AndreaBozzo/ceres-open-data-index huggingface dataset:
<b>Data from: Response of soil carbon and nitrogen to transplanted alfalfa in North Dakota rangeland</b>

<p dir="ltr">Alfalfa (<i>Medicago</i> spp.) interseeded into rangeland has been shown to improve the quantity and quality of forage available for grazing. Information regarding soil responses to interseeded alfalfa in rangeland, however, is lacking. A study was conducted to investigate the effects of alfalfa transplanted into native rangeland on soil organic carbon and total nitrogen. The study was located approximately 5 km south of Mandan, ND USA on a Temvik silt loam soil (USDA: Fine-silty, mixed, superactive frigid Typic Haplustoll). Treatments included three alfalfa cultivars transplanted into rangeland and a native vegetation control. Treatments were applied using a randomized block design with five replications. Soil properties measured during the study included soil bulk density, soil organic carbon, and total soil nitrogen. Measurements were made in 2001 (baseline) and again 2005 following four years of alfalfa growth. Samples were collected using a step-down probe in depth increments of 0-10, 10-20, 20-30, and 30-40 cm. Duplicate cores from each treatment were composited by depth. Soil carbon and nitrogen were quantified by the dry combustion method. Data may be used to understand soil property responses to interseeded alfalfa in rangeland. Data are generally applicable to rangelands under a semiarid Continental climate for the following soil types: Grassna, Linton, Mandan, Temvik, Williams, and Wilton.</p>

Tags: alfalfa, dry-combustion-method, interseeding, northern-great-plains, rangeland, soil-organic-carbon-and-nitrogen
Organization: Department of Agriculture
KINEROS - The kinematic runoff and erosion model

<p>The kinematic runoff and erosion model KINEROS is an event oriented, physically based model describing the processes of interception, infiltration, surface runoff and erosion from small agricultural and urban watersheds. The watershed is represented by a cascade of planes and channels; the partial differential equations describing overland flow, channel flow, erosion and sediment transport are solved by finite difference techniques.  The spatial variation of rainfall, infiltration, runoff, and erosion parameters can be accomodated.  KINEROS may be used to determine the effects of various artificial features such as urban developments, small detention reservoirs, or lined channels on flood hydrographs and sediment yield. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: KINEROS2.</p> <p>File Name: Web Page, url: <a href="https://www.tucson.ars.ag.gov/kineros/">https://www.tucson.ars.ag.gov/kineros/</a> </p><p>Main web site, including links to documentation and downloads for the model.</p></li></ul><p></p>

Tags: ars, data-gov, earth-science-services-models, erosion, runoff, watersheds
Organization: Department of Agriculture
Data from: Five-year timeseries of sap-flux-scaled transpiration reveals inter-annual variation between tree water use and precipitation in a pinyon and juniper woodland

<p dir="ltr">The USDA-ARS conducted a five-year study of transpirational water use of single-leaf pinyon (<i>Pinus monopylla</i>) and Utah juniper (<i>Juniperus osteosperma</i>) at the Porter Canyon Experimental Watershed (PCEW) in the Great Basin of Nevada, USA. A total of 29 pinyon and 16 juniper trees that were representative of the natural size-class variation within the PCEW were selected for long-term sap flow measurements. All trees were instrumented with two sets of 2 cm Granier-style thermal dissipation sap flow probes, as tree core measurements obtained in late 2011 indicated that sapwood depth was greater than 2 cm on average for all trees. Two sets of probes were installed radially into the xylem at approximately north-south orientation, depending on branch architecture, and spaced 15 cm axially with the top probe approximately 50 cm above the ground. This dataset is comprised of nine .CSV files covering the five-year period. The five-year period encompassed five water years from October 1st, 2013 to September 30th, 2018. The dataset includes measurements of mean daily vapor pressure deficit, solar radiation, and volumetric water content at 20 cm. The data set also includes mean daily sap flux density, mean daily whole tree volumetric water use, mean daily water use per basal area, and scaled daily site water use. Lastly, the dataset includes the relationship of mean daytime sap flux density to mean daytime vapor pressure deficit for days within the growing season time periods when: 1) soil volumetric water content was not a sap flux-limiting factor and 2) soil volumetric water content was a sap flux-limiting factor.</p>

Tags: ecohydrology, single-leaf-pinyon, soil-volumetric-water-content, solar-radiation, thermal-dissipation-probes, transpiration, utah-juniper, vapor-pressure-deficit
Organization: Department of Agriculture
Asian giant hornet, Vespa mandarinia, genome assembly

<p>The Asian giant hornet, <em>Vespa mandarinia</em>, has a native range that extends from northern India to East Asia. In 2019, the hornet was confirmed for the first time in North America, posing an invasive threat to honey bees and human health. In September 2019, local beekeepers, tracked down a nest in a park in Nanaimo on Vancouver Island, British Columbia, Canada and exterminated it. The specimen we used for genome sequencing was obtained from that nest, the first one found in North America. DNA was extracted from the thorax for PacBio HiFi sequencing on two cells and data were assembled using IPA to yield a contig assembly of 248 Mb with a 3.14 Mb N50. The assembly was generated by the Agricultural Research Service's Ag100Pest Initiative in collaboration with Pacific Biosciences. This high-quality genome assembly is being released prior to publication in scientific journals as a public service to the research community. </p>
<p>The Primary and Haplotig assemblies, along with the HiFi reads have been archived at NCBI. Relevant accessions include:
SRA: SRR12366675 - PacBio HiFi reads for both cells
BioProject: <a href="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA649644/">PRJNA649644</a>, BioSample: <a href="https://www.ncbi.nlm.nih.gov/biosample/SAMN15675875/">SAMN15675875</a>, GenBank: <a href="https://www.ncbi.nlm.nih.gov/nuccore/JACHAV000000000">JACHAV000000000</a> - Primary contig assembly and mitochondrial genome
BioProject: <a href="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA649643">PRJNA649643</a>, BioSample: <a href="https://www.ncbi.nlm.nih.gov/biosample/SAMN15675875/">SAMN15675875</a>, GenBank: <a href="https://www.ncbi.nlm.nih.gov/nuccore/JACHAW000000000">JACHAW000000000</a> - Alternate (Haplotigs) contig assembly </p>
<div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: IPA contigs purged from haplotigs.</p> <p>File Name: ihVesMand1_IPA_purged_from_htig.fasta</p><p>Resource Description: IPA contigs purged from the haplotigs contig set by purge_dups. Fasta format.</p></li><br><li><p>Resource Title: Mitochondrial PacBio HiFi read set.</p> <p>File Name: ihVesMand1_mt_reads.fasta</p><p>Resource Description: Mitochondrial reads from the PacBio HiFi read set. Fasta format.</p></li><br><li><p>Resource Title: All mitochondrial genome VNTR variants.</p> <p>File Name: ihVesMand1_mtgenome_all_VNTR_variants.fasta</p><p>Resource Description: Multiple contigs of the mitochondrial genome were obtained due to the presence of an extended variable number tandem repeat (VNTR) region corresponding to the control region, with different copy numbers (ranging from 5 to 9) of an 823 bp repeat unit. We designated the most abundant mitochondrial genome variant (6 repeat copies) as the mitochondrial genome sequence and included it with the primary assembly deposited in GenBank.</p></li><br><li><p>Resource Title: Vespa mandarinia sequencing and assembly methods.</p> <p>File Name: Vespa_mandarinia_Sequencing_and_Assembly_Methods.docx</p></li></ul>

Tags: ag100pest, ars, asian-giant-hornet, data-gov, genome-assembly, i5k, vespa-mandarinia
Organization: Department of Agriculture
Data and code from: Extending irrigation reservoir histories for improved groundwater modeling and conjunctive water management in two Arkansas critical groundwater areas

<p dir="ltr">This dataset contains all data and code required to reproduce the time-to-event analysis in the associated manuscript. More detail is found in the associated README.md file.</p><h3>Contents of repository</h3><ul><li><code>Yaeger_ReservoirDataset_Oct2022.csv</code>: comma-separated data file with reservoir characteristics, construction times, and water table depths and percent saturation at 5-year intervals from 1975-2015.</li><li><code>CGA_reservoir_analysis.Rmd</code>: RMarkdown notebook with all code required to reproduce the time-to-event analysis in the manuscript and generate the associated plots.</li><li><code>CGA_reservoir_analysis.html</code>: HTML file rendered from the .Rmd notebook.</li><li><code>README.md</code>: additional details, including column descriptions from the CSV file.</li></ul><h3>Software versions used</h3><p dir="ltr">R version 4.1.2 (https://cran.r-project.org/bin/windows/base/old/4.1.2)</p><p dir="ltr">R packages:</p><ul><li>data.table v1.14.8 (https://rdatatable.gitlab.io/data.table/)</li><li>ggplot2 v3.4.4 (https://ggplot2.tidyverse.org/)</li><li>sf v1.0-14 (https://r-spatial.github.io/sf/)</li><li>survival v3.5-5 (https://cran.r-project.org/package=survival)</li><li>icenReg v2.0.15 (https://cran.r-project.org/package=icenReg)</li></ul><p></p>

Tags: aquifer, arkansas, cache-river-cga, critical-groundwater-area-cga, grand-prairie-cga, groundwater, hydrology, mississippi-river-valley, mississippi-river-valley-alluvial-aquifer, reservoir
Organization: Department of Agriculture
Data From: Gamma-Spectroscopy Method for Soil Water Content Estimation in an Agricultural Field

<p dir="ltr">Gamma-ray spectroscopy (GRS) enables continuous estimation of soil water content (SWC) at the subfield scale with a noninvasive sensor. Hydrological applications, including hyper-resolution land surface models and precision agricultural decision making, could benefit greatly from such SWC information, but a gap exists between established theory and accurate estimation of SWC from GRS in the field. In response, we conducted a robust three-year field validation study at a well instrumented agricultural site in Nebraska, United States. The study involved 27 gravimetric water content sampling campaigns in maize and soybean and <sup>40</sup>K specific activity (Bq kg<sup>−1</sup>) measurements from a stationary GRS sensor. Our analysis showed that the current method for biomass water content correction is appropriate for our maize and soybean field but that the ratio of soil mass attenuation to water mass attenuation used in the theoretical equation must be adjusted to satisfactorily describe the field data. We propose a calibration equation with two free parameters: the theoretical <sup>40</sup>K intensity in dry soil and a, which creates an “effective” mass attenuation ratio. Based on statistical analyses of our data set, we recommend calibrating the GRS sensor for SWC estimation using 10 profiles within the footprint and 5 calibration sampling campaigns to achieve a cross-validation root mean square error below 0.035 g g<sup>−1</sup>.</p>

Tags: gamma-ray-spectroscopy, soil-water-content
Organization: Department of Agriculture
REAP Study for Resilient Economic Agricultural Practices in West Lafayette, Indiana

<p>REAP Study for Resilient Economic Agricultural Practices in West Lafayette, Indiana
Corn stover is an important livestock feed and will probably be a major source of renewable bioenergy, especially in the U.S. Corn Belt. Overly aggressive removal of stover, however, could lead to greater soil erosion and hurt producer yields in the long-run. Good residue management practices could help prevent erosion of valuable topsoil by wind and water while still providing a revenue source for producers, either as livestock feed or for use in renewable bioenergy. Plant residues also contribute to soil structure, nutrient cycling, and help sustain the soil microbiota. Good residue management could also help control the loss of greenhouse gases from agricultural soils that could add to already increasing levels of atmospheric greenhouse gases contributing to global climate change. Cumulative GHG emissions varied widely across locations, by management, and from year-to-year. Despite this high variability, maximum stover removal averaged across all sites, years, and management resulted in lower total emissions of CO2 (-12 ± 11%) and N2O (-13 ± 28%) compared to no stover removal. Decreases in total CO2 and N2O emissions in stover removal treatments were attributed to decreased availability of stover-derived C and N inputs into soils, as well as possible microclimatic differences. Soils at all sites were CH4 neutral or small CH4 sinks. Exceptions to these trends occurred for all GHGs, highlighting the importance of site-specific management and environmental conditions on GHG fluxes in agricultural soils.</p> <div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: West Lafayette, IN REAP Study (INWLREAP) CSV data.</p> <p>File Name: INWLREAP_csv_data.zip</p><p>Resource Description: CSV format data on Experimental Units, Field Sites, Greenhouse Gas Flux, Harvest Fraction, Residue Management, Soil Biology, Soil Chemistry, Soil Physics, Amendments, Growth Stages, Planting, Residue, Persons, Treatments, Weather Daily, Weather Station.</p></li></ul>

Tags: ars, bioenergy, carbon-dioxide, climate-change, corn, data-gov, environment, farming, feedstocks, greenhouse-gases, irrigation, methane, nitrous-oxide, np211, np212, soil, tillage, wind
Organization: Department of Agriculture
Organic Amendment Study for Greenhouse gas Reduction through Agricultural Carbon Enhancement network and Nutrient Use and Outcome Network in Fort Collins, Colorado

<p>Organic Amendment Study for Greenhouse gas Reduction through Agricultural Carbon Enhancement network and Nutrient Use and Outcome Network in Fort Collins, Colorado
Dairy manure is commonly used in place of inorganic N fertilizers but the impacts on trace gas flux, yields and soil N are not well understood in the semiarid western US. CO2, N2O, and CH4 were monitored using surface chamnbers from 5 N treatments to determine their effect on greenhouse gas emissions from a tilled clay loam soil under irrigated, continuous corn production for a 3 yr. time period.  Treatments included (i) partially composed dairy manure (DM) (412 kg N ha -1), (ii) DM + AgrotainPlus (DM + AP), (iii) enhanced efficiency N fertilizer (SuperU, or SUPRU) (179 kg N ha-1), (iv) Urea (179 kg N ha-1), and (v) check.  These results highlight the importance of best-managemnet practices such as immediate irrigation after N application and use of urease and nitrification inhibitors to minimize N losses.</p> <div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Fort Collins, CO Organic Amendment Study (COFOARD4) CSV data.</p> <p>File Name: COFOARD4_csv_data.zip</p><p>Resource Description: CSV format data on Experimental Units, Field Sites, Greenhouse Gas Flux, Harvest Fraction, Nutrient Efficiency, Residue Management, Soil Chemistry, Soil Physics, Amendments, Growth Stages, Planting, Tillage, Persons, Treatments, Weather Daily, Weather Station.</p></li></ul>

Tags: ars, carbon-dioxide, corn, data-gov, environment, farming, fertilizers, grain-yield, greenhouse-gas-emissions, irrigation, methane, nitrogen, nitrous-oxide, np211, np212, soil
Organization: Department of Agriculture
Long-Term Agricultural Research (LTAR) network - Meteorological Collection

<p>The LTAR network maintains stations for standard meteorological measurements including, generally, air temperature and humidity, shortwave (solar) irradiance, longwave (thermal) radiation, wind speed and direction, barometric pressure, and precipitation. Many sites also have extensive comparable legacy datasets. The LTAR scientific community decided that these needed to be made available to the public using a single web source in a consistent manner. To that purpose, each site sent data on a regular schedule, as frequently as hourly, to the National Agricultural Library, which has developed a web service to provide the data to the public in tabular or graphical form.</p>
<p>This archive of the LTAR legacy database exports contains meteorological data through April 30, 2021. For current meteorological data, visit the <a href="https://pdienterprise.azurecloudgov.us/portal/apps/storymaps/stories/e5d539b0565c4a8a948362389a293385">GeoEvent Meteorology Resources page</a>, which provides tools and dashboards to view and access data from the 18 LTAR sites across the United States. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Meteorological data.</p> <p>File Name: ltar_archive_DB.zip</p><p>Resource Description: This is an export of the meteorological data collected by LTAR sites and ingested by the NAL LTAR application. This export consists of an SQL schema definition file for creating database tables and the data itself.</p>
<p>The data is provided in two formats: SQL insert statements (.sql) and CSV files (.csv). Please use the format most convenient for you. Note that the SQL insert statements take much longer to run since each row is an individual insert.</p>
<p><strong>Description of zip files</strong></p>
<p>The ltar<em>archive</em>*.zip files contain database exports. The schema is a .sql file; the data is exported as both SQL inserts and CSV for convenience.
There is a README in markdown and PDF in the zips.</p>
<p><strong>Contains the database export of the schema and data for the site, site_station, and met tables as SQL insert statements.</strong> </p>
<p>ltar_archive_db_sql_export_20201231.zip --> has data until 2020-12-31
ltar_archive_db_sql_export_20210430.zip --> has data until 2021-04-30</p>
<p><strong>Contains the database export of the schema and data for the site, site_station, and met tables as CSV.</strong> </p>
<p>ltar_archive_db_csv_export_20201231.zip --> has data until 2020-12-31
ltar_archive_db_csv_export_20210430.zip --> has data until 2021-04-30</p>
<p><strong>Contains the raw CSV files that were sent to NAL from the LTAR sites/stations.</strong></p>
<p>ltar_rawcsv_archive.zip --> has data until 2021-04-30</p></li></ul><p></p>

Tags: ars, data-gov, ltar-meteorological-stations, meteorological-data, weather-data
Organization: Department of Agriculture
Data from: Genomic features of the host-specific fungal biocontrol agent Ramularia crupinae approved for the management of the federally noxious weed Crupina vulgaris

<p><em>Ramularia crupinae</em> is a foliar and stem blighting fungal pathogen specific to the invasive rangeland weed common crupina (<em>Crupina vulgaris</em>). This fungal plant pathogen was recently approved by the Animal and Plant Health Inspection Service (APHIS) as the first biological control agent for the management of common crupina in the western United States. The genome assembly for <em>R. crupinae</em> 00-010 (<a href="https://mycocosm.jgi.doe.gov/Ramcr1/Ramcr1.info.html">https://mycocosm.jgi.doe.gov/Ramcr1/Ramcr1.info.html</a>) contains 18 contigs totaling 37.9 Mb, and was annotated using the JGI fungal annotation pipeline. The information contained within this Ag Data Commons dataset provides an updated <em>R. crupinae</em> chromosome-level genome assembly. These data are freely available for research purposes. </p>
<p>Resources in this dataset:</p>
<ul>
<li>Resource Title: Ramularia crupinae chromosome-level assembly
File Name: Ramularia crupinae_14chrm.zip
Resource Description: The R. crupinae genome was re-assembled to improve the contiguity of putative chromosome length scaffolds and attempt chromosome-level assembly. This improved assembly was 37,889,040 bp in size with 15 fragments (N50: 2,786,127 bp) and 810x coverage.</li>
</ul>

Tags: ars, data-gov, fungal-genome, genome-assembly, np304, ramularia, ramularia-crupinae
Organization: Department of Agriculture
Data from: Importance of color for artificial clay caterpillars as sentinel prey in maize, soybean, and prairie

<p>Data files for manuscript titled "Importance of color for artificial clay caterpillars as sentinel prey in maize, soybean, and prairie".</p>
<p>Metadata is contained within excel file that describes all variables for each tab.</p>
<p>Abstract from paper:
The use of artificial clay caterpillars to measure predation pressure under real field conditions is one method that has garnered recent support for quantifying ecosystem services that beneficial insects provide. Here, we focus on color and ask whether it is an important variable that should be considered in studies using clay caterpillars as sentinel prey. We deployed a total of 1920 brown, cream, green, gray, terracotta, and white clay caterpillars onto maize, soybean, and prairie plants to test if lighter colored caterpillars will be attacked and retrieved more than caterpillars with darker colors. As hypothesized, color was a significant predictor with green and terracotta caterpillars performing best, whereas brown and gray caterpillars performed the worst. Interestingly, clay caterpillars were also attacked proportionally to the number of insects in the surrounding habitat. Combined, we suggest artificial clay caterpillars could be useful for rapid ecosystem function assessments, but only when their color is considered. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Data for "Importance of color for artificial clay caterpillars as sentinel prey in maize, soybean, and prairie".</p> <p>File Name: Sentinal Prey - Final Data File.xlsx</p><p>Resource Description: Excel file with 3 tabs: Metadata, predation and abundance, and predation and color.</p></li></ul><p></p>

Tags: agriculture, ars, artificial-prey, biological-control, data-gov, dummy-caterpillar, lepidoptera, np304, plasticine-larvae, predation
Organization: Department of Agriculture