AndreaBozzo/ceres-open-data-index huggingface dataset:
Data from: Contemporary United States PRRSV 1-4-4 L1C.5 isolate causes severe disease comparable to historic highly pathogenic PRRSV

<p dir="ltr">This online resource provides source data collected to generate plots and statistics in the work, "Contemporary United States PRRSV 1-4-4 L1C.5 isolate causes severe disease comparable to historic highly pathogenic PRRSV", by Wiarda et al. Weaned pigs were inoculated intranasally with mock inoculum or one of three porcine reproductive and respiratory syndrome viruses (PRRSVs), including a recombinant of the highly pathogenic PRRSV JXwn06 that emerged in Asia in 2006, a 2020 isolate of PRRSV 1-4-4 L1C.5 that has been shown to cause severe morbidity and mortality compared to other contemporary 1-4-4 strains, and moderately pathogenic PRRSV MN184 that emerged in the United States in the early 2000s. Pigs were monitored for signs of disease, and serum samples were collected throughout the study. Animals were necropsied at 2, 6, and 10 days post-infection, or as needed due to development of severe disease. Results demonstrated both PRRSV JXwn06 and the 1-4-4 L1C.5 isolate caused extreme morbidity and mortality that shared very similar disease dynamics. Animal meta data along with data collected for parameters of clinical disease, tissue viral loads, cytokine concentrations, antibody concentrations, gross pathology, and microscopic pathology are available here.</p>

Tags: antibody, ars, cytokines, data-gov, high-pathogenicity, highly-pathogenic, highly-pathogenic-porcine-reproductive-and-respiratory-syndrome, highly-pathogenic-porcine-reproductive-and-respiratory-syndrome-virus, hp-prrs, hp-prrsv, jxwn06, l1c-5, mn184, national-animal-disease-center, np103, pathogenicity, pathology, pig, porcine, porcine-reproductive-and-respiratory-syndrome, porcine-reproductive-and-respiratory-syndrome-prrs, porcine-reproductive-and-respiratory-syndrome-virus, porcine-reproductive-and-respiratory-syndrome-virus-2, prrs, prrsv, prrsv-2, qpcr, swine, swine-diseases, usda, viral-load
Organization: Department of Agriculture
Data from: Insecticidal effect of deltamethrin, pyrethrin, and spinosad on metal and concrete surfaces on six species of stored product insects

<p dir="ltr">The objective of this study was to evaluate three insecticides on metal and concrete surfaces to control six species of stored product insects. Metal and concrete surfaces were constructed in the bottom of a 62 cm<sup>2</sup> plastic petri dish. EverGreen© (active ingredient (a.i.), pyrethrin), Centynal EC™ (a.i. deltamethrin), and Sensat™ (a.i. spinosad), were applied at their label rates, and water was used as a control. Ten adults of one species, <i>Tribolium castaneum </i>(Herbst), <i>Rhyzopertha dominica </i>(F.), <i>Cryptolestes ferrugineus </i>(Stephens), <i>Tribolium confusum </i>Jacquelin du Val, <i>Sitophilus oryzae </i>(L.), or <i>Oryzaephilus surinamensis </i>(L.), were added to individual treated arenas (n=5) along with ~500 mg of diet and held for seven days. Adult beetles were observed after one, three, and seven days for the number of live, affected (those exhibiting uncoordinated movement, twitching or unable to walk) and dead beetles.</p>

Tags: broad-spectrum-insecticide, contact-insecticides, integrated-pest-managment, material-properties, organic, postharvest, stored-product-insects
Organization: Department of Agriculture
Impact of Maternal Antibodies and Weaning stress on the Replication and Transmission of Human H3N2 Influenza A in Piglets

<p dir="ltr">Modern swine production facilitates indoor respiratory contact between human employees and pigs in their care, creating conditions for interspecies transmission of influenza A virus (IAV). Sow vaccination is routinely practiced in the U.S.A. to transfer maternal derived antibodies (MDA) to piglets. Weaning is a highly stressful period for piglets that requires increased human interaction. Weaned piglets potentially have mixed immunity from MDA: matched, mismatched, and naïve. Since there have been multiple introductions of human seasonal H3N2 to swine, we assessed the effect of matched and mismatched MDA acquired from vaccinated sows and the stress of weaning on the susceptibility of piglets to a human-origin H3N2 IAV. The H3N2 virus was generated by reverse genetics to mimic the 2010.1 H3N2 introduction from humans to swine. Challenged seeder piglets were divided by immune and weaning status. Two days post inoculation, naïve direct contact pigs were placed with seeders. IAV quantitative reverse transcription polymerase chain reaction (qRT-PCR) and virus titration were performed on nasal swabs and bronchoalveolar lavage fluid to evaluate shedding and transmission kinetics. Matched MDA were effective in reducing shedding in challenged pigs and minimizing transmission of the human-like H3N2 to contacts. There was an increase in shedding and transmission in weaned pigs compared to littermates that remained on the sow. These results identify critical control points in production where changing practices could mitigate human-to-swine and swine-to-swine transmission to prevent establishment of novel lineages in pig populations.</p>

Tags: influenza-a, maternally-derived-antibodies, reverse-zoonosis, vaccination, weaning
Organization: Department of Agriculture
Wind rose plots for the volcano: 345010  Orosi

This zip folder contains ASCII text files of vectors at the specified volcano at 
12-hour intervals, 
from January 1, 1990 through December 28, 2009.  
The wind vectors are divided into five files, names by their elevation range above 
sea level in the atmosphere: 00-05km.txt; 05-11km.txt; 11-16km.txt; 16-24km.txt; 
and 24-30km.txt. 
The zip folder also contains a subfolder "figures", with Wind rose plots of wind 
direction and speed over 
this time period.  The plots are by season, and by elevation, given a total of 20 
plots (4 seasons, 5 
elevation ranges).  A summary plot is also included which gives the year-round 
wind pattern at the volcano, 
at 0-5 km elevation.  Plots are in both jpg and pdf format.

Tags: meteorology, usgs-58d0170be4b0236b68f5317a, volcanic-ash, volcanic-eruption-forecasting, wind
Organization: Department of the Interior
Data from: Predictive Modeling of Seed Biochemicals Composition Traits using Machine learning algorithms

<p dir="ltr">Sorghum is a versatile cereal crop grown the central U.S. especially in Kansas and Texas and is an important grain for feed, biofuel, and food markets. The growing demand for sorghum has increased the need for enhanced hybrids with superior grain composition, such as high protein and starch content, which are key determinants of its nutritional and economic value. The composition of sorghum grain is highly influenced by genetics, growth conditions, and crop management practices, all of which influence the final yield and quality of the crop. To develop new varieties of sorghum with improved grain traits, grain composition must be measured on large sample sets grown at multiple locations and often with different crop practices, which is currently a labor-intensive and time-consuming process. Thus, this research investigated the ability of machine learning to predict plant growth features and grain composition collected by high throughput techniques and determine relationships between crop management practices and grain composition and ultimately end-use value. By identifying optimal variety-management combinations and leveraging non-invasive, high-throughput plant and grain analysis, this study offers a scalable framework for real-time decision-making and targeted field interventions to improve sorghum varieties. </p><p dir="ltr">This dataset contains grain composition determined by near-infrared spectroscopy used as part of this research project.</p>

Tags: grain, grain-composition, grain-hardness, grain-size, lysine, near-infrared-spectroscopy, protein, sorghum, starch
Organization: Department of Agriculture
Data from: MicroplateGR4: a GUI Matlab program for reducing bias in microbial growth kinetics estimates from microtiter plate optical density data

<p dir="ltr">Data for high-throughput measurements of microbial growth kinetics are typically generated using automated optical density (OD) measurements from microtiter plate readers. There may be significant bias in these measurements which often goes unrecognized, in particular due to variation in background OD measurements and initial cell counts. Curve fitting methods may fail due to atypical growth curves. MicroplateGR4 software was developed to automate the analysis of microtiter plate optical density data from microtiter plate readers, identify sources of error, and generate repeatable and accurate microbial growth kinetics measurements. Example data is included; files consist of Nx97 comma delimited data files consisting of rows (A-H) and columns (col) (1-12). The first column is elapsed time in hours, and subsequent columns are data from 96 well microtiter plates in row-dominant order (A1, A2, A3 ... H11, H12). Microtiter plates were prepared following the general protocol of Anthony and Breidt (protocols.io, https://www.protocols.io/view/microtiter-plate-microbial-growth-measurements-n2bvjny5bgk5/v1).</p><p dir="ltr">EX231020 DifficultCurves.csv, 48 x 97 spreadsheet with OD data, first col is elapsed time, hours (h). Replicate data cells in columns with rows containing 1:2 serial dilutions for the initial OD. No-cell controls included Artificial Cucumber Juice Medium (ACJ), a laboratory medium with similar nutrients as cucumber juice, (col 11) and cucumber juice (CJ, col 12), replicated for all rows. Data for <i>Leuconostoc mesenteroides </i>LA81 in ACJ medium was in cols 1,2, with CJ medium in cols 5,6. Data for <i>Lactiplantibacillus pentosus </i>LA445 in ACJ was in cols 3,4, and for CJ medium, cols 7,8.</p><p dir="ltr">EX240801 B200.csv, 96 x 97 spreadsheet with OD data, first column is elapsed time, 0.5 h. Data included cols 2 and 4 with <i>Escherichia coli </i>B200 in CJ medium (serial dilutions for rows A-F), with controls in cols 11 and 12 (all rows).</p><p dir="ltr">EX250319 microplate.csv, 192 x 97 spreadsheet with OD data, first column in elapsed time 0.25 h. Data included serial 2-fold dilutions (rows A-H) for <i>Lactiplantibacillus pentosus </i>LA445 in columns 1-3 with ACJ medium, columns 4-6 with CJ medium, and columns 7-9  De Man, Rogosa and Sharpe (MRS) medium (a commercial laboratory growth medium for lactic acid bacteria, from De Man, J.C., Rogosa, M., and Sharpe, M.E. (1960). A Medium for the Cultivation of Lactobacilli. <i>Journal of Applied Bacteriology</i>, 23(1), 130–135.). No-cell controls for ACJ (column 10), CJ (column 11), and MRS (column 12) were in all rows.</p><p dir="ltr">EX250319 no header.csv (same as EX250319 but without first row containing row/col labels).</p><p><br></p>

Tags: matlab, measurement-bias, microbial-growth-kinetics, microtiter-plate
Organization: Department of Agriculture
Data from: Development and application of an updated haplotype reference panel for association analysis of spontaneous sex reversal in XX rainbow trout

<p dir="ltr">All-female lines are preferred for rainbow trout production because early sexual maturation in males causes reductions in production efficiency and product quality. However, spontaneous males were reported in genetically all-female XX populations. The objective of this study was to identify single nucleotide polymorphisms (SNPs) associated with spontaneous sex reversal to males in XX rainbow trout (sXX sex reversal). Two families, ST15 and ST22, were genotyped with the Axiom 57K SNP array, and 55 significant SNPs associated with sXX sex reversal were identified and 53 out of the 55 SNPs were located on chromosome OmyA26.</p><p dir="ltr">The genotypes of families ST15 and ST22 are included in this dataset. The chromosome numbers and SNPs locations are based on the Arlee reference genome. SNPs cannot be mapped to the genome were assigned to chromosome 34.</p>

Tags: qtl, rainbow-trout, sex-reversal, snp, spontaneous-male
Organization: Department of Agriculture
Data from: Deep Learning for Sorghum Yield Forecasting using Uncrewed 2 Aerial Systems and Lab-Derived Imagery

<p dir="ltr">Sorghum is an important grain crop in the central plains of the United States and is used for feed, fuel, and food. Sorghum has a wide degree of genetic and phenotypic diversity which can be exploited to improve the agronomic performance and end-use quality and value of the crop. Grain yield is a primary trait that the sorghum breeding industry is working on improving as increased yields directly relate to the value and productivity. Therefore, to take advantage of the genetic diversity of sorghum and develop new lines with improved yield, methods for rapidly determining and predicting yield are necessary. This research evaluated the use of deep learning algorithms to predict yield from images of sorghum and found that yield could be forecast using deep learning processing of images.</p><p dir="ltr">Data includes physical measurements of individual sorghum kernel length and thickness (diameter) used as "ground truth" measurements to help verify seed size measurements determined from bulk grain image analysis.</p>

Tags: grain, image-analysis, kernel-size, sorghum, yield
Organization: Department of Agriculture
Data from: Detection of viral, bacterial, and protozoan pathogens and microbial source tracking markers in paired large- and small-volume water samples

<p dir="ltr">This repository contains data supporting the publication, "Detection of viral, bacterial, and protozoan pathogens and microbial source tracking markers in paired large- and small-volume water samples." The dataset comprises qPCR concentrations of microbial targets in paired large volume and small volume samples from field studies and laboratory recovery experiments, as described in the main publication. </p><p dir="ltr">"Field studies.csv" contains sample data and target concentrations for three field studies, two in groundwater and one in surface water. In the "Groundwater - Private wells (n = 138)" study, large volume samples taken by dead-end ultrafiltration were compared to small volume grab samples. In the remaining two studies, large volume dead-end ultrafiltration and small volume samples were collected synchronously to remove the effect of spatial/temporal heterogeneity during collection. Only the 15 qPCR assays with detections and common to all studies are included. Geographic information is not included to protect the privacy of study participants. </p><p dir="ltr">"Recovery data.csv" contains laboratory data for large volume and small volume method recovery of three microbial targets (a bacterium, a virus, and a protozoan) at varying initial concentrations.</p><p dir="ltr">"Storage data.csv" contains laboratory data for microbial target decay during storage prior to processing. Liquid small volume samples and large volume ultrafilters were stored at 4 C to simulate normal sample storage and transport conditions. Concentrations of three microbial targets (a bacterium, a virus, and a protozoan) were determined for storage times from 0 to 96 hours.</p><p dir="ltr">Descriptive data for all microbial targets is provided in "Target data.csv". An explanation of variables (with units) for all data files can found in "Key to variables.csv".</p>

Tags: bacteria, dead-end-ultrafiltration, groundwater, pathogen, protozoa, sample-volume, surface-water, virus, water-sample-detection
Organization: Department of Agriculture
Data from: Agile Genetics: Single gene resolution without the fuss

<p dir="ltr">These files are 250bp Illumina MiSeq paired-end sequencing reads in fastq format. Libraries were prepared from DNA fragments amplified from tomato bulk (heterogenous) samples around the fruit weight locus.</p>

Tags: id-seq-amplicons, illumina-sequencing-reads, tomato-fruit-weight-gene
Organization: Department of Agriculture
Modular RivGen LCOE Content Model

The Modular RivGen LCOE Content Model contains estimates of levelized cost of energy (LCOE) for three array configurations operating in a theoretical river environment. The LCOE is distinguished by the CapEx, OpEx, and annual energy production and capture for each river environment.

Tags: aep, annual, capex, cec, cost, cross-flow-turbine, economics, efficiency, electrical, energy, energy-capture, energy-production, humboldt-bay, hydrokinetic, lcoe, marine, mechanical, mhk, modular, om, opex, power, power-coefficient, power-matrix, resource, river, rivgen
Organization: Department of Energy
Rock-Eval pyrolysis, vitrinite reflectance, and kerogen microscopy analytical results from Eocene to Pliocene strata in the Susitna Basin, Kenai Peninsula, and Kachemak Bay, Cook Inlet, Alaska

Rock-Eval pyrolysis, vitrinite reflectance, and kerogen microscopy analytical results from Eocene to Pliocene strata in the Susitna Basin, Kenai Peninsula, and Kachemak Bay, Cook Inlet, Alaska, Raw Data File 2025-31, provides analytical results from Rock-Eval pyrolysis, vitrinite reflectance, and kerogen microscopy performed on 51 outcrop samples collected across the Cook Inlet region, including the Susitna Basin, Kenai Peninsula, and Kachemak Bay. These samples were obtained during DGGS Energy Resources Section field campaigns conducted in 2006, 2007, and 2009 to evaluate regional geology and hydrocarbon potential. Eight samples were analyzed by Rock-Eval pyrolysis, and vitrinite reflectance and kerogen microscopy were completed for the full sample set. The samples represent five stratigraphic units: six from the West Foreland Formation, six from the Hemlock Conglomerate, 18 from the Tyonek Formation, 15 from the Beluga Formation, and six from the Sterling Formation. Rock-Eval pyrolysis supports assessment of hydrocarbon-generative potential and thermal maturity. Vitrinite reflectance and kerogen microscopy provide complementary indicators of organic matter type and thermal evolution. Together, these datasets contribute to a more comprehensive understanding of source rock characteristics and maturation history within the Cook Inlet petroleum system. These data are provided as a Raw Data File under an open end-user license and are available on the DGGS website: http://doi.org/10.14509/31800.

Tags: analyses, basin analysis, basins, bedrock, beluga formation, beluga river, bishop creek, capps creek, chichantna river, chigmit mountains, chuitna river, claystone, coal, conglomerate, cook inlet, deep creek, dggs, energy, energy resources, eocene, exploration, falls creek, formations, gas, gas basins, geochemical data, geochemistry, geology, hemlock conglomerate, homer mining district, hydrocarbon, hydrocarbon exploration, hydrocarbon potential, kachemak bay, kenai peninsula, kerogen, kerogen microscopy, lewis river, lignite, methods, mudstone, north capps creek, oil and gas, oil and gas basin, oil basins, oil development, organic geochemistry, outcrop, outcrop samples, petrified wood, petrogenesis, petrographic, petrography, petroleum, petroleum basin study, petroleum geology, petroleum systems, petrology, pliocene, pyrolysis, redoubt mining district, resources, rock-eval pyrolysis, rocks, sandstone, sedimentary, sedimentary rocks, siderite, siltstone, source rock evaluation, source rocks, southcentral alaska, sterling formation, stratigraphy, susitna basin, theodore river, thermal maturity, tyonek formation, visual kerogen, vitrinite, vitrinite reflectance, west foreland formation
Organization: State of Alaska
NYC Honorary Street Names Map (Street Line)

The dataset contains the metadata provided on the <a target="_blank" href="https://streetnamesmap-nyc.hub.arcgis.com/">NYC Honorary Street Names Map</a>. The dataset will include City Council Introduction Number, the local law enactment number and date, category of change, borough, new name of the street or intersection, present name, limits, zip code, Introduced by Council Member(s), Biographical information of the individual, Notes, Longitude and Latitude  coordinates.

Tags: city-council-report, department-of-records, doris, nyc-honorary-street-names, records, street-intersections, street-map
Organization: City of New York
City Council Capital Budget

The dataset reflects funded applications for capital funding allocated by the New York City Council.

Each year, Members of the Council allocate funds to not-for-profit organizations for capital projects that will continue to serve a City purpose (i.e. "limited to the purposes set forth in the New York City Charter" according to Directive 10 from the Office of the Comptroller) for the project's entire useful life. These projects can involve property (acquisition, construction or reconstruction), or moveable property (equipment, furniture, or vehicles).

Recipients of capital funding must:
• hold not for profit status;
• must already hold contracts with the city, with different contract requirements depending on funding type;
• use the grant for stated capital investments at the location of the application.

Organizations must submit their Request Forms online via CapGrants.

For information on the process see: https://www.nyc.gov/site/capitalgrants/guidelines/guidelines.page

For Directive 10 from the Office of the Comptroller see: https://www.nyc.gov/assets/ddc/downloads/not-for-profit/Directive-10-Charges-to-the-Capital-Projects-Fund-Final%20-%20June%202019.pdf

Recipients of capital funding must:
• hold not for profit status;
• must already hold contracts with the city, with different contract requirements depending on funding type;
• use the grant for stated capital investments at the location of the application.

Organizations must submit their Request Forms online via CapGrants.

For more information on the process see: hhttps://www.nyc.gov/site/capitalgrants/guidelines/guidelines.page

Tags: budget, capital, construction, council, infrastructure, investment, ngo, non-profit, nycc, property
Organization: City of New York
Local Law 83 - City Agency Advertising Spend

MOECM functions as financial oversight for all City of New York media placement spend, providing guidance on marketing efficiency and strategy, as well as, monitoring alignment with
the budgetary goals set out in LL83, where each city agency should seek to spend at least 50 percent of applicable media placement budgets with ECM outlets. MOECM is required to report annually on specific city agencies' full advertising spend across all media categories, including ethnic and community (ECM), mainstream, out-of-home, social media, etc. This dataset as well as the dashboards found in this portal reflects the media placement spend of city agencies that had marketing campaigns and their individual alignment with LL83’s goals. 

MOECM works closely with media placement vendors and city agencies to gather accurate media placement spend data through reports, effectively tracking each paid advertisement
placed on behalf of the City of New York. This data is collected, analyzed, and publicly posted to promote transparency regarding media placement budget allocation.

For more information, please visit the MOECM website https://www.nyc.gov/site/ethnicmedia/index.page).

Tags: advertising, community, ecm, ethnic, ll83, local-law-83, media, media-outlets, media-vendor, moecm, publications
Organization: City of New York
City Council Committee Membership (1999 to 2025)

This dataset contains information on the appointments of New York City Council Members from 1999 through 2025. Information before 1999 is not contained in Legistar, the Council's tracking system.

More information on Committees can be found at: https://council.nyc.gov/committees/

To access the Legislative API, you can request a key here: https://council.nyc.gov/legislation/api/

Tags: appointment, city-council, committee, council-member, hearing, legislation
Organization: City of New York
Emergency Food Supply Gap

The Supply Gap Map is a robust metric that tracks neighborhood-by-neighborhood levels of unmet food need, alongside the various supplies of food going into each neighborhood. Data is analyzed by Neighborhood Tabulation Area (NTA).
https://www.nyc.gov/site/foodpolicy/reports-and-data/supply-gap.page

Tags: emergency-food, food, food-needs, supply-gap
Organization: City of New York