AndreaBozzo/ceres-open-data-index huggingface dataset:
Data and code from: Wild sources for host plant resistance to <i>Bemisia tabaci</i> in watermelon: insights from behavioral and chemical analyses

<p dir="ltr">This dataset includes all raw data and statistical software code required to reproduce the analyses and graphics in the manuscript:</p><p dir="ltr">McKenzie-Reynolds, P., Owolabi, I.A., Biswas, A., Read, Q.D., Burke, G.R., Levi, A. & Simmons, A.M. (2026). Wild sources for host plant resistance to <i>Bemisia tabaci</i> in watermelon: insights from behavioral and chemical analyses. <i>Crop Protection</i>, 199, 107411. <a href="https://doi.org/10.1016/j.cropro.2025.107411" rel="noreferrer" target="_blank">https://doi.org/10.1016/j.cropro.2025.107411</a> (ARIS log 426869)</p><p dir="ltr">Whitefly infestations, primarily caused by <i>Bemisia tabaci</i>, pose a significant threat to watermelon production, leading to severe yield losses and increased reliance on chemical pesticides. We did a study to evaluate the potential of the desert watermelon <i>Citrullus colocynthis</i> and other <i>Citrullus </i>species genotypes for resistance to <i>B. tabaci</i> using oviposition assays, vertical Y-tube olfactometer assays, and gas chromatography-mass spectrometry (GC-MS) analysis of plant volatiles. This dataset contains all the raw and processed data and statistical software code to reproduce the analyses and graphics in the associated manuscript. Our statistical analysis includes Bayesian generalized linear mixed models fit to the oviposition and Y-tube olfactometer datasets, with posterior distributions of the model parameters used to estimate means for each genotype and test hypotheses comparing them. In this dataset we have included CSV files of the raw data, R statistical software code contained in RMarkdown notebooks, HTML rendered output of the notebooks including all figures, tables, and textual description of the results, and pre-fit model objects so that the notebooks may be rendered without refitting the models. The findings in the accompanying manuscript provide critical insights into resistance mechanisms in <i>C. colocynthis</i> and advance sustainable watermelon production, reducing chemical pesticide dependence and enhancing economic returns for growers.</p><p dir="ltr">A full description of all files included in the dataset is found in README.pdf.</p><p><br></p>

Tags: bemisia-tabaci, citrullus-colocynthis, citrullus-lanatus, gas-chromatography-mass-spectrometry-gcms, integrated-pest-management, olfactometer-bioassay, oviposition, oviposition-deterrence, plant-volatiles, watermelon, whitefly, whitefly-resistance
Organization: Department of Agriculture
Data from: Using empirical performance data to source bluebunch and Snake River wheatgrass plant materials to restoration sites in the eastern Great Basin, USA

<p dir="ltr">Twelve populations of bluebunch wheatgrass (7) and Snake River wheatgrass (5) were tested from 2011 (establishment year) through 2016 at three locations (Malta, ID; Nephi, UT; Millville, UT) chosen for low, medium, and high precipitation, respectively. Plots at the three locations were established from transplants at the three locations. Each plot consisted of 12 plants of a population. Each replicate consisted of 12 plots, one for each population. Each location planting consisted of 12 replicates. Plots were arranged in a randomized complete block design with replicates as plots. The purpose of the research was to assess the relative adaptation of the two species and among the populations within each species for the establishment (2011) and post-establishment (2012-2016) stages.</p><p>.</p>

Tags: ecological-restoration, native-plants, plant-adaptation, rangelands
Organization: Department of Agriculture
The Triticeae Toolbox

<p><a href="https://triticeaetoolbox.org/">The Triticeae Toolbox</a> (T3) webportal hosts data generated by the Triticeae Coordinated Agricultural Project (CAP), funded by the National Institute for Food and Agriculture (NIFA) of the United States Department of Agriculture (USDA). T3 contains SNP, phenotypic, and pedigree data from wheat and barley germplasm in the Triticeae CAP integrating rapidly expanding DNA marker and sequence data with traditional phenotypic data to provide access to predictive analyses mapping genotype to phenotype and enabling breeders to select on marker data alone. T3 will also link to related genomic and crop diversity databases (GrainGenes, Gramene, Ensembl Plants, and GRIN) for functional analyses to identify causal polymorphisms and networks affecting phenotypes. The software and data structure for T3 were developed as part of the Barley CAP project for its database, The Hordeum Toolbox (THT), carried forward as part of the Triticeae CAP in the T3 databases. T3 Barley holds data generated for Hordeum vulgare L. T3 Wheat holds data generated for Triticum spp. T3 Oat holds data generated for Avena. All are being enhanced in database performance, community curation and user tools. T3 contains germplasm line information, pedigree, genotype and phenotypic data from breeding programs participating in the CAP and core germplasm collections maintained by the <a href="http://www.ars.usda.gov/Main/docs.htm?docid=21891">USDA National Small Grains Collection</a>. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Website Pointer to The Triticeae Toolbox (T3).</p> <p>File Name: Web Page, url: <a href="https://triticeaetoolbox.org/">https://triticeaetoolbox.org/</a> </p><p>T3 is the webportal for the data generated by the Triticeae Coordinated Agricultural Project (CAP), funded by the National Institute for Food and Agriculture (NIFA) of the United States Department of Agriculture (USDA). Databases accessed via the portal: T3 Wheat, T3 Barley, T3 Oat.</p></li></ul><p></p>

Tags: ars, data-gov, np301
Organization: Department of Agriculture
Data from: Selenium geochemistry in reclaimed phosphate mine soils and its relationship with plant bioavailability

<p>Selenium accumulation in vegetation has resulted in toxicity in livestock grazing on phosphate mine soils in Southeastern Idaho. Plant and soil samples were collected from sites located near phosphate mines. Soil physicochemical properties, Se speciation, and Se distribution from a sequential extraction procedure (SEP) were examined in relation to bioavailability in the Se-hyperaccumulator, western aster (<em>Symphyotrichum ascendens</em> Lindl.). Selenium-hyperaccumulators are plants that can absorb over 1000 mg Se kg<sup>−1</sup> DM (Dry Matter). Chemical analyses revealed that western aster contained Se exceeding 6000 mg kg<sup>−1</sup> DM. Soil speciation results indicated that selenite (SeO3<sup>2−</sup>) was dominant with lower levels of selenate (SeO4<sup>2−</sup>) present. This was expanded using an SEP that accounted for six fractions. Regression analyses indicated a strong relationship for western aster Se and the water-soluble and phosphate-extractable SEP fractions combined (R<sup>2</sup> = 0.85). Once carbonate, amorphous Fe-oxide, organic, and residual Se fractions were factored into the analysis, the relationship decreased. A strong relationship between selenate and the water-soluble Se fraction was also observed (R<sup>2</sup> = 0.83). Soluble and phosphate-extractable Se were determined to be "bioavailable fractions" for western aster. Thus, simple water extractions can be used for quick assessment of Se bioavailability and provide a means to identify potentially hazardous areas locations. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Supplementary Tables - Download docx.</p> <p>File Name: 11104_2017_3299_MOESM1_ESM.docx, url: <a href="https://static-content.springer.com/esm/art:10.1007/s11104-017-3299-5/MediaObjects/11104_2017_3299_MOESM1_ESM.docx">https://static-content.springer.com/esm/art:10.1007/s11104-017-3299-5/MediaObjects/11104_2017_3299_MOESM1_ESM.docx</a> </p><p>Table 1.  Selenite and selenate soil speciation with standard deviations for 10 soils in duplicate.
Table 2. Sequential extraction procedure fractionation for 6 extractions with duplicate standard deviations for 78 soils.</p></li></ul><p></p>

Tags: ars, data-gov, reclaimed-phosphate-mine-soils
Organization: Department of Agriculture
Mortality data of navel orangeworm, Amyelois transitella, in response to nitric oxide fumigation treatment

<p>Mortality data of navel orangeworm, <em>Amyelois transitella</em>, in response to nitric oxide fumigation treatments, are presented.</p>
<p>This data set is associated with the study on responses of navel orangeworm (NOW), <em>Amyelois transitella</em> (Walker), to nitric oxide (NO) fumigation treatments. In the study, NO fumigation was evaluated for efficacy against eggs, larvae, and pupae of NOW. Larvae and pupae were fumigated both on artificial diet and in infested walnuts. Insects were fumigated with NO at different concentrations for different durations. Numbers of dead and alive insects at each life stages were collected for each treatment. NO fumigation was conducted under ultralow oxygen (ULO) conditions. So, each test included two controls: CK (in normal atmosphere) and ULO (under ultralow oxygen condition). Mortality rates from different treatments for each life stage were compared statistically to determine efficacy of NO fumigation. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Data for manuscript JEN-2020-0214.</p> <p>File Name: NO fumigation of NOW Original 10-7-20.xlsx</p><p>Resource Description: This data set is associated with the study on responses of navel orangeworm (NOW), Amyelois transitella (Walker), to nitric oxide (NO) fumigation treatments.  In the study, NO fumigation was evaluated for efficacy against eggs, larvae, and pupae of NOW. Larvae and pupae were fumigated both on artificial diet and in infested walnuts. Insects were fumigated with NO at different concentrations for different durations. Numbers of dead and alive insects at each life stages were collected for each treatment. NO fumigation was conducted under ultralow oxygen (ULO) conditions. So, each test included two controls: CK (in normal atmosphere) and ULO (under ultralow oxygen condition). Mortality rates from different treatments for each life stage were compared statistically to determine efficacy of NO fumigation. </p></li></ul><p></p>

Tags: ars, data-gov, mortality-of-navel-orangeworm, nitric-oxide-fumigation, np304
Organization: Department of Agriculture
Data from: Metagenomes and Metagenome-Assembled Genomes from Ex Vivo Fecal Incubations of Six Unique Donors

<p dir="ltr">This is a dataset consisting of donor-specific collections of 78 metagenomes (13 / donor) and 143 metagenome-assembled genomes (MAGs) representing the gut microbiomes of six healthy adult human donors. Raw sequencing data and MAG sequence data will be available in NCBI under BioProject accession PRJNA961974 (<a href="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA961974">https://www.ncbi.nlm.nih.gov/bioproject/PRJNA961974</a>). Spreadsheets attached to this dataset include individual accession numbers and sequencing depth for the raw data; and assembly and NCBI accession numbers, binning information, quality metrics, and taxonomic assignments for the MAGs.</p><p dir="ltr">Resources in this dataset:</p><ul><li>Resource Title: Metagenome assembled genome (MAG) information File Name: MAGs_information_table.csv</li><li>Resource Title: Metagenome sample information File Name: Metagenomes_information_table.csv</li><li>Resource Title: Metagenome metadata table File Name: Metagenome_metadata_table.xlsx</li><li>Resource Title: MAG metadata table File Name: MAG_metadata_table.xlsx</li></ul><p></p>

Tags: ars, data-gov, gut-microbiome, metagenome-assembled-genomes, metagenomics, np306
Organization: Department of Agriculture
Data from: The pathogenesis of a 2022 North American highly pathogenic clade 2.3.4.4b H5N1 avian influenza virus in mallards (Anas platyrhynchos)

<p>Treatment groups of ducks were exposed to different virus doses (2, 4, 6 log10 50% egg infectious doses) and by different routes (contact or intrachoanal). The experimental setting was a laboratory with animal care as approved by the institutional animal care and use committee as appropriate for the species and age of bird. Data are the virus titers shed by the oral and cloacal route for individual mallard ducks exposed to H5N1 highly pathogenic avian influenza virus by day post exposure. Samples were collected through 11 days post exposure. Virus titer equivalents were determined by quantitative real-time RT-PCR. Serological data are serum antibody titers to the challenge virus as determined by hemagglutination inhibition assay (reciprocal of the log2 dilution) determined with serum collected 10 or 11 days post exposure.  </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Virus_shed_data.</p> <p>File Name: Spackman_et_al_virus_shedData from H5_mallard_study_2022.csv</p><p>Resource Description: Virus shed data determined by quantitative real-time RT-PCR</p></li><br><li><p>Resource Title: Serology data for H5 challenged mallards.</p> <p>File Name: Spackman_et_al_Serology_Data from H5_mallard_study_2022.csv</p><p>Resource Description: Serology determined by hemagglutination inhibition assay. NS= no serum (sample not run)</p></li></ul><p></p>

Tags: ars, avian-influenza, data-gov, mallard-disease, np103
Organization: Department of Agriculture
Data from: Genomic survey of the ectoparasitic mite Varroa destructor, a major pest of the honey bee Apis mellifera

<p>These data represent <em>V. destructor</em> genomic annotations to be used for evolutionary comparison with other arthropods.</p>
<p>The ectoparasitic mite <em>Varroa destructor</em> has emerged as the primary pest of domestic honey bees (<em>Apis mellifera</em>). 
Here we present an initial survey of the <em>V. destructor</em> genome carried out to advance our understanding of <em>Varroa</em> biology and to identify new avenues for mite control. This sequence survey provides immediate resources for molecular and population-genetic analyses of <em>Varroa-Apis</em> interactions and defines the challenges ahead for a comprehensive <em>Varroa</em> genome project.</p>
<div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Data Dictionary - BLAST - annotated Varroa contigs.</p> <p>File Name: Data Dictionary genomic survey ectoparasitic mite varroa.csv</p></li><br><li><p>Resource Title: BLAST-annotated Varroa contigs.</p> <p>File Name: 1471-2164-11-602-s3.csv</p><p>Resource Description: Spreadsheet of Varroa destructor genomic contigs with significant similarity to the GenBank nr database by BLAST search. This is Additional File 3 from Cornman, et al. 2010.

We used BLASTX (for genomic contigs) and BLASTP (for ORFs of 90 residues or more) to identify genic sequences in the assembly. Sequences were initially searched against a database of five arthropod peptide predictions (Drosophila melanogaster, Anopheles gambiae, Pediculus humanus [a representative non-Dipteran insect], Daphnia pulex, and I. scapularis), with a minimum expectation of 10-8, and then secondarily against the eukaryotic Refseq database at the same expectation. In total, 13,031 contigs were identified with BLAST-detected similarity to database sequences.</p></li></ul><p></p>

Tags: ars, data-gov, insects, np305, varroa-destructor
Organization: Department of Agriculture
FoodData Central

<p>Several USDA food composition databases, including the Food and Nutrient Database for Dietary Studies (FNDDS), Standard Reference (SR) Legacy, and the USDA Branded Food Products Database, have transitioned to FoodData Central, a new and harmonized USDA food and nutrient data system. FoodData Central also includes expanded nutrient content information as well as links to diverse data sources that offer related agricultural, environmental, food, health, dietary supplement, and other information.  The new system is designed to strengthen the capacity for rigorous research and policy applications through its search capabilities, downloadable datasets, and detailed documentation. Application developers can incorporate the information into their applications and web sites through the application programming interface (API) REST access.</p>
<p>The constantly changing and expanding food supply is a challenge to those who are interested in using food and nutrient data. Including diverse types of data in one data system gives researchers, policymakers, and other audiences a key resource for addressing vital nutrition and health issues.</p>
<p>FoodData Central:</p>
<ul>
<li>Includes five distinct types of data containing information on food and nutrient profiles, each with a unique purpose: Foundation Foods; Experimental Foods; Standard Reference; Food and Nutrient Database for Dietary Studies; USDA Global Branded Food Products Database.</li>
<li>Provides a broad snapshot in time of the nutrients and other components found in a wide variety of foods and food products.</li>
<li>Presents data that come from a variety of sources and are updated as new information becomes available.</li>
<li>Includes values that are derived through a variety of analytic and computational approaches, using state-of-the-art methodologies and transparent presentation.</li>
</ul>
<p>FoodData Central is managed by the Agricultural Research Service and hosted by the National Agricultural Library.</p>
<div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Website Pointer for FoodData Central.</p> <p>File Name: Web Page, url: <a href="https://fdc.nal.usda.gov/index.html" target="_blank">https://fdc.nal.usda.gov/index.html</a> </p><p>Includes Search, Download data, API Guide, Data Type Documentation, and Help pages.</p></li></ul>

Tags: ars, data-gov, fooddata-central, np107, online-database
Organization: Department of Agriculture
Assessing the attractiveness of native wildflower species to bees (Hymenoptera: Anthophila) in the southeastern United States

<p>Pesticide use, disease, climate change, and habitat loss associated with agricultural intensification and urbanization have contributed to the decline of numerous insect groups. Recent government incentives have recognized the importance of supplementary wildflower plantings to support native bee populations, yet little information exists on the attractiveness of recommended plant species to bees. We evaluated the bee attractiveness of 18 native wildflower species belonging to 6 families (Apiaceae, Apocynaceae, Asteraceae, Fabaceae, Lamiaceae, and Verbenaceae) commonly recommended by the U.S. Department of Agriculture – Natural Resource Conservation Service (USDA-NRCS) to land managers in the southeastern United States. To accomplish this, we planted the 18 wildflower species in separate 1 m2 plots arranged in a randomized block design with four replicates in Auburn, Alabama, USA. We conducted floral counts and timed sweep netting events to assess each species’ attractiveness to bees from May-November 2019. We also evaluated the floral preferences of seven bee taxa (<em>Apis mellifera</em>, <em>Halictus poeyi/ligatus</em>, <em>Bombus griseocollis, Bombus impatiens, Lasioglossum </em>spp., <em>Megachile </em>spp., and <em>Xylocopa virginica</em>) to the planted wildflower species. We found that <em>Asclepias tuberosa, Gaillardia pulchella, </em>and <em>Verbena hastata </em>attracted the greatest abundance, richness, and diversity of native bees compared to the other wildflower species. While several wildflower species attracted low abundance, richness, and diversity of native bees, they are still ecologically important for attracting uncommon or specialist bee species. Each bee taxa were attracted to a particular combination of planted wildflower species; collectively, <em>Asclepias tuberosa, Gaillardia pulchella, </em>and <em>Verbena hastata </em>attracted 89% of all be taxa in the study, which exemplifies the importance of including them in a wildflower mixture to attract native bees. Our results highlight that each species of native wildflower varies in the abundance, richness, and diversity of native bees they attract; this could be considered in the decision-making of landowners and land managers to promote wildflower plantings to reflect their needs.</p>

Tags: bee-visitation, native-bees, native-wildflowers, pollination, sweep-netting, wildflower-attractiveness
Organization: Department of Agriculture
Residue Removal Study for Greenhouse gas Reduction through Agricultural Carbon Enhancement network and Resilient Economic Agricultural Practices in Brookings, South Dakota

<p>Residue Removal Study for Greenhouse gas Reduction through Agricultural Carbon Enhancement network and Resilient Economic Agricultural Practices in Brookings, South Dakota</p>
<div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: GeoData catalog record.</p> <p>File Name: Web Page, url: <a href="https://geodata.nal.usda.gov/geonetwork/srv/eng/catalog.search#/metadata/16fa0ab9-c011-4550-a15c-8286d3d5b716" target="_blank">https://geodata.nal.usda.gov/geonetwork/srv/eng/catalog.search#/metadata/16fa0ab9-c011-4550-a15c-8286d3d5b716</a> </p></li></ul>

Tags: agricultural-economics, ars, carbon, data-gov, environment, farming, greenhouse-gases, np211, np212
Organization: Department of Agriculture
USDA Branded Food Products Database

<p>The USDA Branded Food Database was integrated as part of FoodData Central on April 2019.  For more information on FoodData Central and the USDA Branded Food Database:</p>
<ul>
<li>Website: <a href="https://fdc.nal.usda.gov/">https://fdc.nal.usda.gov/</a></li>
<li>Ag Data Commons link: <a href="https://data.nal.usda.gov/dataset/fooddata-central">https://data.nal.usda.gov/dataset/fooddata-central</a></li>
</ul>

Tags: ars, bfpd, branded-food-products-database, data-gov, np107, online-database
Organization: Department of Agriculture
Data and code from: Predictions of Aboveground Herbaceous Production from Satellite-Derived APAR Are More Sensitive to Ecosite than Grazing Management Strategy in Shortgrass Steppe

<p dir="ltr">This study set out to accurately estimate the amount of herbaceous biomass grown in rangelands, which is difficult to observe directly. Herbaceous biomass is the total weight of all living plant material, such as grasses, forbs, and small shrubs, some of which are edible forage for livestock. We used a combination of satellite data and ground-based measurements to estimate herbaceous biomass.</p><p dir="ltr">The data provided here allows others to reproduce our statistical analysis. We also provide cleaned datasets for herbaceous biomass, grazing periods, satellite, and photosynthetic active radiation collected at the Central Plains Experimental Range, which is a Long-Term Agroecosystem Research network site. The time frame for this data spans 2014 – 2022.</p><p dir="ltr">The .zip archive </p><p dir="ltr"><code>Peirce_etal_2024_APAR_grazing.zip</code></p><p dir="ltr"> contains data and code files.</p><p dir="ltr">This dataset contains all code and data necessary to reproduce the statistical analyses in the manuscript:</p><p dir="ltr">Peirce, E.S.; Kearney, S.P.; Santamaria, N.; Augustine, D.J.; Porensky, L.M. Predictions of Aboveground Herbaceous Production from Satellite-Derived APAR Are More Sensitive to Ecosite than Grazing Management Strategy in Shortgrass Steppe. Remote Sens. 2024, 16, 2780.</p><p dir="ltr"><a href="https://doi.org/10.3390/rs16152780" target="_blank">https://doi.org/10.3390/rs16152780</a></p><p dir="ltr"><br></p><p dir="ltr">This research used resources provided by the SCINet project and/or the AI Center of Excellence of the USDA Agricultural Research Service, ARS project numbers 0201-88888-003-000D and 0201-88888-002-000D.</p>

Tags: anhp, apar, ecological-site, grazing-management, herbaceous-biomass, ndvi, remote-sensing
Organization: Department of Agriculture