AndreaBozzo/ceres-open-data-index huggingface dataset:
Data from: Precision, quantitative measurement of sunflower capitulum inclination: a trigonometry-based approach

<p dir="ltr"><b>headinclination_allmodels.xlsx:</b></p><p dir="ltr">Excel file containing the raw data and calculated angles for sunflower head inclination measurements. This dataset includes:</p><p dir="ltr">Plot identifiers and location information</p><p dir="ltr">Plant measurements (flower height, maturity height, stem length, head height)</p><p dir="ltr">Calculated values (height difference, incline length)</p><p dir="ltr">Angle measurements using different methods (trigonometry-based, linear model)</p><p dir="ltr"><b>supplementarymaterial_angle 20240619.stl:</b></p><p dir="ltr">STL file containing a 3D model related to the angle measurement apparatus used in the study.</p><p dir="ltr"><b>supplementarymaterial_mount 20240619.stl:</b></p><p dir="ltr">STL file containing a 3D model of the mounting mechanism used for the measurement apparatus.</p>

Tags: crop-genetics, crop-growth-and-development, data-acquisition-and-assimilation, field-evaluations, germplasm-enhancement, math-solutions, other-approaches, statistics, sunflowers
Organization: Department of Agriculture
Data from: Evaluating impacts of radiation-induced sterilization on the performance and gut microbiome of mass-reared Mediterranean fruit fly (Ceratitis capitata) in Hawai’i

<p dir="ltr">Mediterranean fruit fly males reared for sterile insect technique (SIT) have been shown to have differences in their microbiomes relative to other population sources, which has been postulated to be a factor in the how well flies compete with wild conspecifics. To identify baseline performance metrics on the effects of irradiation on the gut microbiome of mass-reared flies in Hawai’i, a study was performed to assess performance metrics and microbiome (bacterial 16S-rRNA) variation across multiple timepoints. Mediterranean fruit fly pupae were selected from mass-reared trays intended for release, and paired samples were either irradiated or remained as controls and transported to the laboratory for evaluation.</p>

Tags: 16s-rrna, bacteria, digestive, gut, microbiome, sterile-insect-technique, tephritidae
Organization: Department of Agriculture
Data and scripts from: Revealing reassortment in influenza A viruses with TreeSort

<p dir="ltr">This repository contains scripts and data to replicate the experiments from<br>Markin, A., Macken, C.A., Baker, A.L., and Anderson, T.K., 2024. <b>Revealing reassortment in influenza A viruses with TreeSort</b>. bioRxiv 2024.11.15.623781; doi: <a href="https://doi.org/10.1101/2024.11.15.623781" rel="noreferrer" target="_blank">https://doi.org/10.1101/2024.11.15.623781</a></p><p><br></p><p><br></p><p dir="ltr">For the TreeSort tool and tutorial, see <a href="https://github.com/flu-crew/TreeSort" rel="noreferrer" target="_blank">https://github.com/flu-crew/TreeSort</a>.</p><p dir="ltr">Unzip TreeSort-experiments.zip and see the nested directories and README files for instructions to replicate the study.</p><p dir="ltr">- See 'simulations' directory for code and instructions to replicate the simulation study.<br>- See 'IAV-reasortment-analysis' directory for data and code to replicate the analysis of reassortment rates and patterns among avian, swine, and human IAV lineages.</p><p dir="ltr"><br></p><p dir="ltr">Contact alexey.markn@usda.gov for questions.</p><p dir="ltr"><br></p>

Tags: influenza-a, reassortment
Organization: Department of Agriculture
Population dynamics of<i> Floracarus perrepae </i>and a predatory mite in a screenhouse environment

<p dir="ltr">This research investigated observations of an increase in a predatory mite within galls for a screenhouse mass rearing colony. The survey consisted of counted the galls on 5 haphazardly selected plants and then dissecting 5 galls for each plant. The number of <i>Floracarus perrepae</i> biological control mites and the number of predatory mites were recorded for each gall. The survey was intended to run a full early starting 9/29/2021, but it concluded early in July 2022 when the screenhouse became too hot for a colony to be maintained there. Predatory mite presence is correlated with a reduction in <i>F. perrepae </i>numbers. Sequenced samples of predatory mite from the colony and indicated that the predatory mite is <i>Amblyseius rematavensis</i>.</p><p dir="ltr">Partially funded by the USDA through the Comprehensive Everglades Restoration Plan (CERP) (USDA agreement 58-6032-1-001), through the Southwest Florida Water Management District (USDA agreement 58-6032-3-003).</p>

Tags: biological-control, ferns, floracarus-perrepae, galls, invasive-species, lygodium-microphyllum, mites, predatory-mite, usda
Organization: Department of Agriculture
Data and Code: Temperature influences desiccation resistance of bumble bees

<p dir="ltr">In this experiment, we crossed temperature (20, 25, and 30C) with humidity (<5%, 50%, and >95% RH) and measured the effects on bumble bee (<i>Bombus impatiens</i>) water balance. We had 10 replicates per treatment, with 6 source colonies, resulting in a total of 540 bees. We placed bees singly into tubes and checked for mortality every 2 hours for the first 12 hours and then every 4 hours until 5/10 bees from each temperature, humidity, colony treatment had reached mortality (52h and 48h for the two trials). We measured mass before and after mortality to evaluate water loss and then dried bees to a constant dry weight to get the initial water content and dry mass of each bee. </p>

Tags: bombus-impatiens, critical-water-content, desiccation-resistance, water-loss-rates
Organization: Department of Agriculture
Data From: Two haplotype-resolved genomes reveal important flower traits in bigleaf hydrangea (Hydrangea macrophylla) and insights into Asterid evolution

<p dir="ltr">These files represent the final annotations for two hydrangea genomes derived from BRAKER2 using total RNAs extracted from seven tissue types, including sepals, buds, flowers, nodes, internodes, leaves, and roots, and subjected to library preparation according to the manufacturer’s instructions. The publicly available Iso-seq reads on NCBI (PRJDB9979) were used for genome annotation. Files include normal gff3 format and coding sequence (CDS) files.</p>

Tags: flowers, gene-annotation, horticulture-production, hydrangea
Organization: Department of Agriculture
CMAQv5.5 CRACMM2 Predictions for Select Locations during 2023 in the U.S.: Northeast U.S. (v2.0)

2023 CMAQ Simulation output for select sites in the Northeast US
- CMAQ simulations performed by Havala Pye ORD/CEMM/AESMD 
- simulation labels: cmaq55plus (base) and cmaq55plus_nofire (wildfire, agricultural fire, and prescribed fire emissions in US and outside US set to zero)
- Description: CMAQv5.5+ public version downloaded 2/13/2025. (SHA: 783dc11668a83b9ec243c2cf7d20471ecd34dfae). Last Merge on 5.5 plus: Jan 31. Chemical mechanism: CRACMM2. Dry deposition: STAGE with Emerson et al. 2020 aerosol parameters. Vertical diffusion: acm. Windblown dust emissions: on. Sea spray emissions: on. Lightning NOx: on. Land surface model: PX. Bidirectional ammonia exchange: on. Fertilizer NH3 emissions: computed in-line. HONO production on ground surfaces: on. Gravitational settling of aerosols: on. Scale free trop O3 to potential vorticity: off. Biogenic emissions: BEIS in-line. Aerosol optics: approx of Mie Theory for internally homogeneous particle. WRF v4.6.0. BCON: GEOSCF mapped to cracmm2. Solver: EBI. Compiler: Intel 23.2. OMI file set to use 2019 data. Entire month of December 2022 (using representative days) discarded as spinup. HAP emissions are from explicit emission factors rather than VOC speciation.  Species definitions file for post processing concentrations updated 2/27/2025. Simulations and post-processing performed by Havala Pye.
- Original file locations: /work/MOD3DEV/has/2023cracmm_ages/runs/

Files were created by the write site program distributed with CMAQ (https://github.com/USEPA/CMAQ/blob/main/POST/writesite/README.md). Species included are defined in terms of raw models species in SpecDef_Conc_cracmm2_v2.txt. The description of raw model species is at https://github.com/USEPA/CRACMM/blob/main/metadata/cracmm2/cracmm2_metadata.csv. Log files for the write site program are included as writesite*.txt. A jupyter notebook in ipynb and html format shows some of the data.

Please cite the following for CMAQ with CRACMM2:
Skipper, T. N., D'Ambro, E. L., Wiser, F. C., McNeill, V. F., Schwantes, R. H., Henderson, B. H., Piletic, I. R., Baublitz, C. B., Bash, J. O., Whitehill, A. R., Valin, L. C., Mouat, A. P., Kaiser, J., Wolfe, G. M., St. Clair, J. M., Hanisco, T. F., Fried, A., Place, B. K., and Pye, H. O. T.: Role of chemical production and depositional losses on formaldehyde in the Community Regional Atmospheric Chemistry Multiphase Mechanism (CRACMM), Atmos. Chem. Phys., 24, 12903–12924, https://doi.org/10.5194/acp-24-12903-2024, 2024.

DISCLAIMER: This data product has been reviewed in accordance with U.S. Environmental Protection Agency policy and approved for public release. At the time of release, the data had not yet been published in peer-reviewed literature. The data is provided for research and the user should verify the data is suitable for their intended use.

Tags: air-quality, cmaq, ozone, pm2-5
Organization: U.S. Environmental Protection Agency
ESR_Manuscript_Data

Development of band ratio from Sentinel-2 and SCHISM model input and output files. Portions of this dataset are inaccessible because: The file is 42GB and too large to be uploaded to ScienceHub or hosted in EDG. They can be accessed through the following means: Contact the Principal Investigator, Blake Schaeffer at schaeffer.blake@epa.gov. Format: Development of band ratio from Sentinel-2 and SCHISM model input and output files. 

This dataset is associated with the following publication:
Lebrasse, M., B. Schaeffer, D.R. Bohnenstiehl, C.L. Osburn, M. Coffer, R. He, P. Whitman, W. Salls, and D. Graybill. Winter-Spring dynamics of dissolved organic carbon fluxes driven by precipitation in a North Carolina tidal marsh.   ESTUARINE, COASTAL AND SHELF SCIENCE. Elsevier Science Ltd, New York, NY, USA, 322: 109361, (2025).

Tags: blue-carbon, dissolved-organic-carbon, numerical-modeling, sentinel-2, tidal-marshes
Organization: U.S. Environmental Protection Agency
Land Cover Data: Lake Powell Backwaters, 2009-2021

This dataset contains spatial and tabular data documenting land cover and surface exposure ages along the Colorado and San Juan Rivers within the backwaters of Lake Powell Reservoir. Data were derived from aerial imagery collected as part of the USDA NAIP Program between 2009-2021, along with topobathymetric elevation data collected from Lake Powell Reservoir. For more information on the data contained here, please see "0-README.txt" within the attached .zip folder.

Tags: colorado-river, dams-and-reservoirs, drought, water-resources
Organization: U.S. Environmental Protection Agency
Data from "Estimating power plant contributions to surface pollution in a wintertime Arctic environment"

This dataset is non-EPA-owned. Some of the analyses are based on previous use of CMAQ emissions and meteorological files for the ALPACA period.  The links to those ScienceHub entries are attached. Portions of this dataset are inaccessible because: Non-EPA-owned data by the first author. They can be accessed through the following means: Contact Natalie Brett (natalie.brett@latmos.ipsl.fr) or Steve Arnold (S.Arnold@leeds.ac.uk). Format: Analyses in this paper are based on model simulations (described in a previous paper) that used EPA data (netCDF files containing CMAQ emissions and meteorological inputs). See the associated links above which will be published upon publication of the associated manuscripts. 

This dataset is associated with the following publication:
Brett, N., S. Arnold, K. Law, J. Raut, T. Onishi, B. Barret, E. Dieudonné, M. Cesler-Maloney, W. Simpson, S. Bekki, J. Savarino, S. Albertin, R. Gilliam, K. Fahey, G. Pouliot, D. Huff, and B. D'Anna. Estimating Power Plant Contributions to Surface Pollution in a Wintertime Arctic Environment.   ACS ES&T Air. American Chemical Society, Washington, DC, USA, 2(5): 943-956, (2025).

Tags: alpaca, fairbanks, power-plant-emissions, winter-pollution
Organization: U.S. Environmental Protection Agency
EPA Facility Registry Service (FRS): FRP

This dataset contains location and facility identification information from EPA's Facility Registry System (FRS) for the subset of facilities that are active oil facilities subject to FRP. It includes FRP id, harm/determination category, OSRO, and harm factors,  Using vigorous verification and data management procedures, FRS integrates facility data from EPA's national program systems, other federal agencies, and State and tribal master facility records and provides EPA with a centrally managed, single source of comprehensive and authoritative information on facilities.   Additional information on FRS is available at the EPA website https://www.epa.gov/enviro/facility-registry-service-frs. Data Dictionary available: https://ordsext.epa.gov/FLA/www3/ESF10_Supplemental_Metadata.docx

Tags: 020:072, alabama, alaska, american samoa, arizona, arkansas, california, cleanup, colorado, compliance, connecticut, contaminant, conterminous united states (conus), delaware, district of columbia, emergency response, environmental management, esf10, facilities, florida, georgia, hawaii, idaho, illinois, indiana, iowa, kansas, kentucky, louisiana, maine, maryland, massachusetts, michigan, minnesota, mississippi, missouri, montana, nebraska, nevada, new hampshire, new jersey, new mexico, new york, north carolina, north dakota, ohio, oklahoma, oregon, pennsylvania, puerto rico, regulatory, remediation, resources, rhode island, sites, south carolina, south dakota, tennessee, texas, toxics, united states, united states (us) (usa), utah, vermont, virgin islands, virginia, washington, washington dc, waste, west virginia, wisconsin, wyoming
Organization: U.S. Environmental Protection Agency
TigerRAY Moored Deployment Data

This respiratory contains TigerRAY moored deployment data for each day in which data was collected between January 10, 2024 and March 3, 2024. For sensors on and inside TigerRAY, there is one .mat file for each day in which TigerRAY operated and collected data. These files are labeled as: "DDMMMYYYY_TigerRAYdata.mat" corresponding to the date collected. These .mat files contain a single variable, data, formatted into:
- time stamps and load cell readings from the heave plate 
- time stamps and data from the two heave plate mounted pressure sensors
- structure containing data from the heave plate mounted IMU
- data collected by the central data acquisition system in the nacelle
- timestamps and data from encoder 1
- timestamps and data from encoder 2
- structure containing data from the nacelle mounted IMU
- data from the satellite compass mounted to the mast of the nacelle

For SWIFT data, there is one data file that contains all reprocessed SWIFT data for the entire deployment. This repository contains three structures, named SWIFT22_rp, SWIFT23_rp, and SWIFT24_rp. Reprocessing of the data was done to remove frequency components in the wave spectra with frequencies < 0.2 Hz. The remaining energy is distributed between 0.2 Hz and 1 Hz. New significant wave height, peak period, energy period, and peak direction were then calculated from these trimmed energy spectra.

See attached data guide for a complete summary of data included in this submission, description of the data products (TigerRAY and SWIFT data), and deployment setup information and figures. 

Tags: code, deployment-data, energy, field-deployment, hydrokinetic, imu, load-cell, marine, matlab, mhk, moored-deployment, power, pressure-sensors, processed-data, reprocessed-data, swift, swift-data, tigerray, tigerray-data, tigerray-moored-deployment, usa, wa, washington, wave-energy
Organization: Department of Energy
EPA Facility Registry Service (FRS): Oil Compliance Activity

This dataset contains location and facility identification information from EPA's Facility Registry System (FRS) for the subset of facilities that contain Oil compliance inspection activities for all active Oil facilities. It includes inspection start date, end date and outcome information. Using vigorous verification and data management procedures, FRS integrates facility data from EPA's national program systems, other federal agencies, and State and tribal master facility records and provides EPA with a centrally managed, single source of comprehensive and authoritative information on facilities.   Additional information on FRS is available at the EPA website https://www.epa.gov/enviro/facility-registry-service-frs. Data Dictionary available: https://ordsext.epa.gov/FLA/www3/ESF10_Supplemental_Metadata.docx

Tags: 020:072, alabama, alaska, american samoa, arizona, arkansas, california, cleanup, colorado, compliance, connecticut, contaminant, conterminous united states (conus), delaware, district of columbia, emergency response, environmental management, esf10, facilities, florida, georgia, hawaii, idaho, illinois, indiana, iowa, kansas, kentucky, louisiana, maine, maryland, massachusetts, michigan, minnesota, mississippi, missouri, montana, nebraska, nevada, new hampshire, new jersey, new mexico, new york, north carolina, north dakota, ohio, oklahoma, oregon, pennsylvania, puerto rico, regulatory, remediation, resources, rhode island, sites, south carolina, south dakota, tennessee, texas, toxics, united states, united states (us) (usa), utah, vermont, virgin islands, virginia, washington, washington dc, waste, west virginia, wisconsin, wyoming
Organization: U.S. Environmental Protection Agency
EPA Facility Registry Service (FRS): OIL OSRO

This dataset contains OSRO information from EPA's Facility Registry System (FRS) for the subset of facilities that are active oil facilities subject to FRP. Using vigorous verification and data management procedures, FRS integrates facility data from EPA's national program systems, other federal agencies, and State and tribal master facility records and provides EPA with a centrally managed, single source of comprehensive and authoritative information on facilities.   Additional information on FRS is available at the EPA website https://www.epa.gov/enviro/facility-registry-service-frs. Data Dictionary available: https://ordsext.epa.gov/FLA/www3/ESF10_Supplemental_Metadata.docx

Tags: 020:072, alabama, alaska, american samoa, arizona, arkansas, california, cleanup, colorado, compliance, connecticut, contaminant, conterminous united states (conus), delaware, district of columbia, emergency response, environmental management, esf10, facilities, florida, georgia, hawaii, idaho, illinois, indiana, iowa, kansas, kentucky, louisiana, maine, maryland, massachusetts, michigan, minnesota, mississippi, missouri, montana, nebraska, nevada, new hampshire, new jersey, new mexico, new york, north carolina, north dakota, ohio, oklahoma, oregon, pennsylvania, puerto rico, regulatory, remediation, resources, rhode island, sites, south carolina, south dakota, tennessee, texas, toxics, united states, united states (us) (usa), utah, vermont, virgin islands, virginia, washington, washington dc, waste, west virginia, wisconsin, wyoming
Organization: U.S. Environmental Protection Agency
EPA Facility Registry Service (FRS): Oil Discharge History

This dataset contains location and facility identification information from EPA's Facility Registry System (FRS) for the subset of facilities that are active oil facilities. It contains Oil incidents information for all active Oil facilities. It includes incident cause, type, location and volume. Using vigorous verification and data management procedures, FRS integrates facility data from EPA's national program systems, other federal agencies, and State and tribal master facility records and provides EPA with a centrally managed, single source of comprehensive and authoritative information on facilities.   Additional information on FRS is available at the EPA website https://www.epa.gov/enviro/facility-registry-service-frs. Data Dictionary available: https://ordsext.epa.gov/FLA/www3/ESF10_Supplemental_Metadata.docx

Tags: 020:072, alabama, alaska, american samoa, arizona, arkansas, california, cleanup, colorado, compliance, connecticut, contaminant, conterminous united states (conus), delaware, district of columbia, emergency response, environmental management, esf10, facilities, florida, georgia, hawaii, idaho, illinois, indiana, iowa, kansas, kentucky, louisiana, maine, maryland, massachusetts, michigan, minnesota, mississippi, missouri, montana, nebraska, nevada, new hampshire, new jersey, new mexico, new york, north carolina, north dakota, ohio, oklahoma, oregon, pennsylvania, puerto rico, regulatory, remediation, resources, rhode island, sites, south carolina, south dakota, tennessee, texas, toxics, united states, united states (us) (usa), utah, vermont, virgin islands, virginia, washington, washington dc, waste, west virginia, wisconsin, wyoming
Organization: U.S. Environmental Protection Agency
EPA Facility Registry Service (FRS): Oil Capacity

This dataset contains location and facility identification information from EPA's Facility Registry System (FRS) for the subset of facilities that are active oil facilities.  It includes aboveground Oil storage containers and buried Oil storage containers. Using vigorous verification and data management procedures, FRS integrates facility data from EPA's national program systems, other federal agencies, and State and tribal master facility records and provides EPA with a centrally managed, single source of comprehensive and authoritative information on facilities.   Additional information on FRS is available at the EPA website https://www.epa.gov/enviro/facility-registry-service-frs. Data Dictionary available: https://ordsext.epa.gov/FLA/www3/ESF10_Supplemental_Metadata.docx

Tags: 020:072, alabama, alaska, american samoa, arizona, arkansas, california, cleanup, colorado, compliance, connecticut, contaminant, conterminous united states (conus), delaware, district of columbia, emergency response, environmental management, esf10, facilities, florida, georgia, hawaii, idaho, illinois, indiana, iowa, kansas, kentucky, louisiana, maine, maryland, massachusetts, michigan, minnesota, mississippi, missouri, montana, nebraska, nevada, new hampshire, new jersey, new mexico, new york, north carolina, north dakota, ohio, oklahoma, oregon, pennsylvania, puerto rico, regulatory, remediation, resources, rhode island, sites, south carolina, south dakota, tennessee, texas, toxics, united states, united states (us) (usa), utah, vermont, virgin islands, virginia, washington, washington dc, waste, west virginia, wisconsin, wyoming
Organization: U.S. Environmental Protection Agency
EPA Facility Registry Service (FRS): FRS_ESF10

This web service contains the following layers: RMP, TRI, FRP, RCRATSD, CERCLIS, TSCA, and E-PLAN facilities and their associated CONTACTS, CHEMICALS, NAIP, SIC, and STATE IDs information. Layers are drawn at scale of 1: 18,489,297 and lower. Data used to create this web service are available as a separate download at the Secondary Linkage listed above. Full FGDC metadata records for each layer may be found by clicking the layer name in the web service table of contents (available through the online link provided above) and viewing the layer description. Data Dictionary available: https://ordsext.epa.gov/FLA/www3/ESF10_Supplemental_Metadata.docx

Tags: air, cleanup, compliance, environment, esf-10, esf10, facilities, permits, regulatory, remediation, sites, toxics
Organization: U.S. Environmental Protection Agency