Analysis Software Tool Multi-zone modeling of probable sars virus transmission by airflow between flats in block e, amoy gardens Investigating a safe ventilation rate for the prevention of indoor sars transmission: an attempt based on a simulation approach Multi-zone simulation of outdoor particle penetration and transport in a multi-story building Significance of two-way airflow effect due to temperature difference in indoor air quality The transport of gaseous pollutants due to stack effect in high-rise residential buildings Air infiltration induced inter-unit dispersion and infectious risk assessment in a high-rise residential building Principles and applications of probability-based inverse modeling method for finding indoor airborne contaminant sources Experimental and numerical study on particle distribution in a two-zone chamber Model-based optimal control of a dedicated outdoor air-chilled ceiling system using liquid desiccant and membrane-based total heat recovery Identifying index (source), patient location of sars transmission in a hospital ward Airborne contagion and air hygiene: an ecological study of droplet infections An advanced numerical model for the assessment of airborne transmission of influenza in bus microenvironments Evaluation of airborne disease infection risks in an airliner cabin using the lagrangian-based wells-riley approach Cfd simulation of spread risks of infectious disease due to interactive wind and ventilation airflows via window openings in high-rise buildings Modelling the transmission of airborne infections in enclosed spaces Infection risk of indoor airborne transmission of diseases in multiple spaces Preventing airborne disease transmission: review of methods for ventilation design in health care facilities Risk assessment of airborne infectious diseases in aircraft cabins Risk of indoor airborne infection transmission estimated from carbon dioxide concentration A probabilistic transmission dynamic model to assess indoor airborne infection risks. key: cord-354254-89vjfkfd authors: Peng, Shanbi; Chen, Qikun; Liu, Enbin title: The role of computational fluid dynamics tools on investigation of pathogen transmission: Prevention and control date: 2020-08-31 journal: Sci Total Environ DOI: 10.1016/j.scitotenv.2020.142090 sha: doc_id: 354254 cord_uid: 89vjfkfd Transmission mechanics of infectious pathogen in various environments are of great complexity and has always been attracting many researchers' attention.
    keywords: aerosol; airborne; airborne transmission; airflow; algorithms; analysis; bacteria; boltzmann; boundary; building; calculation; cfd; cfd method; cfd simulation; characteristics; computational; concentration; contaminant; control; data; different; diffusion; dispersion; distribution; droplet; dynamics; effect; effective; environment; epidemic; equation; et.al; exhaust; experiment; fig; flow; fluid; forecasting; gas; great; high; hospital; human; impact; indoor; infected; infection; investigations; lattice; law; mask; media; method; model; modeling; multi; necessary; number; numerical; order; particle; pathogen; pathogen transmission; people; phase; pollutant; pollution; pressure; process; r n; rate; research; researchers; result; review; rise; risk; role; room; sars; scale; simulation; single; source; spread; study; system; temperature; time; toilet; tracer; tracer gas; transmission; transport; transportation; type; unsteady; velocity; ventilation; virus; virus transmission; vof; volume; way; web; wind; work; zone
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        item: #61 of 61
          id: cord-355165-xc6ythgp
      author: van den Wijngaard, Cees
       title: Validation of Syndromic Surveillance for Respiratory Pathogen Activity
        date: 2008-06-17
       words: 4565
      flesch: 35
     summary: Negative associations (e.g., between enteroviruses, which peak in summer, vs. respiratory syndromes, which peak in winter) were excluded to avoid noncausal effects. To discriminate between primary and secondary infections by S. pneumoniae (as a complication of respiratory virus infection) (16) (17) (18) (19) , we used the residuals from regressing S. pneumoniae counts on other pathogens as the variable for S. pneumoniae (instead of its counts) for all the earlier described models for respiratory syndromes.
    keywords: absenteeism; activity; clinical; counts; data; detection; disease; earlier; early; elevations; explained; extent; general; health; higher; hospital; illness; infectious; infl; infl uenza; laboratory; lagged; medical; models; mortality; netherlands; observed; pathogen; peaks; pharmacy; pneumoniae; refl; registries; registry; regression; respiratory; rhinovirus; rsv; seasonal; series; specifi; study; submissions; surveillance; syndrome; syndromic; system; table; terms; time; timeliness; uenza; van; variations; virus; weeks; winter
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