AndreaBozzo/ceres-open-data-index huggingface dataset:
PhenoCam images from JERSAND site, Jornada Experimental Range, New Mexico, USA since 2014

<p>This data set consists of repeat digital imagery from the tower-mounted digital cameras (hereafter, PhenoCams) at the Jornada Experimental Range. JER is a member of the PhenoCam network, which has as its mission to serve as a long-term, continental-scale, phenological observatory. Imagery is uploaded to the PhenoCam server every 30 minutes. The archived images provide a permanent record that can be visually-inspected to determine the phenological state of the vegetation at any point in time. Vegetation greenness metrics (e.g., GCC) derived from the ratio of the green color band to sum of red, green, and blue color bands serve as proxies for vegetation greenness.  Greenness metrics can be extracted from the images using simple image processing methods in 1-day or 3-day increments.</p>
<p>This dataset is available to the public and may be freely downloaded. Please keep the designated Contact person informed of any plans to use the dataset. Consultation or collaboration with the original investigators is strongly encouraged. Publications and data products that make use of the dataset must include proper acknowledgement.</p>
<p>The development of PhenoCam has been supported by multiple entities. Those include the Northeastern States Research Cooperative, NSF’s Macrosystems Biology program (award EF-1065029), DOE’s Regional and Global Climate Modeling program (award DE-SC0016011), the US National Park Service Inventory and Monitoring Program, the USA National Phenology Network (grant number G10AP00129 from the United States Geological Survey), and is currently supported by the Department of Agriculture (USDA) Agricultural Research Service.</p>
<p>This research is a contribution from the Long-Term Agroecosystem Research (LTAR) network. LTAR and the Jornada Experimental Range are supported by the United States Department of Agriculture (USDA) Agricultural Research Service.</p>
<div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: PhenoCam images from JERSAND.</p> <p>File Name: Web Page, url: <a href="https://phenocam.sr.unh.edu/webcam/sites/jersand/" target="_blank">https://phenocam.sr.unh.edu/webcam/sites/jersand/</a> </p></li></ul>

Tags: ars, data-gov, digital-image, long-term-monitoring-sites, ltar, new-mexico, np216, phenocam, phenology, primary-productivity
Organization: Department of Agriculture
Data from: Steroidal saponin concentrations in switchgrass cultivars Liberty and Independence in North America

<p>Switchgrass (<em>Panicum virgatum</em> L.) is a warm-season grass native to the tallgrass prairie in North America with various ecosystem benefits and enhance the resiliency of ecosystems. These resilient qualities of switchgrass may be due to the steroidal saponins produced by the grass. Steroidal saponins are plant secondary metabolites in the group of terpenes. Steroidal saponins are triterpenes that have antibacterial and antifungal characteristics. Switchgrass cultivars “Liberty” and “Independence” are two prominent bioenergy switchgrass cultivars for the Great Plains and Midwest. This dataset shows the relative steroidal saponin concentration in leaf and stem tissues from both Liberty and Independence switchgrass. The steroidal saponins, protodioscin, dichotomin, and saponin B, were detected in all leaf and stem tissues of both Liberty and Independence cultivars.</p>

Tags: ars, data-gov, np216, saponins, switchgrass-independence, switchgrass-liberty
Organization: Department of Agriculture
Agricultural Research Service Culture Collection (NRRL - Northern Regional Research Laboratory) Database

<p dir="ltr">The ARS Culture Collection is one of the largest public collections of microorganisms in the world, containing approximately 93,000 strains of bacteria and fungi. The collection is split into subcollections of molds, prokaryotes, and yeasts. In addition, the online catalog is searchable by genus, species, subvar type, and subspecies.</p><p dir="ltr">The collection is housed within the <a href="http://www.ars.usda.gov/main/site_main.htm?modecode=36-20-71-00">Mycotoxin Prevention and Applied Microbiology Research Unit</a> at the <a href="http://www.ars.usda.gov/main/site_main.htm?modecode=36-20-00-00">National Center for Agricultural Utilization Research</a> in Peoria, Illinois. The scientists and staff of the ARS Culture Collection conduct and facilitate microbiological research that advances agricultural production, food safety, public health, and economic development. These goals are pursued through in-house research that improves understanding and utilization of microbiological diversity and through efforts to enhance the value and accessibility of microbial accessions in the Agricultural Research Service Culture Collection.</p><p dir="ltr">Resources in this dataset:</p><ul><li>Resource Title: The ARS Culture (NRRL) Collection Online Catalog.File Name: Web Page, url: <a href="https://nrrl.ncaur.usda.gov" rel="noreferrer" target="_blank">https://nrrl.ncaur.usda.gov/</a> Online catalog and database server for the ARS Culture Collection (NRRL).</li></ul><p><br></p>

Tags: ars, bacteria, biological, cell, cultures, data-gov, food-safety, fungi, living-cell, microbiology, molds, northern-regional-research-laboratory, online-database, prokaryotes, public-health, tissue, tissue-cultures, yeasts
Organization: Department of Agriculture
Economic Model of Deficit Irrigation II (spreadsheet)

<p>This spreadsheet model calculates the net income for irrigated agricultural production.  The model is designed to evaluate the economics of deficit irrigation (irrigation at less than the amount required to produce maximum yield).</p>
<p>The spreadsheet first models the water production function for a crop, then uses that relationship along with crop price and production costs to calculate net income and the irrigation amount that maximizes net income.</p>
<p>This spreadsheet is similar to another posted at Ag Data Commons:  "Economic Model of Deficit Irrigation" (<a href="http://dx.doi.org/10.15482/USDA.ADC/1504421">http://dx.doi.org/10.15482/USDA.ADC/1504421</a>).  That model was designed primarily to evaluate deficit irrigation as a means to compare revenue with reduced water consumption to income gained by transferring the saved water.</p>
<p>The model includes two common scenarios:  1)  irrigation water supply is adequate but expensive, and 2)  irrigation water supply is inadequate to fully irrigate the available land.  In the first scenario, net income is maximized when the marginal costs of production, including water, is equal to the marginal revenue.  In the second scenario, net income is maximized when the value of the water is maximized by selecting the portion of the land that should be irrigated.  In the second scenario, the value and costs of the un-irrigated land are included.</p>
<p>The first worksheet of the spreadsheet describes the relationships used in each worksheet and the input parameters required.  Additional worksheets calculate the water production function, the irrigation water production function, and the net income for each of the two scenarios. The worksheets allow the user to input the various biophysical and economic parameters relevant to their conditions and allows evaluating various parameter combinations.  Each worksheet contains graphs to visualize the results.   </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Economic Model of Deficit Irrigation II (spreadsheet).</p> <p>File Name: WPF Econ Model V2 Mod.xlsx</p><p>Resource Description: Spreadsheet contains 5 worksheets.  The first worksheet describes the relationships in the remaining worksheets and the parameters required by the model.</p><p>Resource Software Recommended: Microsoft Excel 365 (may work on earlier versions),url: <a href="https://www.microsoft.com/en-us/microsoft-365/get-started-with-office-2019">https://www.microsoft.com/en-us/microsoft-365/get-started-with-office-2019</a> </p></li><br><li><p>Resource Title: Description of the Model.</p> <p>File Name: DataDictionary.pdf</p><p>Resource Description: Description of the model and input parameters.</p><p>Resource Software Recommended: Adobe Reader,url: <a href="https://get.adobe.com/reader/otherversions/">https://get.adobe.com/reader/otherversions/</a> </p></li></ul><p></p>

Tags: agricultural-economics, ars, data-gov, deficit-irrigation, economic-model, irrigation-and-water-use, np211
Organization: Department of Agriculture
Data from: Near-Surface Soil Property Responses to Forage Production in a Semiarid Region

<p dir="ltr">Use of perennial forages in cropping systems can improve soil quality. The length of time needed to accrue improvements in soil condition under perennial forages is unclear, particularly in semiarid regions. A study was conducted to quantify soil responses to perennial grasses, legumes, and grass-legume mixtures over a 5-yr period on a Parshall fine sandy loam near Mandan, ND USA. Five forage treatments and an annual crop treatment were evaluated. Forage treatments included field pea (<i>Pisum sativum </i>L.), intermediate wheatgrass [IMWG; <i>Thinopyrum intermedium</i> (Host) Barkw. & D.R. Dewey subsp. <i>Intermedium</i>], switchgrass (SWG; <i>Panicum virgatum</i> L.), an intermediate wheatgrass-field pea mixture, and a switchgrass-field pea mixture. After the establishment year (2006), alfalfa (<i>Medicago</i> spp.) was seeded in treatments where field pea was present the year before. Continuous spring wheat (<i>Triticum aestivum</i> L.) represented the annual crop treatment. In April of 2008-2011, soil samples within each fall-converted forage treatment and continuous annual crop treatment were collected prior to seeding spring wheat. Samples were collected from the 0-30 cm depth in increments of 0-5, 5-10, 10-20, 20-30 cm using a step-down probe with an inner tip diameter of 3.13 cm. Soil samples were evaluated for soil bulk density, water-stable aggregation, soil pH, total carbon and nitrogen, and particulate organic matter carbon and nitrogen. Assessments of carbon and nitrogen were determined by dry combustion. Water-stable aggregation was measured using the 1-2 mm aggregate fraction. Data may be used to understand soil responses to perennial forages under rainfed conditions in a semiarid continental climate. Applicable USDA soil types include Parshall, Cabba, Farland, Flasher, Lehr, Lihen, Manning, Morton, Straw, Tally, Vebar and Williams.</p>

Tags: northern-great-plains, particulate-organic-matter-carbon, perennial-forages
Organization: Department of Agriculture
Raw data for imidacloprid effects on native bees

<p>Field and Lab data regarding the effects of 4 sublethal concentrations of a neonicotinoid insecticide (Imidacloprid) on honey bees and about a dozen native bee species. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Weighted Tolerance Index (WTI) .</p> <p>File Name: WTI Calculation.docx</p><p>Resource Description: Calculating the weighted tolerance index (WTI) for bee species imbibing sublethal quantities of imidacloprid</p></li><br><li><p>Resource Title: Weighted tolerance index for 10 bee genera subjected to sublethal concentrations of imidacloprid insecticide (5 - 100ppb).</p> <p>File Name: Table 4 WTI.docx</p><p>Resource Description: These data show to what degree representative species of 10 bee genera were tolerant to the side-effects of imidacloprid intoxication. Higher WTI index indicates greater relative tolerance</p></li><br><li><p>Resource Title: Raw data and preliminary analyses.</p> <p>File Name: BEETOX RAW DATA AGCOMMONS 1.csv</p><p>Resource Description: These data represent the raw dataset for bioassays conducted on 12 species of bees representing 10 genera.</p></li><br><li><p>Resource Title: Beetox raw data - data dictionary.</p> <p>File Name: BEETOX raw data DD.csv</p></li><br><li><p>Resource Title: Bioassay Data Beetox 2016.</p> <p>File Name: BIOASSAY DATA BEETOX 2016 2017 4.xlsx</p></li></ul><p></p>

Tags: ars, data-gov, np305
Organization: Department of Agriculture
LTAR Great Basin Wyoming Big Sagebrush Phenocam, Reynolds Creek Experimental Watershed

<p>A Year-round stationary camera from a fixed position overlooking sagebrush rangeland dominated by Wyoming Big sagebrush (Artemisia tridentata ssp. Wyomingensis). Color and infrared images are taken every 30 minutes between 10 am and 2 pm Mountain Standard Time. The camera points north and incorporates a view of the Nancy Gulch watershed weir house and meteorology station. The camera is part of the instrumentation suite for the LTAR "common experiment" comparing agricultural and environmental results from "business as usual" and "aspirational best practices."</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/1ea5610e-e4f1-4c67-b218-496f691ebab1" target="_blank">https://geodata.nal.usda.gov/geonetwork/srv/eng/catalog.search#/metadata/1ea5610e-e4f1-4c67-b218-496f691ebab1</a> </p></li></ul>

Tags: ars, artemisia-tridentata-ssp-wyomingensis, biological-resources-wyoming-big-sagebrush, biota, continent-north-america-united-states-of-america-idaho, continent-north-america-united-states-of-america-in-situ-laboratory-instruments-photon-optical-, data-gov, earth-science-agriculture-agricultural-plant-science, earth-science-agriculture-agricultural-plant-science-reclamation-revegetation-restoration-veget, earth-science-biosphere-vegetation, earth-science-biosphere-vegetation-biomass, earth-science-biosphere-vegetation-canopy-characteristics, earth-science-biosphere-vegetation-chlorophyll, earth-science-biosphere-vegetation-leaf-characteristics, earth-science-biosphere-vegetation-plant-phenology, earth-science-biosphere-vegetation-vegetation-cover, environment, farming, np211, np215, rangeland, reynolds-creek-experimental-watershed
Organization: Department of Agriculture
Data and code from: A natural polymer material as a pesticide adjuvant for mitigating off-target drift and protecting pollinator health

<p dir="ltr">This dataset contains all data and code required to clean the data, fit the models, and create the figures and tables for the laboratory experiment portion of the manuscript:</p><p dir="ltr">Kannan, N., Q. D. Read, and W. Zhang. 2024. A natural polymer material as a pesticide adjuvant for mitigating off-target drift and protecting pollinator health. <i>Heliyon</i>, in press. https://doi.org/10.1016/j.heliyon.2024.e35510.</p><p dir="ltr">In this dataset, we archive results from several laboratory and field trials testing different adjuvants (spray additives) that are intended to reduce particle drift, increase particle size, and slow down the particles from pesticide spray nozzles. We fit statistical models to the droplet size and speed distribution data and statistically compare different metrics between the adjuvants (sodium alginate, polyacrylamide [PAM], and control without any adjuvants). </p><p dir="ltr">The following files are included:</p><ul><li>RawDataPAMsodAlgOxfLsr.xlsx: Raw data for primary analyses</li><li>OrganizedDataPaperRevision20240614.xlsx: Raw data to produce density plots presented in Figs. 8 and 9</li><li>raw_data_readme.md: Markdown file with description of the raw data files</li><li>R_code_supplement.R: All R code required to reproduce primary analyses</li><li>R_code_supplement2.R: R code required to produce density plots presented in Figs. 8 and 9</li></ul><p dir="ltr">Intermediate R output files are also included so that tables and figures can be recreated without having to rerun the data preprocessing, model fitting, and posterior estimation steps:</p><ul><li>pam_cleaned.RData: Data combined into clean R data frames for analysis</li><li>velocityscaledlogdiamfit.rds: Fitted **brms** model object for velocity</li><li>lnormfitreduced.rds: Fitted **brms** model object for diameter distribution</li><li>emm_con_velo_diam_draws.RData: Posterior distributions of estimated marginal means for velocity</li><li>emm_con_draws.RData: Posterior distributions of estimated marginal means for diameter distribution</li></ul><p dir="ltr">The following software and package versions were used:</p><ul><li>R version 4.3.1</li><li>CmdStan version 2.33.1</li><li>R packages:</li><li><ul><li>brms version 2.20.5</li><li>cmdstanr version 0.5.3</li><li>fitdistrplus version 1.1-11</li><li>tidybayes version 3.0.4</li><li>emmeans version 1.8.9</li></ul></li></ul><p><br></p>

Tags: cotton, honeybee, lower-mississippi-delta, pesticide, pesticide-adjuvant, polyacrylamide, sodium-alginate, soybean
Organization: Department of Agriculture
Data from: Soil resistance under grazed intermediate wheatgrass

<p>Intermediate wheatgrass [Thinopyrum intermedium (Host) Barkw. & D.R. Dewey subsp. intermedium] is a high-yielding cool-season grass with adaptable uses for grazing, haying, and soil restoration. Despite its adaptability, adoption of intermediate wheatgrass has been limited due to inadequate stand longevity under grazing stress. A study was conducted near Mandan, ND USA to investigate if stand longevity of intermediate wheatgrass was affected by changes in soil properties due to grazing. Soil data from this study included measurements of soil bulk density, soil pH, soil organic carbon, and total soil nitrogen on a Wilton silt loam soil (USDA: Fine-silty, mixed, superactive frigid Pachic Haplustoll). Measurements were made in May 1997 (baseline) and again in May 2004 following four years of grazing. Data may be used to understand soil property responses to grazed perennial forages. Data are generally applicable to rainfed conditions under a semiarid Continental climate for the following associated soil types: Temvik, Grassna, Linton, Mandan, and Williams.</p>
<p>Resources in this dataset:</p>
<p>Resource title: Intermediate Wheatgrass Grazing Study Data Dictionary
File name: IWGS_Data Dictionary.xlsx
Resource description: Data dictionary for associated dataset.</p>
<p>Resource title: Intermediate Wheatgrass Grazing Study_Soil Data for Aggregated Depths
File name: IWGS_Soil Data_Aggregated Depths.xlsx
Resource description: File includes data for 0-30 cm depth.</p>
<p>Resource title: Intermediate Wheatgrass Grazing Study_Soil Data for Separated Depths
File name: IWGS_Soil Data_Separated Depths.xlsx
Resource description: Soil data for 0-5, 5-10, 10-20, and 20-30 cm depths.</p>
<p>Resource title: Intermediate Wheatgrass Grazing Study_Soil Data_Aggregated Depths
File name: IWGS_Soil Data_Aggregated Depths.csv
Resource description: Data for aggregated depths in csv format.</p>
<p>Resource title: Intermediate Wheatgrass Grazing Study_Metadata_Aggregated Depths
File name: IWGS_Soil Data_Aggregated Depths_Metadata.csv
Resource description: Metadata for aggregated depths.</p>
<p>Resource title: Intermediate Wheatgrass Grazing Study_Soils Data_Separated Depths
File name: IWGS_Soil Data_Separated Depths.csv
Resource description: Soil data for 0-5, 5-10, 10-20, and 20-30 cm depths.</p>
<p>Resource title: Intermediate Wheatgrass Grazing Study_Metadata_Separated Depths
File name: IWGS_Soil Data_Separated Depths_Metadata.csv
Resource description: Metadata for soils data separated by depth increment.</p>

Tags: ars, data-gov, northern-great-plains, np215, perennial-forages, soil-bulk-density, soil-organic-carbon, soil-ph
Organization: Department of Agriculture
Data from: Modulation of the Gut Microbiota Structure and Function by Two Structurally Different Lemon Pectins

<p>In vitro study of the effects on the human gut microbiota of lemon pectins with two different molecular weights and having varying degrees of esterification.  Data collected following incubations include: amplicon sequencing of the V1-V2 regions of the 16S rRNA gene (found in the NCBI Sequence Read Archive associated with BioProject PRJNA903836: <a href="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA903836">https://www.ncbi.nlm.nih.gov/bioproject/PRJNA903836</a>), RT-qPCR of Bifidobaterium sp. 16S rRNA genes, and short-chain fatty acid concentrations. </p>
<p>Resources in this dataset:</p>
<ul>
<li>
<p>Resource Title: Short Chain Fatty Acid concentrations
File Name: pectin_SCFA_data.csv</p>
</li>
<li>
<p>Resource Title: Pectin_total_bacterial_qPCR_data
File Name: pectin_total_bacterial_qPCR_data.csv</p>
</li>
<li>
<p>Resource Title: Pectin_bifidobacterium_genus_qPCR_data
File Name: pectin_bifidobacterium_genus_qPCR_data.csv</p>
</li>
<li>
<p>Resource Title: Sample metadata</p>
</li>
<li>
<p>File Name: pectin_sample_attributes.csv</p>
</li>
</ul>

Tags: 16s-rrna-sequence-data, ars, data-gov, np306, pectin, rt-qpcr, short-chain-fatty-acids
Organization: Department of Agriculture
Nitrogen Decision Aid

<p>The Nitrogen Decision Aid is a computerized program that predicts the amount of N mineralized from planting to side-dress or 5-leaf growth-stage. By applying just enough N-fertilizer to reach the critical soil nitrate concentration it is possible reduce this waste. This model is designed for Northern climates that will have some frost in the soil during the winter.</p>
<p>Each Year more than 10 billion kg of nitrogen fertilizer are applied to croplands in the United States at a cost of more that $3.5 billion (USDA Economics and Statistics System, 1998). It is estimated that the efficiency of this applied nitrogen (N) ranges from about 30% to about 70% (Pilbeam, 1998); thus, large amounts of fertilizer N are lost or wasted each year.</p>
<p>The Nitrogen Decision Aid is a computerized program that predicts the amount of N mineralized from planting to side-dress or 5-leaf growth-stage. By applying just enough N-fertilizer to reach the critical soil nitrate concentration it is possible reduce this waste. This model is designed for Northern climates that will have some frost in the soil during the winter. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Nitrogen Decision Aid.</p> <p>File Name: Web Page, url: <a href="https://www.ars.usda.gov/research/software/download/?softwareid=85&modecode=50-60-05-00">https://www.ars.usda.gov/research/software/download/?softwareid=85&modecode=50-60-05-00</a> </p><p>download page</p></li></ul><p></p>

Tags: ars, data-gov, earth-science-agriculture-soils-nitrogen, fertilizer, fertilizer-recommendations
Organization: Department of Agriculture