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The genomic and epidemiological virulence patterns of Salmonella enterica serovars in the United States
<p>The serovars of <i>Salmonella enterica </i>display dramatic differences in pathogenesis and host preferences. We developed a process (patent pending) for grouping <i>Salmonella</i> isolates and serovars by their public health risk. We collated a curated set of 12,337 <i>S. enterica</i> isolate genomes from human, beef, and bovine sources in the US. After annotating a virulence gene catalog for each isolate, we used unsupervised random forest methods to estimate the proximity (similarity) between isolates based upon the genomic presentation of putative virulence traits We then grouped isolates (virulence clusters) using hierarchical clustering (Ward's method), used non-parametric bootstrapping to assess cluster stability, and externally validated the clusters against epidemiological virulence measures from FoodNet, the National Outbreak Reporting System (NORS), and US federal sampling of beef products. We identified five stable virulence clusters of <i>S. enterica</i> serovars. Cluster 1 (higher virulence) serovars yielded an annual incidence rate of domestically acquired sporadic cases roughly one and a half times higher than the other four clusters combined (Clusters 2-5, lower virulence). Compared to other clusters, cluster 1 also had a higher proportion of infections leading to hospitalization and was implicated in more foodborne and beef-associated outbreaks, despite being isolated at a similar frequency from beef products as other clusters. We also identified subpopulations within 11 serovars. Remarkably, we found <i>S.</i> Infantis and<i> S.</i> Typhimurium subpopulations that significantly differed in genome length and clinical case presentation. Further, we found that the presence of the pESI plasmid accounted for the genome length differences between the <i>S. </i>Infantis subpopulations. Our results show that <i>S. enterica</i> strains associated with highest incidence of human infections share a common virulence repertoire. This work could be updated regularly and used in combination with foodborne surveillance information to prioritize serovars of public health concern. </p><p>Files contained in this repository will reproduce elements of figures 3,4,6, and 7 of the accompanying PLOS One manuscript. </p><p> </p>
Data from: Climatic damage cause variations of agricultural insurance loss for the Pacific Northwest region of the United States
<p>Agricultural crop insurance is an important component for mitigating farm risk, particularly given the potential for unexpected climatic events. Using a 2.8 million nationwide insurance claim dataset from the United States Department of Agriculture (USDA), this research study examines spatiotemporal variations of over 31,000 agricultural insurance loss claims across the 24-county region of the inland Pacific Northwest (iPNW) portion of the United States, from 2001 to 2022. Wheat is the dominant insurance loss crop for the region, accounting for over 2.8 billion dollars in indemnities, with over 1.5 billion dollars resulting in claims due to drought (across the 22 year time period). While fruit production generates considerably lesser insurance losses (400 million dollars) as a primary result of freeze, frost, and hail, overall revenue ranks number one for the region, with 2 billion dollars in sales, across the same time range. Principal components analysis of crop insurance claims showed distinct spatial and temporal differentiation in wheat and apple insurance losses using the range of damage causes as factor loadings. The first two factor loadings for wheat accounts for approximately 50 percent of total variance for the region, while a separate analysis of apples accounts for over 60 percent of total variance. These distinct orthogonal differences in losses by year and commodity in relationship to damage causes suggest that insurance loss analysis may serve as an effective barometer in gauging climatic influences.</p>
Figure 3 in Acmaeodera (Coleoptera: Buprestidae): A new species of Acmaeodera Eschscholtz, 1829 from the southwestern United States, with three new synonymies, new state and host records, and a key to species occurring east of the Rocky Mountain states
Figure 3. Acmaeodera conoidea Fall, paralectotype ♂. a) Dorsal view. b) Ventral view. c) Lateral view. d) Broadly arcuate clypeus e) Third stria split near umbone. f) Protarsal claw.
Figure 2. Male genitalia, Acmaeodera tubulus species group. a in Acmaeodera (Coleoptera: Buprestidae): A new species of Acmaeodera Eschscholtz, 1829 from the southwestern United States, with three new synonymies, new state and host records, and a key to species occurring east of the Rocky Mountain states
Figure 2. Male genitalia, Acmaeodera tubulus species group. a) A. natlovei new species. b) A. neoneglecta. c) A. tubulus. d) A. neglecta. e) A. opuntiae.
Figure 1. Acmaeodera natlovei new species. a in Acmaeodera (Coleoptera: Buprestidae): A new species of Acmaeodera Eschscholtz, 1829 from the southwestern United States, with three new synonymies, new state and host records, and a key to species occurring east of the Rocky Mountain states
Figure 1. Acmaeodera natlovei new species. a) Holotype, dorsal view. b) Holotype, ventral view. c) Holotype, lateral view. d) Holotype, clypeus. e) Paratype protarsal claw ♂. f) Paratype protarsal claw ♀.
MCIT storm tracks with updraft radar data for large hail cases in the United States (2013 - 2023)
<p>Storm tracking data from 114 hail days in the United States between 2013 and 2023. Cases were selected based on the availability of abundant Storm Prediction Center (SPC) hail reports (either at least 20 reports of hail > 1 cm or five reports > 10 cm) in a range between 20 and 90 km from a NEXRAD radar site. Only cases in a geographic area from 28-48°N and 105-90°E, roughly corresponding to the U.S. Great Plains, were considered. Cells are quality filtered based on these criteria: (1) Cell center within 120 km of the radar range, and (2) continuous tracking for at least 6 timesteps (approx. 30 minutes, depending on radar scan rate). SPC hail data is matched to tracking timesteps. We used this data to train a Random Forest model for hail size nowcasting.</p> <p>Further metadata can be requested from the authors.</p>
Potential near-term wetting of the Southwestern United States if the Eastern Pacific cooling trend reverses
<p>Data for the manuscript "Potential near-term wetting of the Southwestern United States if the Eastern Pacific cooling trend reverses."</p>
Heat pumps for all? Distributions of the costs and benefits of residential air-source heat pumps in the United States
<p>Dataset for the "<span>Heat pumps for all? Distributions of the costs and benefits of residential air-source </span><span>heat pumps in the United States" paper</span></p>
MaStR power unit registry for eGon-data (legacy)
<p>The data set contains selected data from the <a href="https://www.marktstammdatenregister.de/MaStR">Marktstammdatenregister</a> for eGon-data pipeline.<br><strong>Note:</strong> This dataset is legacy and should be only used for compatibility reasons in eGon-data.</p> <p><strong>Dump version: 2021-04-30</strong></p> <p>The data set has been downloaded and processed with a very early version of the software <a href="https://github.com/OpenEnergyPlatform/open-MaStR">open-MaStR</a>.</p> <p>License information:<br>Marktstammdatenregister - © Bundesnetzagentur für Elektrizität, Gas, Telekommunikation, Post und Eisenbahnen | <a href="https://www.govdata.de/dl-de/by-2-0">DL-DE-BY-2.0</a></p>
MaStR power unit registry for eGon-data
<p>The data set contains selected data from the <a href="https://www.marktstammdatenregister.de/MaStR">Marktstammdatenregister</a> for eGon-data pipeline.</p> <p><strong>Dump version: 2022-11-17</strong></p> <p>The data set has been downloaded and processed with the software <a href="https://github.com/OpenEnergyPlatform/open-MaStR">open-MaStR</a>.<br>Compared to the <a href="../doi/10.5281/zenodo.6807425">official open-MaStR releases</a> a custom format postprocessing has been applied.</p> <p>License information:<br>Marktstammdatenregister - © Bundesnetzagentur für Elektrizität, Gas, Telekommunikation, Post und Eisenbahnen | <a href="https://www.govdata.de/dl-de/by-2-0">DL-DE-BY-2.0</a></p>
Data for: Characterization of large-scale preferential flow across continental United States
<p>Understanding preferential flow (PF) at large scales is critical for improving land management and groundwater (GW) quality. However, limited knowledge of this process, due to soil surface heterogeneity and observational constraints, hampers progress. In this study, we propose estimating effective PF at remote sensing footprint scale (4 – 9 km) by examining its impact on soil moisture (SM) distribution and shallow GW (SGW) table fluctuations (depth 5 m). Effective PF encompasses macropore, funnel, and finger flow pathways influencing SGW table fluctuations. We compiled daily SGW observations (2019-2021) from 19 continental US (CONUS) sites through USGS. Using inverse modeling in HYDRUS-1D, SGW data, and CHIRPS precipitation data, we inversely estimated soil hydraulic parameters of the dual porosity model (DPM) simulating vertical flow from soil surface to subsurface. Effective PF presence was inferred using three criteria: (1) daily precipitation >= the site-specific average across multiple (calibration) years, (2) daily observed SGW table increase, and (3) daily difference between observed and DPM simulated SGW tables 50% of the site-specific RMSE. Leveraging optimized DPM parameters and associated soil texture, classified PF events, and Soil Moisture Active Passive (SMAP L3E) satellite-based SM, a Random Forest algorithm with 10-fold cross validation predicted large-scale effective PF events. Results indicate seasonal dependence, with spring having the highest occurrence of PF events. The Random Forest model achieved 98% accuracy in predicting large-scale PF events, with SMAP SM and saturated hydraulic conductivity (Ks) among the 4 most impactful variables. Our approach provides a soil hydraulic property, site characteristic, soil texture and remote sensing based generalized tool to analyze large-scale effective PF.</p>
FIG. 7 in A new operculate symmoriiform chondrichthyan from the Late Mississippian Fayetteville Shale (Arkansas, United States)
FIG. 7. — Consensus of eight most parsimonious trees. Bootstrap values are shown above branches; bootstrap values below 50 are not shown. New taxon Cosmoselachus n. gen. indicated by yellow highlight, holocephalan group and symmoriiform group indicated in differing shades of gray.
FIG. 5. — Cosmoselachus mehlingi n. gen., n in A new operculate symmoriiform chondrichthyan from the Late Mississippian Fayetteville Shale (Arkansas, United States)
FIG. 5. — Cosmoselachus mehlingi n. gen., n. sp., specimen AMNH FF 20509: A, cross section through the posterior half of the specimen, at the point indicated by the inset 3D reconstruction, showing multilayered opercular structure made of cartilaginous branchial rays, fused to one another. Layer of rays from the first branchial arch (behind the hyoid arch) indicated by the second-from-left arrowhead. The right-most arrowhead marks the second row of pharyngeal rays (first branchial arch); another layer (second branchial arch) can be found just beneath it (second arrowhead from the right). Hyoid operculum appears to fold at the arrowhead furthest to the left; B, longitudinal section of posterior half of AMNH FF 20509 showing hyoid operculum (right-most arrowhead) and additional elongate branchial rays (left two arrowheads). Anterior to left, slice location within the specimen indicated by 3D reconstruction in the upper right corner. Scale bars: 5 cm.
FIG. 3. — A in A new operculate symmoriiform chondrichthyan from the Late Mississippian Fayetteville Shale (Arkansas, United States)
FIG. 3. — A, Tooth families of Cosmoselachus n. gen. on the Meckel's cartilages, with denticles between tooth families. Teeth make contact but have no fused bases, dorsal oblique labial view; B, detail of tooth batteries in axial section, anterior to right, showing denticles between each tooth family, on the scalloped Meckel's cartilage. Abbreviations: d, denticles; mc, Meckel's cartilage; t, teeth. Scale bars: A, B, 4 cm; C, 2 mm.
FIG. 2. — Cosmoselachus mehlingi n. gen., n in A new operculate symmoriiform chondrichthyan from the Late Mississippian Fayetteville Shale (Arkansas, United States)
FIG. 2. — Cosmoselachus mehlingi n. gen., n. sp., three-dimensional renderings of specimen AMNH FF 20509, produced by computed tomographic (CT) scanning: A, ventral view of posterior half of specimen, anterior to top; B, ventral view of anterior part of the specimen, anterior to right, with opercular elements removed; C, dorsal view of anterior half of specimen, anterior to right. Note loss of anterior portion of cranium due to taphonomy. Abbreviations: add, depression potentially for adductor musculature; c, cranium; cb, ceratobranchials; ch, ceratohyals; d, denticles; mc, Meckel's cartilage; op, opercular cartilage; pa f, pharyngeal arch fragments; pq, palatoquadrate fragment; t, teeth. Scale bars: 5 cm.
FIG. 1. — Cosmoselachus mehlingi n. gen., n in A new operculate symmoriiform chondrichthyan from the Late Mississippian Fayetteville Shale (Arkansas, United States)
FIG. 1. — Cosmoselachus mehlingi n. gen., n. sp., specimen AMNH FF 20509, anterior to right: A, entire specimen, ventral view. Abbreviations: mc, Meckel's cartilage; op, opercular flap; B, detail of opercular flap. Scale bars: A, 5 cm; B, 2 cm. Photographs by Lorraine Meeker.
FIG. 6. — Cosmoselachus mehlingi n. gen., n in A new operculate symmoriiform chondrichthyan from the Late Mississippian Fayetteville Shale (Arkansas, United States)
FIG. 6. — Cosmoselachus mehlingi n. gen., n. sp., partial basicranium of specimen AMNH FF 20509: A, dorsal view; B, ventral view. Anterior to top. Abbreviations: da?, possible opening for the dorsal aorta; occ, occiput; ot cap, otic capsule. Scale bar: 3 cm.
Text-fig. 1. Map of the early Eocene Okanagan Highlands British Columbia, Canada and Washington, United States of America. Modified from Archibald et al. 2014: fig. 2, courtesy of Bruce Archibald. in The Early Eocene Flora Of Horsefly, British Columbia, Canada And Its Phytogeographic Significance
Text-fig. 1. Map of the early Eocene Okanagan Highlands British Columbia, Canada and Washington, United States of America. Modified from Archibald et al. 2014: fig. 2, courtesy of Bruce Archibald.
Operating diagram of hatching module, this module consists of two clearly separated sections, each consisting of two long tanks (2 × 0.2 × 0.2 m) designed to accommodate hatching boxes, a filtration tank and an independent water circulation pump with a cooling unit and UV sterilizer. This allows simultaneous monitoring of 16 batches of eggs. in Reproduction of Zingel asper (Linnaeus, 1758) in controlled conditions: an assessment of the experiences realized since 2005 at the Besançon Natural History Museum
Operating diagram of hatching module, this module consists of two clearly separated sections, each consisting of two long tanks (2 × 0.2 × 0.2 m) designed to accommodate hatching boxes, a filtration tank and an independent water circulation pump with a cooling unit and UV sterilizer. This allows simultaneous monitoring of 16 batches of eggs.
Operating diagram of hatching module in Zoug jars, this system consists of a 300-litre temperature-controlled isothermal enclosure containing 10 one-litre Zoug jars, each able to accommodate several hundred eggs. An ascending current holds the eggs in suspension and carries the larvae to the surface. Another bottle connected to this device collects the larvae. The water circulating in the jars is independent of that used in the filtration circuit. A cooling unit and UV sterilizer complete the installation. in Reproduction of Zingel asper (Linnaeus, 1758) in controlled conditions: an assessment of the experiences realized since 2005 at the Besançon Natural History Museum
Operating diagram of hatching module in Zoug jars, this system consists of a 300-litre temperature-controlled isothermal enclosure containing 10 one-litre Zoug jars, each able to accommodate several hundred eggs. An ascending current holds the eggs in suspension and carries the larvae to the surface. Another bottle connected to this device collects the larvae. The water circulating in the jars is independent of that used in the filtration circuit. A cooling unit and UV sterilizer complete the installation.
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
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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.