AndreaBozzo/ceres-open-data-index huggingface dataset:
RZWQM2

<p>Root Zone Water Quality Model 2 (RZWQM2) is a whole-system model for studying crop production and environmental quality under current and changing climate conditions. It emphasizes the effects of agricultural management practices on physical, chemical and biological processes. RZWQM2 is a one-dimensional model with a pseudo 2-dimensional drainage flow. Crop simulation options include the generic plant growth model, DSSAT-CSM 4.0 and HERMES SUCROS models. It also can simulate surface energy balance with components from the SHAW model and water erosion from the GLEAMS model. An automated parameter estimation algorithm (PEST) was added to RZWQM2 for objective model calibration and uncertainty analysis. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: RZWQM2 download page.</p> <p>File Name: Web Page, url: <a href="https://www.ars.usda.gov/research/software/download/?softwareid=412&modecode=30-12-30-25">https://www.ars.usda.gov/research/software/download/?softwareid=412&modecode=30-12-30-25</a> </p></li></ul><p></p>

Tags: adsorption, algorithms, ammonium, best-management-practices, bulk-density, carbon, carbon-dioxide, climate-change, climatic-factors, colorado, computer-software, corn, crop-models, crop-production, crop-residues, crop-rotation, crops, databases, denitrification, drainage, energy-balance, environmental-impact, environmental-sustainability, evaporation, fertilizers, furrows, georgia, gleams-model, groundwater, growth-models, heat-flow, humus, irrigation, irrigation-scheduling, macropores, melting, micropores, mineralization, mortality, nematoda, nitrates, nitrification, nitrogen, nutrients, organic-matter, pesticides, planting-date, pollutants, pollution-load, potatoes, probability-distribution, rain, rangelands, relative-humidity, rhizosphere, root-growth, root-zone-water-quality-model, runoff, soil-density, soil-ph, soil-profiles, soil-solution, soil-water, statistics, surface-roughness, temperature, tile-drainage, transpiration, uncertainty-analysis, volatilization, water-content, water-erosion, water-quality, water-table, watersheds, weather, wheat, wind
Organization: Department of Agriculture
Data from: Crop Diversity Effects on Near-Surface Soil Condition under Dryland Agriculture

<p dir="ltr">Crop rotations significantly affect economic and environmental outcomes on agricultural land. In the context of environmental outcomes related to key soil attributes, crop rotations can alter soil structure, soil water properties, and nutrient retention and availability. A study was conducted to quantify crop rotation effects on a suite of soil properties across four long-term cropping systems and a nearby grazed pasture. The cropping systems, differing in cropping intensity and rotational diversity, were located on the Area IV Soil Conservation Districts Cooperative Research Farm near Mandan, North Dakota USA. The pasture was located approximately 2.5 km east of the cropped fields, possessed the same soil type and landscape attributes, had never been tilled, and was grazed by cattle at a low stocking rate (2.6 ha/steer) as part of an experiment established in 1916. Samples were collected in spring 2012 from the 0-10 cm depth using a step-down probe. Soil samples were evaluated for soil bulk density, electrical conductivity, soil pH, total nitrogen, organic carbon, microbial biomass carbon, and particulate organic matter carbon and nitrogen. In-field measurements of infiltration rate were conducted at the time of sampling. Laboratory methods followed accepted protocols, while infiltration rate was estimated using a single ring infiltrometer. Data may be used to better understand soil property responses to cropping system diversity under rainfed conditions within a semiarid continental climate. Applicable USDA soil types include Temvik, Wilton, Grassna, Linton, Mandan, and Williams.</p>

Tags: crop-diversity, dryland-farming, northern-plains, soil-properties
Organization: Department of Agriculture
Data from: Transcriptomes of bovine ovarian follicular and luteal cells

<p>Affymetrix Bovine GeneChip® Gene 1.0 ST Array RNA expression analysis was performed on four somatic ovarian cell types: the granulosa cells (GCs) and theca cells (TCs) of the dominant follicle and the large luteal cells (LLCs) and small luteal cells (SLCs) of the corpus luteum. The normalized linear microarray data was deposited to the NCBI GEO repository (GSE83524). Subsequent ANOVA determined genes that were enriched (≥2 fold more) or decreased (≤−2 fold less) in one cell type compared to all three other cell types, and these analyzed and filtered datasets are presented as tables. Genes that were shared in enriched expression in both follicular cell types (GCs and TCs) or in both luteal cells types (LLCs and SLCs) are also reported in tables. The standard deviation of the analyzed array data in relation to the log of the expression values is shown as a figure. These data have been further analyzed and interpreted in the companion article "Gene expression profiling of ovarian follicular and luteal cells provides insight into cellular identities and functions", Romereim et al., (2017) <em>Mol. Cell. Endocrinol.</em> 439:379-394. <a href="https://doi.org/10.1016/j.mce.2016.09.029">https://doi.org/10.1016/j.mce.2016.09.029</a> </p>
<div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: RNA Expression Data from Four Isolated Bovine Ovarian Somatic Cell Types.</p> <p>File Name: Web Page, url: <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE83524" target="_blank">https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE83524</a> </p><p>NCBI Gene Expression Omnibus (GEO) Accession Display. Analysis of the RNA present in each bovine cell type using Affymetrix microarrays yielded new cell-specific genetic markers, functional insight into the behavior of each cell type via Gene Ontology Annotations and Ingenuity Pathway Analysis, and evidence of small and large luteal cell lineages using Principle Component Analysis. Enriched expression of select genes for each cell type was validated by qPCR. This expression analysis offers insight into the lineage and differentiation process that transforms somatic follicular cells into luteal cells.
The orignal Affymetrix .CEL files and the normalized linear expression data are included in this submission.</p></li></ul>

Tags: ars, bos-taurus, data-gov, granulosa-cells, large-luteal-cells, small-luteal-cells, somatic-ovarian-cell-types, theca-cells
Organization: Department of Agriculture
Climate Shield Bull Trout (50% Brook Trout), 2040 (Feature Layer)

This feature class represents the mid-century (2030-2059) scenario for bull trout, derived from the Climate Shield fish distribution models. These models provide stream-specific probabilistic predictions about the occurrence of juvenile bull trout and cutthroat trout in association with three different scenarios for climate change and brook trout invasions. These datasets indicate all potential cold-water habitats less than 11 degrees Celsius. The attribute fields BT_0BRK - BT_100BRK indicate the probabilities of bull trout occurrence within a cold-water habitat based on the prevalence of brook trout at 0%, 25%, 50%, 75%, or 100% of the sites within a habitat. The probabilities were predicted using the Climate Shield native trout models developed from known species occurrence in greater than 500 cold-water streams. The stream centerlines were based on the National Hydrography Dataset (NHD) but were modified for purposes of modeling and cross-walking to other datasets.

Tags: biota, bull-trout, climate-change, climate-shield, climatologymeteorologyatmosphere, crowd-sourcing, ectotherm, environment, geostatistics, health, inlandwaters, invasive-species, models, open-data, refugia, salmonid, species-distribution, stream-temperature, usfs
Organization: Department of Agriculture
Data from: Venereal Transmission of Vesicular Stomatitis Virus by Culicoides sonorensis Midges

<p>Culicoides sonorensis biting midges are well-known agricultural pests and transmission vectors of arboviruses such as vesicular stomatitis virus (VSV). The epidemiology of VSV is complex and encompasses a broad range of vertebrate hosts, multiple routes of transmission, and diverse vector species. In temperate regions, viruses can overwinter in the absence of infected animals through unknown mechanisms, to reoccur the next year. Non-conventional routes for VSV vector transmission may help explain viral maintenance in midge populations during inter-epidemic periods and times of adverse conditions for bite transmission. In this study, we examined whether VSV could be transmitted venereally between male and female midges. Our results showed that VSV-infected females could venereally transmit virus to uninfected naïve males at a rate as high as 76.3% (RT-qPCR), 31.6% (virus isolation) during the third gonotrophic cycle. Additionally, VSV-infected males could venereally transmit virus to uninfected naïve females at a rate as high as 76.6% (RT-qPCR), 49.2% (virus isolation). Immunofluorescent staining of micro-dissected reproductive organs, immunochemical staining of midge histological sections, examination of internal reproductive organ morphology, and observations of mating behaviors were used to determine relevant anatomical sites for virus location and to hypothesize the potential mechanism for VSV transmission in C. sonorensis midges through copulation.</p>

Tags: culicoides-midges, mating-behavior, non-conventional-transmission, reproductive-anatomy, venereal-transmission, vesicular-stomatitis-virus
Organization: Department of Agriculture
Data from: Visualizing Plant Responses: Novel Insights Possible through Affordable Imaging Techniques in the Greenhouse

<p dir="ltr">Data of image calculation averages, coefficient of variations, and experimental measurements that were presented in the manuscript, <i>Visualizing Plant Responses: Novel Insights Possible through Affordable Imaging Techniques in the Greenhouse</i>, is provided.</p><p dir="ltr">Abstract: Global climatic pressures and increased human demands create a modern necessity for efficient and affordable plant phenotyping unencumbered by arduous technical requirements. The analysis and archival of imagery have become easier as modern camera technology and computers are leveraged. This facilitates the detection of vegetation status and changes over time. Using a custom lightbox, an inexpensive camera, and common software, turfgrass pots were photographed in a greenhouse environment over an 8-week experiment period. Subsequent imagery was analyzed for area of cover, color metrics, and sensitivity to image corrections. Findings were compared to active spectral reflectance data and previously reported measurements of visual quality, productivity, and water use. Results indicate that Red Green Blue-based (RGB) imagery with simple controls is sufficient to measure the effects of plant treatments. Notable correlations were observed for corrected imagery, including between a percent yellow color area classification segment (%Y) with human visual quality ratings (VQ) (R = -0.89), the dark green color index (DGCI) with clipping productivity in mg d-1 (mg) (R = 0.61), and an index combination term (COMB2) with water use in mm d-1 (mm) (R = -0.60). The calculation of green cover area (%G) correlated with Normalized Difference Vegetation Index (NDVI) (R = 0.91) and its RED reflectance spectra (R = -0.87). A CIELAB b*/a* chromatic ratio (BA) correlated with Normalized Difference Red-Edge index (NDRE) (R = 0.90), and its Red-Edge (RE) (R = -0.74) reflectance spectra, while a new calculation termed HSVi correlated strongest to the Near-Infrared (NIR) (R = 0.90) reflectance spectra. Additionally, COMB2 significantly differentiated between the treatment effects of date, mowing height, deficit irrigation, and their interactions (p < 0.001). Sensitivity and statistical analysis of typical image file formats and corrections that included JPEG (JPG), TIFF (TIF), geometric lens correction (LC), and color correction (CC) were conducted. Results underscore the need for further research to support image corrections standardization and better connect image data to biological processes. This study demonstrates the potential of consumer-grade photography to capture plant phenotypic traits.</p>

Tags: agricultural-innovations, camera-efficiency, color-calculation, cover-abundance, imagery, phenotyping-experiments, turf-surfaces
Organization: Department of Agriculture
Data from: Effects of mate availability on egg production in the marsh ramshorn snail, <i>Planorbella trivolvis</i>, and ghost ramshorn snail, <i>Biomphalaria havanensis</i>

<p dir="ltr">Pulmonate snails are the first intermediate host in the life cycle of <i>Bolbophorus damnificus</i>, an important digenetic trematode in Mississippi catfish aquaculture. Two species, the marsh ramshorn snail <i>Planorbella trivolvis</i> and the ghost ramshorn snail <i>Biomphalaria havanensis</i>, commonly inhabit commercial catfish ponds in northwest Mississippi, USA. Low-level, repeated applications of copper sulfate have negative effects on snail reproduction and are effective in reducing snail populations in commercial catfish ponds, although they must be applied judiciously to minimize the phytotoxic and ichthyotoxic effects of copper. At present, little is known regarding population dynamics of these snails and underlying mechanisms driving their proliferation in catfish aquaculture ponds. This study investigated effects of mate availability on egg production in both snail species. Twelve individuals of each species were assigned to one of three treatments based on access to potential mates: continuously (“control”), weekly (“cyclic”), or at a single timepoint (“solitary”). Eggs were collected weekly, and the number of clutches, eggs, and non-viable eggs counted. The study ended at 21 weeks, one week after the final <i>B. havanensis</i> had died. More than 93,000 eggs were counted during the study, with over 60% from <i>P. trivolvis</i>.</p>

Tags: aquaculture-disease, ars, catfish, data-gov, mate-availability, parasite-vector, planorbid-snail-hosts, pulmonate-snails, reproduction
Organization: Department of Agriculture
USDA Agricultural Research Service - Patented Bioenergy and Environment Technologies

<p>Recent USDA/ARS patented technologies on bioenergy and the environment that are available for licensing are described, including summary, contact, benefits, and applications. Updated June 2018. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Bioenergy and Environment - Available Technologies, June 2018.</p> <p>File Name: Bioenergy and Environment.pptx</p><p>Resource Description: Slides presenting title, contact, docket number(s), description, image, benefits, and applications of each new technology.</p></li><br><li><p>Resource Title: Patented Technologies Data Dictionary.</p> <p>File Name: patented-technologies-data-dictionary.csv</p><p>Resource Description: Defines fields, data type, allowed values etc. in patented technology tables.</p></li><br><li><p>Resource Title: Bioenergy and Environment - June 2018.</p> <p>File Name: Bioenergy_and_Environment_2018-06.csv</p><p>Resource Description: Listing of technologies to convert materials to bioproducts from agriculture and food production into fuels and other marketable products, and technologies to monitor and conserve the environment and resources. This CSV file provides the title, technology type, docket number, contact, description, and category for each item. Machine-readable content extracted from corresponding slides accompanying this dataset.</p></li></ul><p></p>

Tags: aerate, ars, bio-oils, biofuels, chars, chemical, data-gov, emissions, energy, ethanol, fluids, gas, manure, oil, oxygen, rangeland, water
Organization: Department of Agriculture
Data from: Short- and long-term changes in sugarbeet (Beta vulgaris L.) gene expression due to postharvest jasmonic acid treatment - Data

<p>Jasmonic acid is a natural plant hormone that induces native defense responses in plants. Sugarbeet (<em>Beta vulgari</em>s L.) root unigenes that were differentially expressed 2 and 60 days after a postharvest jasmonic acid treatment are presented. Data include changes in unigene expression relative to water-treated controls, unigene annotations against nonredundant (Nr), Swiss-Prot, Clusters of Orthologous Groups (COG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) protein databases, and unigene annotations with Gene Ontology (GO) terms. Putative defense unigenes are compiled and annotated against the sugarbeet genome. Differential gene expression data were generated by RNA sequencing. Interpretation of the data is available in the research article, "Jasmonic acid causes short- and long-term alterations to the transcriptome and the expression of defense genes in sugarbeet roots" (K.K. Fugate, et al., <em>Plant Gene</em> 9:50-63) </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Short- and long-term changes in sugarbeet (Beta vulgaris L.) gene expression due to postharvest jasmonic acid treatment - Data.</p> <p>File Name: Web Page, url: <a href="https://www.sciencedirect.com/science/article/pii/S2352340917300276">https://www.sciencedirect.com/science/article/pii/S2352340917300276</a> </p><p>Data in Brief: Data on sugarbeet root unigenes that were differentially expressed due to a postharvest jasmonic acid (JA) treatment are presented. Data identify unigenes that were differentially expressed 2 and 60 d after JA treatment. Data include the logarithm of the fold change in expression due to JA treatment, relevant statistics related to changes in expression, unigene annotations generated by BLASTx search against nonredundant (Nr), Swiss-Prot, Clusters of Orthologous Groups (COG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) protein databases, and Gene Ontology (GO) annotations (Tables 1 and 2). In addition, differentially expressed genes with putative defense functions were identified, compiled, and further annotated by comparison to the sugarbeet genome.</p></li></ul><p></p>

Tags: ars, data-gov, plant-defense, priming, taproots
Organization: Department of Agriculture
Data from: Dataset of proinflammatory cytokine and cytokine receptor gene expression in rainbow trout (Oncorhynchus mykiss) measured using a novel GeXP multiplex, RT-PCR assay

<p>A GeXP multiplex, RT-PCR assay was developed and optimized that simultaneously measures expression of a suite of immune-relevant genes in rainbow trout (<em>Oncorhynchus mykiss</em>), concentrating on tumor necrosis factor and interleukin-1 ligand/receptor systems and acute phase response genes. The dataset includes expression values for <em>drpt, il11a, il1b1, il1b2, il1b3, il1r-like-1(e3-5), il1r-like-1(e9-11), il1r1-like-a, il1r1-like-b, il1r2, saa, tnfa1, tnfa2, tnfa3, tnfrsf1a, tnfrsf1a-like-a, tnfrsf1a-like-b, tnfrsf5</em>, and <em>tnfrsf9</em>. Gene expression was measured at four time-points post-challenge in both a resistant line (ARS-Fp-R) and a susceptible line (ARS-Fp-S) of rainbow trout. In addition, fish body weight, spleen index and the <em>Flavobacterium psychrophilum</em> load are reported. These data are an extension of information presented and discussed in the article "Proinflammatory cytokine and cytokine receptor gene expression kinetics following challenge with <em>Flavobacterium psychrophilum</em> in resistant and susceptible lines of rainbow trout (<em>Oncorhynchus mykiss</em>)" (Kutyrev et al., 2016). </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Dataset of proinflammatory cytokine and cytokine receptor gene expression in rainbow trout (Oncorhynchus mykiss) measured using a novel GeXP multiplex, RT-PCR assay.</p> <p>File Name: Web Page, url: <a href="https://www.sciencedirect.com/science/article/pii/S2352340917300331">https://www.sciencedirect.com/science/article/pii/S2352340917300331</a> </p><p><em>Data in Brief</em> data article providing expression values for a suite of immune-relevant genes in rainbow trout (<em>Oncorhynchus mykiss</em>), concentrating on tumor necrosis factor and interleukin-1 ligand/receptor systems and acute phase response genes. Data are available for download as Excel spreadsheet.</p><p>Resource Software Recommended: Microsoft Excel,url: <a href="https://office.microsoft.com/excel/">https://office.microsoft.com/excel/</a> </p></li></ul><p></p>

Tags: ars, cytokine-receptor-gene-expression, data-gov, gexp-multiplex-rt-pcr-assay, proinflammatory-cytokine
Organization: Department of Agriculture
County FS revised 2020 Census

<div style="text-align:Left;"><div><div><p>This feature class includes States, Counties or Boroughs, Congressional Districts, Alaska Recording Districts, County Subdivisions, and Places boundaries that are derived from the latest official Census Bureau and Alaska Department of Natural Resources datasets. Features within Forest Service Administrative Forest boundaries may have been modified by the Forest Service for improved accuracy and spatial coincidence(vertical integration).</p></div></div></div>

Tags: alp-geopolitical-dataset, boundaries, land-status, usda-forest-service
Organization: Department of Agriculture
Data from: Microarray analysis of subcutaneous adipose tissue from mature cows with divergent body weight gain after feed restriction and realimentation

<p>Body weight response to periods of feed restriction and realimentation is critical and relevant to the agricultural industry. The purpose of this study was to evaluate differentially expressed genes identified in subcutaneous adipose tissue collected from cows divergent in body weight (BW) gain after feed restriction and realimentation. We compared adipose samples from cows with greater gain based on average daily gain (ADG) during realimentation with samples from cows with lesser gain. Specifically, there were four comparisons including two comparing the high and low gain animals across each feeding period (feed restriction and realimentation) and two that compared differences in feed restriction and realimentation across high or low gain classifications. Using microarray analysis, we provide a set of differentially expressed genes identified between the high and low gain at both periods of nutrient restriction and realimentation. These data identify multiple differentially expressed genes between these two phenotypes across both nutritional environments. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: NCBI Gene Expression Omnibus (GEO) Accession GSE94746 Display .</p> <p>File Name: Web Page, url: <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE94746">https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE94746</a> </p><p>Evaluation of the naturally occurring transcriptome variation among beef cows with divergent gain. </p></li></ul><p></p>

Tags: adipose-tissue, agricultural-industry, average-daily-gain, beef-cows, body-weight, cows, genes, microarray-technology, phenotype, repletion, restricted-feeding, subcutaneous-fat, transcriptome
Organization: Department of Agriculture