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ShareScore release 0.9.0
Dataset results
8 results for “Foodborne pathogens”
Dataset for publication: An inter-laboratory study characterizes the impact of bioinformatic approaches on genome-based cluster detection for foodborne bacterial pathogens
<p>This dataset is part of a dry-lab interlaboratory study conducted across Germany, regarding bacterial outbreak detection based on NGS data, with a focus on bioinformatic analysis of four species to identify potential variability caused by different data analysis approaches and human interpretation. Participants were asked to follow their usual in-house protocols while adhering to the general guidelines. A quality assessment (with sample exclusion) was followed by 7-gene Multilocus-Sequence Typing (MLST), core genome Multilocus Sequencing Typing (cgMLST), and SNP calling. The participants were then asked to identify clusters. The study was not intended to resemble a standard proficiency test with a passing/failing grade, but rather to investigate and quantify obvious variability in the results and, where possible, the reasons for it. For this purpose, the datasets included borderline cases in terms of quality.</p>
A trait-based framework for predicting foodborne pathogen risk from wild birds
<p>Recent foodborne illness outbreaks have heightened pressures on growers to deter wildlife from farms, jeopardizing conservation efforts. However, it remains unclear which species, particularly birds, pose the greatest risk to food safety. Using >11,000 pathogen tests and 1,565 bird surveys covering 139 bird species from across the western U.S.A., we examined the importance of 11 traits in mediating wild bird risk to food safety. We tested whether traits associated with pathogen exposure (<i>e.g</i>., habitat associations, movement, and foraging strategy) and pace-of-life (clutch size and generation length) mediated foodborne pathogen prevalence and proclivities to enter farm fields and defecate on crops. <i>Campylobacter </i>spp. were the most prevalent enteric pathogen (8.0%), while <i>Salmonella</i> and Shiga-toxin producing <i>E. coli </i>(STEC) were rare (0.46% and 0.22% prevalence, respectively). We found that several traits related to pathogen exposure predicted pathogen prevalence. Specifically, <i>Campylobacter </i>and STEC-associated virulence genes were more often detected in species associated with cattle feedlots and bird feeders, respectively. <i>Campylobacter </i>was also more prevalent in species that consumed plants and had longer generation lengths. We found that species associated with feedlots were more likely to enter fields and defecate on crops. Our results indicated that canopy-foraging insectivores were less likely to deposit foodborne pathogens on crops, suggesting growers may be able to promote pest-eating birds and birds of conservation concern (<i>e.g.</i>, via nest boxes) without necessarily compromising food safety. As such, promoting insectivorous birds may represent a win-win-win for bird conservation, crop production, and food safety. Collectively, our results suggest that separating crop production from livestock farming may be the best way to lower food safety risks from birds. More broadly, our trait-based framework suggests a path forward for co-managing wildlife conservation and food safety risks in farmland by providing a strategy for holistically evaluating the food safety risks of wild animals, including under-studied species.</p>
A trait-based framework for predicting foodborne pathogen risk from wild birds
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Data from: Assessing foodborne pathogen survival in bird feces to co-manage farms for bird conservation, production, and food safety
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Dataset of paper "Assessment of Photoactivated Chlorophyllin Production of Singlet Oxygen and Inactivation of Foodborne Pathogens"
<p>Dataset of paper "Assessment of Photoactivated Chlorophyllin Production of Singlet Oxygen and Inactivation of Foodborne Pathogens"</p>
Dietary antigens drive the generation of functional cytotoxic intraepithelial lymphocytes for early defense against foodborne pathogens
GEO Series GSE299783. Mus musculus. 6 samples. Type: Expression profiling by high throughput sequencing.
Probing the pan genome of a foodborne bacterial pathogen Listeria monocytogenes
GEO Series GSE20367. Listeria monocytogenes FSL J1-194; Listeria monocytogenes FSL J2-003; Listeria monocytogenes FSL J2-064; Listeria monocytogenes FSL N1-017; Listeria monocytogenes F6900; Listeria monocytogenes 10403S; Listeria monocytogenes FSL F2-515; Listeria monocytogenes FSL J2-071; Listeria monocytogenes J0161; Listeria monocytogenes HPB2262; Listeria monocytogenes FSL F2-208; Listeria monocytogenes serotype 4b str. H7858; Listeria monocytogenes FSL J1-208; Listeria monocytogenes FSL N3-165; Listeria monocytogenes LO28; Listeria monocytogenes; Listeria monocytogenes EGD-e; Listeria monocytogenes serotype 4b str. F2365; Listeria monocytogenes serotype 1/2a str. F6854; Listeria monocytogenes FSL J1-175; Listeria monocytogenes FSL R2-503; Listeria monocytogenes J2818. 18 samples. Type: Genome variation profiling by genome tiling array.
Host mechanisms potentially associated with foodborne pathogen Escherichia coli O157 shedding in feedlot beef cattle
GEO Series GSE85277. Bos taurus. 60 samples. Type: Expression profiling by high throughput sequencing.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.