AndreaBozzo/ceres-open-data-index huggingface dataset:
Long-term tillage and cropping system experiment for Greenhouse gas Reduction through Agricultural Carbon Enhancement network and Nutrient Use and Outcome Network in Lincoln, Nebraska

<p>Long-term tillage and cropping system experiment for Greenhouse gas Reduction through Agricultural Carbon Enhancement network and Nutrient Use and Outcome Network in Lincoln, Nebraska
Lincoln NE Long-term Tillage Project Overview of NELITCSE: Long-term Tillage and Cropping System Experiment (Lincoln, NE) The objectives of this experiment is to evaluate the agronomic and environmental impacts of long-term tillage and crop rotation practices in a rainfed agroecosystem. This experiment was initiated in 1981 with continuous corn only under six tillage practices (chisel, tandem disk, moldboard plow, no-till, ridge-tillage, and subsoil tillage). In 1985, the experimental design was modified to include 3 crop rotation systems (continuous corn, corn-soybean, and continuous soybean) under 6 tillage practices. Each year, both the corn phase and soybean phase of the two-year rotation system are present. In 2015, all tillage practices were converted to no-till to evaluate the magnitude, direction, and rate of agronomic and soil changes to this management shift. In addition, the continuous soybean system was converted to continuous corn with a 3-species winter cover crop (hairy vetch, purple-topped radish, and cereal rye). Prepared 13 Sep 2016 (V. Jin)</p> <div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Lincoln, NE Long-term tillage and cropping system experiment (NELITCSE) CSV data.</p> <p>File Name: NELITCSE_csv_data.zip</p><p>Resource Description: CSV format data on Experimental Units, Field Sites, Nutrient Efficiency, Residue Management, Soil Chemistry, Soil Physics, Amendments, Planting, Tillage, Persons, Treatments, Weather Daily, Weather Station.</p></li></ul>

Tags: air-temperature, ars, climate-change, crop-rotation, crops, data-gov, environment, environmental-impact, farming, grain-yield, greenhouse-gas, np211, np212, precipitation, soils, soybeans, tillage
Organization: Department of Agriculture
Data from: Bivalent hemagglutinin and neuraminidase influenza replicon particle vaccines protect without causing vaccine associated enhanced respiratory disease in swine

<p>Influenza A virus is a major respiratory pathogen in swine that leads to significant economic loss in the swine industry, and there is a critical need to improve on commercial vaccines. Traditional vaccines target the hemagglutinin (HA) portion of the IAV virus, lose protection to as viruses change, and may even lead to vaccine-associated enhanced respiratory disease (VAERD) after infection with a dissimilar influenza virus. A newer replicon particle (RP) vaccine platform targeting the influenza HA protein offers multiple advantages over traditional vaccines for swine, but have not yet been evaluated for the ability to avoid VAERD or the use of HA along with an additional viral vaccine target, such as neuraminidase (NA). In this work we demonstrated RP HA and NA influenza vaccines stimulate immune responses, protect from disease, and avoid VAERD following infection with a distantly related virus. This demonstrates the potential utility of RP vaccines against influenza and the importance in utilizing the NA in influenza vaccine design. Such improvement of IAV vaccines will reduce influenza disease and economic loss in commercial swine and reduce the risk of influenza transmission to people. These data include individual pig responses used in statistical analyses and figures to support the conclusions of the paper. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Data from: Bivalent hemagglutinin and neuraminidase influenza replicon particle vaccines protect without causing vaccine associated enhanced respiratory disease in swine.</p> <p>File Name: Data Repository.xlsx</p></li></ul><p></p>

Tags: ars, data-gov, influenza-a-virus, np103, replicon-particle, rna-vaccine, vaccine, vaccine-associated-enhanced-respiratory-disease-vaerd
Organization: Department of Agriculture
Data from: Interspecies Transmission from Pigs to Ferrets of Antigenically Distinct Swine H1 Influenza A Viruses with Reduced Reactivity to Candidate Vaccine Virus Antisera as Measures of Relative Zoonotic Risk

<p>The dataset includes clinical data from an experimental swine and ferret challenge and transmission study with 3 strains of swine H1 influenza A virus. Data are presented in two spreadsheets, one for pigs and one for ferrets. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Interspecies transmission from pigs to ferrets of antigenically distinct swine H1 influenza A viruses with loss in reactivity to human vaccine virus antisera as measures of relative zoonotic risk.</p> <p>File Name: Kimble swine and ferret data.xlsx</p></li></ul><p></p>

Tags: antigenic-drift, ars, data-gov, influenza-a-virus, np103, pandemic-preparedness, risk-assessment, variant, zoonosis
Organization: Department of Agriculture
Data from: A catalog of natural products occurring in watermelon - Citrullus lanatus

<p>In support of nutrition research, concentrations of compounds from different parts of the watermelon plant are provided. The parts of the plant for which data are tabulated include (red) flesh, heart tissue, juice, seed, rind, peel, yellow flesh, seedling, leaf, root, other parts of the plant, and detected but plant part undeclared. The collected data include the low value in the range, the high value in the range, deviation from those values, and units (assumed to be fresh or wet weight unless noted). This table also provides for all compounds the citations to the literature and database sources. The “AFC” identifier represents the Agricultural Research Service (ARS) Food Compound; PubChem refers to the identifier from this resource of chemical compounds.</p>
<div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Catalog of natural products occurring in watermelon.</p> <p>File Name: Watermelon_NP_catalog_20210623.tsv</p><p>Resource Description: This is a table of chemical compounds found in watermelon</p></li><br><li><p>Resource Title: Data dictionary.</p> <p>File Name: Data_dictionary_Watermelon_compounds_NAL_20210623.xlsx</p><p>Resource Description: This is the data dictionary</p><p>Resource Software Recommended: Microsoft Excel,url: <a href="https://products.office.com/en-us/access" target="_blank">https://products.office.com/en-us/access</a> </p></li></ul>

Tags: ars, data-gov, food-chemistry, natural-compounds, natural-products, np107, phytochemicals, watermelon
Organization: Department of Agriculture
ASRU Study for Greenhouse gas Reduction through Agricultural Carbon Enhancement network in Sidney, Montana

<p>Information is needed to mitigate dryland soil greenhouse gas (GHG) emissions by using novel management practices. We evaluated the effects of cropping sequence and N fertilization on dryland soil temperature and water content at the 0- to 15-cm depth and surface CO2, N2O, and CH4 fluxes in a Williams loam in eastern Montana. Treatments were no-tilled continuous malt barley (Hordeum vulgaris L.) (NTCB), no-tilled malt barley-pea (Pisum sativum L.) (NTB-P), and conventional-tilled malt barley-fallow (CTB-F) (control), each with 0 and 80 kg N ha-1. Gas fluxes were measured at 3 to 14 d intervals using static, vented chambers from March to November, 2008 to 2011. Soil temperature varied but water content was greater in CTB-F than in other treatments. The GHG fluxes varied with date of sampling, peaking immediately after substantial precipitation (>15 mm) and N fertilization during increased soil temperature. Total CO2 flux from March to November was greater in NTCB and NTB-P with 80 kg N ha-1 than in other treatments from 2008 to 2010. Total N2O flux was greater in NTCB with 0 kg N ha-1 and in NTB-P with 80 kg N ha-1 than in other treatments in 2008 and 2011. Total CH4 uptake was greater with 80 than with 0 kg N ha-1 in NTCB in 2009 and 2011. Because of intermediate level of CO2 equivalent of GHG emissions and known favorable effect on malt barley yield, NTB-P with 0 kg N ha-1 might mitigate GHG emissions and sustain crop yields compared to other treatments in eastern Montana. For accounting global warming potential of management practices, however, additional information on soil C dynamics and CO2 associated with production inputs and machinery use are needed.  </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/60e0612c-8144-46fc-a41a-07fc83b4ad83">https://geodata.nal.usda.gov/geonetwork/srv/eng/catalog.search#/metadata/60e0612c-8144-46fc-a41a-07fc83b4ad83</a> </p></li></ul><p></p>

Tags: ars, crop-management, data-gov, environment, farming, greenhouse-gas-emissions, np211, np212, soil-temperature, tillage, yield
Organization: Department of Agriculture
Data and code from: Comparison of infestation rates of fall armyworm (Lepidoptera: Noctuidae) neonates for maize resistance screening

<p dir="ltr">This document contains all data and R statistical software code needed to reproduce the analyses presented in the manuscript:</p><p dir="ltr">Woolfolk, S., G. Matthews, and Q. D. Read. 2024. Comparison of infestation rates of fall armyworm (Lepidoptera: Noctuidae) neonates for maize resistance screening. <i>Journal of Insect Science. </i>(Citation to be updated)</p><h2>Summary</h2><p dir="ltr">The data included here come from an experiment to assess a technique for measuring resistance of maize to fall armyworm. An economically important global maize pest, fall armyworm (FAW, <i>Spodoptera frugiperda</i>), causes damage mainly to the above-ground parts of maize plants, primarily the whorl tissues. One of our research unit missions is to identify and develop maize germplasm with resistance to FAW. One method to measure resistance in maize to FAW is visual rating of leaf-feeding damage after infestation with neonates into the whorl. The data presented here are from a replicated experiment crossing eleven maize lines (four susceptible and seven resistant) with five FAW infestation rates; the experiment was repeated in two consecutive years. The measured response was leaf feeding damage on a categorical scale. </p><p dir="ltr">The statistical model presented here is a cumulative logistic mixed model. It treats the response variable (leaf damage rating) as an ordered categorical response. We include a random effect to account for the split-plot design, and include three-way interactions between fixed effects of genotype, treatment, and year. We present means for each genotype and treatment based on the underlying modeled probabilities of each category (weighted averages of the modeled probabilities).</p><h2>Files</h2><ul><li><b>FAW_combinedyears.csv</b>: All experimental data, with the following columns:</li><li><ul><li>Year: Year of data collection (2023 or 2024)</li><li>Row: Numeric identifier of row</li><li>Rep: Numeric identifier of replicate block</li><li>Entry: Numeric identifier of genotype</li><li>Pedigree: Text identifier of genotype</li><li>Treatment: Number of neonates per whorl (10, 20, 30, 40, 50)</li><li>Plant: Numeric identifier of individual plant within row</li><li>Rating: Categorical leaf-feeding damage rating (scale of 0-9)</li></ul></li><li><b>FAW_analysis.Rmd</b>: RMarkdown notebook with all R statistical code to reproduce analyses</li><li><b>FAW_analysis.html</b>: HTML rendered output of Rmd notebook</li></ul><p></p>

Tags: damage-score, fall-armyworm, host-plant-resistance, leaf-feeding, maize, visual-rating
Organization: Department of Agriculture
Data from: Gene expression during the early stages of host perception and attachment in adult female Rhipicephalus microplus ticks

<p>This study produced a comprehensive transcriptome from newly molted adult ticks and will provide a useful resource for studies of tick feeding and host perception and also assist genome annotation refinements.</p>
<p>The goal was to develop a comprehensive transcriptome of adult female Rhipicephalus microplus ticks and discover transcriptome changes that are related to feeding and host-perception prior to feeding. We have sequenced the transcriptomes of unfed newly molted adult female ticks, newly molted adult females that were feeding upon a bovine host for 3 hours following attachment to the host, and newly molted adult females that were placed in a gas-permeable bag attached to a bovine host for 3 hours (attachment to host prevented but host odors available to the ticks). There were 2 biological replicates and transcriptomes assembled from each individual experimental condition. A collective adult female transcriptome was assembled from sequence data pooled from all 3 conditions (using data from all replicates). Differential gene expression was examined using all possible comparisons to detect putative feeding-associated and host perception-associated transcripts. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Gene expression during the early stages of host perception and attachment in adult female Rhipicephalus microplus ticks.</p> <p>File Name: Web Page, url: <a href="https://doi.org/10.1007/s10493-019-00420-1">https://doi.org/10.1007/s10493-019-00420-1</a> </p></li></ul><p></p>

Tags: ars, cattle-tick, data-gov, feeding-response, gene-expression, host-perception, np104, transcriptomics
Organization: Department of Agriculture
T3 Barley

<p><a href="https://barley.triticeaetoolbox.org">The Triticeae Toolbox Barley</a> (T3 Barley) is an extension of The Hordeum Toolbox (THT), which was created by the preceding Barley CAP. T3 Barley incorporates all of the THT data.</p>
<p>The Triticeae Toolbox (T3) is the web portal for data generated by the <a href="http://triticeaecap.org/">Triticeae Coordinated Agricultural Project</a> (T-CAP), funded by the National Institute for Food and Agriculture (NIFA) of the United States Department of Agriculture (USDA). It also contains data from US Uniform Regional Nurseries, supported by the <a href="http://scabusa.org/">US Wheat and Barley Scab Initiative</a>. The database was initially developed as The Hordeum Toolbox (THT) to hold barley data generated by the Barley CAP project (2006-2010). T3 Barley hods 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: T3 Barley.</p> <p>File Name: Web Page, url: <a href="https://barley.triticeaetoolbox.org">https://barley.triticeaetoolbox.org</a> </p><p>T3 Barley is an extension of The Hordeum Toolbox (THT), which was created by the preceding Barley CAP. T3 Barley incorporates all of the THT data.</p></li></ul><p></p>

Tags: ars, barley, data-gov, genomics, hordeum-vulgare-l, np301, online-database, phenotype, plants-crops
Organization: Department of Agriculture
Data from: Monitoring standing herbaceous biomass and thresholds in semiarid rangelands from harmonized Landsat 8 and Sentinel-2 imagery to support within-season adaptive management

<p>Tabular data from the manuscript "Monitoring standing herbaceous biomass and thresholds in semiarid rangelands from harmonized Landsat 8 and Sentinel-2 imagery to support within-season adaptive management" published in the journal Remote Sensing of Environment. Data are plot-scale values of (1) ground-sampled herbaceous standing biomass estimated using visual obstruction (VO) methods, (2) ground sampled percent cover by vegetation type using the line-point intercept (LPI) method, (3) percent midgrass derived from hyperspectral aerial imagery (1 m) collected by the NEON AOP (see Gaffney et al. 2021 cited within the manuscript), and (4) satellite-derived indices and bands. Only seasonal data used to develop the standing biomass model is included. The bounding box coordinates of each plot are also included. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Tabular ground and satellite-derived data.</p> <p>File Name: Kearney_Biomass_from_HLS_data.csv</p><p>Resource Description: Seasonal plot-scale tabular ground and satellite-derived data along with four fields (minx, miny, etc.) for the bounding box of the plots (EPSG:32613 - UTM 13N, WGS 84). Data includes (1) ground-sampled biomass estimate using visual obstruction (VO) poles, (2) ground sampled vegetation cover estimated using the line-point intercept (LPI) method, (3) percent mid-grass estimated from a plant community map derived from hyperspectral aerial imagery (1 m) acquired by the NEON AOP, (4) satellite-derived indices and bands interpolated daily from the Harmonized Landsat-Sentinel (HLS) dataset (30 m). See Metadata_column_headers.csv for descriptions of the fields (columns) in this dataset.</p></li><br><li><p>Resource Title: Metadata: Description of column headers for tabular dataset.</p> <p>File Name: Kearney_Biomass_from_HLS_data_metadata.csv</p><p>Resource Description: Descriptions of each field (column) in the tabular dataset.</p></li></ul><p></p>

Tags: aboveground-biomass, ars, data-gov, harmonized-landsat-sentinel, landsat, ltar, np215, rangeland-ecology, remote-sensing, sentinel, vegetation
Organization: Department of Agriculture
Eddy Covariance Data from Office of Naval Research Biofuel project on Maui

<p>These data come from three eddy covariance (EC) towers that were installed as part of a project to assess the productivity of sugarcane agricultural systems for biofuel production. These towers were operated from 2011-2013 in Maui, USA.  Major observational parameters include net carbon exchange, evapotranspiration, and energy fluxes. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Link to data for EC tower site Sugarcane Sheltered/Lee.</p> <p>File Name: SuS.zip</p><p>Resource Description:<br>
Continuous, irrigated, sugarcane cultivation for >100 years. Practice is to grow plant sugarcane for 2 years, drydown, burn leaves, harvest cane, and then till and replant very shortly after harvest. First cycle of observations were from July 2011 to November 2012. Second cycle was from April 2013 to December 2013. Site differs from Sugarcane Windy and Sugarcane Middle in soil type and meteorology.</p>
<p>Find the site data and information at <a href="https://ameriflux.lbl.gov/sites/siteinfo/US-SuS">https://ameriflux.lbl.gov/sites/siteinfo/US-SuS</a></p></li><br><li><p>Resource Title: Link to data for EC tower site Sugarcane Windy.</p> <p>File Name: SuW.zip</p><p>Resource Description:<br>
Continuous, irrigated, sugarcane cultivation for >100 years. Practice is to grow plant sugarcane for 2 years, drydown, burn leaves, harvest cane, and then till and replant very shortly after harvest. Site differs from Sugarcane Lee/Sheltered and Sugarcane Middle in soil type and site meteorology.</p>
<p>Find the site data and information at <a href="https://ameriflux.lbl.gov/sites/siteinfo/US-SuW">https://ameriflux.lbl.gov/sites/siteinfo/US-SuW</a></p></li><br><li><p>Resource Title: Link to data for EC tower site Sugarcane Middle.</p> <p>File Name: SuM.zip</p><p>Resource Description: Continuous, irrigated, sugarcane cultivation for >100 years. Practice is to grow plant sugarcane for 2 years, drydown, burn leaves, harvest cane, and then till and replant very shortly after harvest. Site differs from Sugarcane Windy and Sugarcane Lee/sheltered in soil and meteorology.</p>
<p>Find the site data and information at <a href="https://ameriflux.lbl.gov/sites/siteinfo/US-SuM">https://ameriflux.lbl.gov/sites/siteinfo/US-SuM</a></p></li></ul><p></p>

Tags: ars, carbon-dioxide-flux, data-gov, earth-science-atmosphere-atmospheric-radiation-heat-flux, evapotranspiration, latent-energy-flux, np211, online-database
Organization: Department of Agriculture
Data from: Performance of a cotton gin machine that removes plastic contamination from seed cotton

<p>This is USDA-ARS data from the publication: "Performance of a cotton gin machine that removes plastic contamination from seed cotton." The study was conducted during the Fall of 2020 with continued data analysis thru September 2021. Plastic contamination is the most pressing issue for the U.S. cotton industry today. Due to this problem, U.S. cotton has lost the 7 cents per pound premium it brought on international cotton markets. Plastic contaminants are often introduced prior to ginning, but cotton gin machinery can tear and shred the plastics so that they become more difficult to remove.  A cotton gin machine developed and used to combat the plastic contamination problem in Chinese cotton was tested to compare its performance at removing typical plastics found in U.S. cotton to that of conventional cotton gin seed cotton cleaners.</p>

Tags: ars, contamination, cotton-fiber, cotton-gin, data-gov, extraction, machinery, np306, plastic
Organization: Department of Agriculture
Honey bee (Apis mellifera) and Varroa mite (Varroa destructor) toxicity data

<p>Toxicological data generated for <em>Apis mellifera</em> honey bees and an ectoparasitic mite (<em>Varroa destructor</em>) in laboratory toxicity trials are presented. Data were generated over a four-year period by members of the Varroacide Research and Testing Team (VRTT) as part of a foundational grant from the Foundation for Food and Agricultural Research (FFAR). Data may be used to explore toxicological responses of honey bees and <em>Varroa</em> mites to a wide range of natural and synthetic chemical treatments against <em>Varroa</em> infestations in honey bee colonies. Data may be collected and analyzed together with other data sets not generated by VRTT. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Toxicity data generated from vial and jar assays by USDA-ARS Beltsville bee lab in summer, 2019.</p> <p>File Name: Vial & Jar Data Summer 2019 USDA .csv</p><p>Resource Description: Toxicity data generated for Apis mellifera honey bees and Varrroa destructor mites from laboratory vial and jar assays in 2019 by the USDA-ARS Bee Research Lab, Beltsville MD</p></li><br><li><p>Resource Title: Honey bee (Apis mellifera) and Varroa destructor toxicity data from 2019 cage trials at USDA laboratory.</p> <p>File Name: Cage Data Summer 2019 USDA ultimate.csv</p><p>Resource Description: Bees and mites were housed together in 1 L plastic deli containers modified into cages. Toxicants were applied to acetate strips hung from the center of the upper lid. Bee and mite mortality were gauged at 3 time points, 4 hours, 24 hours, and 48 hours after exposure to toxicants.</p></li><br><li><p>Resource Title: Vial and Jar toxicity data 2018 USDA.</p> <p>File Name: Vial Jar toxicity data Summer 2018_USDA.csv</p><p>Resource Description: Honey bee (Apis mellifera) and Varroa destructor mite toxicity data from vial and jar assays 2018 USDA</p></li><br><li><p>Resource Title: Vial and Jar toxicity data OSU 2018.</p> <p>File Name: Vial and Jar toxicity data OSU 2018.csv</p><p>Resource Description: Toxicity data for Varroa destructor mites and Apis mellifera honey bees completed for various active ingredients conducted by laboratory of Dr. Reed Johnson at the Ohio State University in 2018.</p></li><br><li><p>Resource Title: Vial and Jar toxicity data OSU 2019.</p> <p>File Name: Vial and Jar toxicity data OSU 2019.csv</p><p>Resource Description: Toxicity data for Varroa destructor mites and Apis mellifera honey bees completed for various active ingredients conducted by laboratory of Dr. Reed Johnson at the Ohio State University in 2019.</p></li></ul><p></p>

Tags: acari, ars, data-gov, honey-bees, hymenoptera, np305, toxicity, varroa-destructor
Organization: Department of Agriculture