AndreaBozzo/ceres-open-data-index huggingface dataset:
Minimum Inhibitory Concentration (MIC) data for third generation cephalosporin resistant E. coli and extended spectrum beta-lactamase producing Enterobacteriaceae from feedlot cattle

<p>The data presents the antimicrobial susceptibility testing results in three separate files: 1) third generation cephalosporin resistant <em>E. coli</em> isolates obtained on cefotaxime supplemented media; 2) extended spectrum beta-lactamase (ESBL) producing <em>E. coli</em>, and 3) ESBL-producing <em>Klebsiella</em>, <em>Enterobacter</em> and <em>Citrobacter</em> species obtained on chromogenic media. The data was generated as part of a research project that evaluated the impact of tylosin supplementation of feedlot cattle on the dynamics of antimicrobial resistant fecal bacteria.  The study was a longitudinal design with periodic sampling of fecal samples from individual animals over the entire feeding period. Two publications from the project, one describing the study design in detail, and the other specifically reporting on these data, are linked to the database.</p>
<p>Resources in this dataset:</p>
<ul>
<li>
<p>Resource Title: Third generation cephalosporin resistant E. coli
File Name: TYAMR-TGC Combined Data.xlsx
Resource Description: Third generation cephalosporin resistant E. coli from TyAMR project.</p>
</li>
<li>
<p>Resource Title: ESBL-producing E. coli
File Name: TyAMR-ESBLs isolates-combined AST data.xlsx
Resource Description: </p>
</li>
<li>
<p>Resource Title: ESBL-producing Klebsiella, Enterobacter and Citrobacter spp.
File Name: TyAMR KEC-with AST interpretation.xlsx
Resource Description: ESBL-producing Klebsiella, Enterobacter and Citrobacter obtained as part of TyAMR project.</p>
</li>
</ul>

Tags: antimicrobial-resistance, ars, beef-cattle, data-gov, esbl, extended-spectrum-beta-lactamase-producing-bacteria, food-safety, np108, third-generation-cephalosporin-resistance
Organization: Department of Agriculture
Data from: Experiments on Jackson trap efficiency capturing Bactrocera dorsalis and Zeugodacus cucurbitae

<p>Jackson traps baited with male lures with or without insecticides are essential components of surveillance and monitoring programs against pest tephritid fruit flies. The ability of a trap to capture a fly that enters, sometimes termed “trap efficiency”, is dependent on many factors including the trap/lure/toxicant combination. We tested the effects of three important components of Jackson traps on efficiency of capture of two important fruit fly species, using the “standard” (i.e., as they are used in the state-wide surveillance program in California) and alternatives: Insecticide (Naled, DDVP or None), type of adhesive on the sticky panel (Seabright Laboratories Stickem Special Regular or Stickem Special HiTack), and use of a single or combination male lure (Methyl eugenol and/or cuelure). Experiments were conducted in large outdoor carousel olfactometers with known numbers of <em>Bactrocera dorsalis</em> and <em>Zeugodacus cucurbitae</em> and by trapping wild populations of the same two species. Lures were aged out to eight weeks to develop a comprehensive dataset on trap efficiency of the various combinations.  </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Olfactometer data.</p> <p>File Name: olfactometer-data-rows.csv</p><p>Resource Description: Number of flies per trap captured in the olfactometers</p></li><br><li><p>Resource Title: Field data.</p> <p>File Name: field-data-rows.csv</p><p>Resource Description: Number of flies caught per trap in the field</p></li><br><li><p>Resource Title: Metadata.</p> <p>File Name: Metadata.txt</p><p>Resource Description: Information on columns in each data file</p></li></ul><p></p>

Tags: ars, data-gov, fruit-fly, insect-pests, np304, surveillance, tephritidae
Organization: Department of Agriculture
The GRIN-Global Project

<p>GRIN-Global is an ongoing international collaborative project to develop shared and open-source applications that help manage plant germplasm collections. The software was jointly developed by the Agricultural Research Service of USDA, Global Crop Diversity Trust, and Bioversity International, with the first version released in December 2011. The ARS has used GRIN-Global to manage its plant germplasm collections, the U.S. National Plant Germplasm System, since November 2015. GRIN-Global is an extension of Germplasm Resources Information Network (GRIN) information management system, which was first developed by ARS beginning in the mid-1980s. </p>
<p>GRIN-Global is comprised of a suite of computer applications that are used internally by genebank staff to curate collections, as well as a public website through which scientists can query the database and request samples of germplasm through a shopping cart process. </p>
<div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: The GRIN-Global Project website pointer.</p> <p>File Name: Web Page, url: <a href="https://www.grin-global.org/" target="_blank">https://www.grin-global.org/</a> </p></li></ul>

Tags: angiosperms, animals, arid-land-plant, ars, biofluids, cell-cultures, cotton, data-gov, food-security, genetics, germplasm, grains, gymnosperms, legumes, livestock, maize, national-arboretum, np301, organisms, ornamental-plant, pea, plants, potato, pteridophytes, rice, seeds, soybean, species, tissue-cultures, tomato, u-s-forest-service
Organization: Department of Agriculture
Ecological site identification, soil observations, and geomorphology data collected by the Assessment, Inventory, and Monitoring (AIM) terrestrial program between 2012 and 2021 in the western United States

<p>This metadata is the documentation for the field soil observations, ecological site identification, and geomorphology characteristics collected by the Assessment, Inventory, and Monitoring (AIM) terrestrial program between 2012 and 2021 in 14 states of the western United States. The AIM program is conducted by the Bureau of Land Management (BLM)’s and provides information to guide site-specific management of ecosystem functions and services. There are 31,267 monitoring plots (79% of plots) with identified ecological sites and 29,228 plots (74% of plots) containing soil morphology descriptions of soil horizons examined in excavated pits. While soil texture class is observed in most soil horizons (98%), rock fragment volume is the soil property with the least data availability (75%). The consistency of soil data (e.g., clay content observations within the ranges of texture classes) increases as a function of time following guidance in soil profile description training for AIM data collectors. Nearly 47% of AIM plots are found on gentle slopes of 0-5% steepness and on Flat/Plain and Hill/Mountain landscape types. The AIM database is a source of georeferenced soil and geomorphology information that can be used for land management and research on land potential, soil geography, and assessment of soil health indicators across the western United States.</p>
<p>Resources in this dataset:</p>
<ul>
<li>
<p>Resource title: Plot characteristics
File name: PlotCharacteristics.csv
Resource description: Plot characteristics table contains information on GPS coordinates, ecological site ID, and geomorphological settings, such as slope, aspect, landscape type, etc.</p>
</li>
<li>
<p>Resource title: Soil horizon
File name: SoilHorizon.csv
Resource description: The soil horizon table has information on soil morphology attributes, such as color, texture class, effervescence, soil structure, etc.</p>
</li>
<li>
<p>Resource title: Plot characteristics data dictionary
File name: PlotCharacteristicsDataDictionary.csv</p>
</li>
<li>
<p>Resource title: Soil horizon data dictionary
File name: SoilHorizonDataDictionary.csv</p>
</li>
<li>
<p>Resource title: Methods
File name: Methods.txt</p>
</li>
</ul><p></p>

Tags: ars, data-gov, ecological-site-descriptions-esd, geomorphology, landscape-position, np216, soil-depth, soil-morphology, soil-profiles, soil-texture
Organization: Department of Agriculture
Data from: Measured and simulated carbon dynamics in Midwestern US corn-soybean rotations

<p>The dataset includes information on soil properties collected from two conventionally managed fields under corn-soybean rotation in October 2005 and October 2016, respectively. The fields are located in Story County, Central Iowa. 42 sampling locations per field and year were sampled within a 50 m × 50 m grid, and 1 to 2 samples per location were collected using a hydraulic soil sampler (d= 38.2 mm) from the 0 - 120 cm soil layer. The samples were analyzed to determine carbon and nitrogen concentration, and soil pH in five soil layers (0-15, 15-30, 30-60, 60-90, and 90-120 cm). Presented is the raw data per location (mean of duplicates) with which carbon and nitrogen content can be calculated with either the equivalent soil mass method or by using bulk density.</p>
<p>For more information about this dataset contact:
Tom Sauer: tom.sauer@usda.gov
Christian Dold: c.dold@fz-juelich.de </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Data Dictionary.</p> <p>File Name: data-dictionary_CD.csv</p><p>Resource Description: Defines variables and their units for the data table, also provided as a separate sheet within xlsx file.</p></li><br><li><p>Resource Title: Soil Properties.</p> <p>File Name: Soil Chemical Analysis.xlsx</p></li></ul><p></p>

Tags: ars, corn-soybean-rotation, data-gov, np212, np216
Organization: Department of Agriculture
Alternative Biomass Production Study for Resilient Economic Agricultural Practices in Morris, Minnesota

<p>Alternative Biomass Production Study for Resilient Economic Agricultural Practices in Morris, Minnesota
The Tillage Study was established in 1997 to assess the effect of a variety of tillage intensities on soil C. The initial eight treatments included no-tillage, moldboard + disk tillage, chisel tillage, and fall and spring residue management, with or without strip-tillage and strip-tillage + subsoiling (Archer and Reicosky, 2009). In 2004, treatments were reduced to no-tillage, moldboard tillage, and fall and spring residue management without strip-tillage, but all had an early or late planting date. The last comprehensive set of soil samples were collected in 2006. In 2008, the strip-tilled subset of the Tillage Study plots were repurposed for the Alternative Biomass Production Systems study, which was designed to explore alternative strategies to support bioenergy including planting of cellulosic feedstock. The Alternative Biomass Production plots included perennials in an extended 6-year rotation, winter cereal rye cover crops in a corn-soybean rotation, and an alternative Sorghum-Sudan grass hybrid forage system, all of which have and will continue to be monitored for agronomic and soil properties.</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/cafbf65e-2056-4aac-af33-ab3896fb3c6d" target="_blank">https://geodata.nal.usda.gov/geonetwork/srv/eng/catalog.search#/metadata/cafbf65e-2056-4aac-af33-ab3896fb3c6d</a> </p></li></ul>

Tags: andropogon-gerardii, ars, autumn, bioenergy, biomass-production, combustion, corn, corn-stover, cover-crops, crop-management, cutting, data-gov, developmental-stages, discing, drying, energy-crops, environment, farming, feedstocks, forage-grasses, grain-yield, herbicides, hybrids, lakes, live-mulches, lolium, morris-mn-abp, natural-resources-and-genomics, no-tillage, np211, np212, on-farm-research, panicum-virgatum, perennials, planting-date, production-technology, reap, rye, seed-set, seedbeds, soil-depth, soil-nutrients, soil-sampling, sorghum-bicolor-subsp-drummondii, soybeans, spring, statistics, straw, strip-tillage, subsoiling, trifolium-pratense
Organization: Department of Agriculture
Data from: An Exploratory Analysis of Barriers to Usage of the USDA Dietary Guidelines for Americans

<p>The average American’s diet does not align with the Dietary Guidelines for Americans (DGA) provided by the U.S. Department of Agriculture and the U.S. Department of Health and Human Services (2020). The present study aimed to compare fruit and vegetable consumption among those who had and had not heard of the DGA, identify characteristics of DGA users, and identify barriers to DGA use. A nationwide survey of 943 Americans revealed that those who had heard of the DGA ate more fruits and vegetables than those who had not. Men, African Americans, and those who have more education had greater odds of using the DGA as a guide when preparing meals relative to their respective counterparts. Disinterest, effort, and time were among the most cited reasons for not using the DGA. Future research should examine how to increase DGA adherence among those unaware of or who do not use the DGA. </p>
<p>Comparative analyses of fruit and vegetable consumption among those who were aware/unaware and use/do not use the DGA were completed using independent samples t tests. Fruit and vegetable consumption variables were log-transformed for analysis.   Binary logistic regression was used to examine whether demographic features (race, gender, and age) predict DGA awareness and usage. Data were analyzed using SPSS version 28.1 and SAS/STAT® version 9.4 TS1M7 (2023 SAS Institute Inc).</p>

Tags: adherence, adults, ars, attitudes, data-gov, diet, dietary-guidelines, dietary-recommendations, food, health-belief-model, np107, nutrition, opinions
Organization: Department of Agriculture
Greenhouse Gas Study for Greenhouse gas Reduction through Agricultural Carbon Enhancement network in Bowling Green, Kentucky

<p>Greenhouse Gas Study for Greenhouse gas Reduction through Agricultural Carbon Enhancement network in Bowling Green, Kentucky
Alternative N fertilizers that produce low greenhouse gas (GHG) emissions from soil are needed to reduce the impacts of agricultural practices on global warming potential (GWP). We quantified and compared growing season fluxes of N2O, CH4, and CO2resulting from applications of different N fertilizer sources, urea (U), urea-ammonium nitrate (UAN), ammonium nitrate (NH4 NO3), poultry litter, and commercially available, enhanced-efficiency N fertilizers as follows: polymer-coated urea (ESN), SuperU, UAN + AgrotainPlus, and poultry litter + AgrotainPlus in a no-till corn (Zea maysL.) production system. Greenhouse gas fluxes were measured during two growing seasons using static, vented chambers. The ESN delayed the N2O flux peak by 3 to 4 wk compared with other N sources. No significant differences were observed in N2O emissions among the enhanced-efficiency and traditional inorganic N sources, except for ESN in 2009. Cumulative growing season N2O emission from poultry litter was significantly greater than from inorganic N sources. The N2O loss (2-yr average) as a percentage of N applied ranged from 0.69% for SuperU to 4.5% for poultry litter. The CH4–C and CO2–C emissions were impacted by environmental factors, such as temperature and moisture, more than the N source. There was no significant difference in corn yield among all N sources in both years. Site specifics and climate conditions may be responsible for the differences among the results of this study and some of the previously published studies. Our results demonstrate that N fertilizer source and climate conditions need conideration when selecting N sources to reduce GHG emissions.</p> <div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Bowling Green, KY Greenhouse Gas Study (KYBGGHG) CSV data.</p> <p>File Name: KYBGGHG_csv_data.zip</p><p>Resource Description: CSV format data on Experimental Units, Field Sites, Greenhouse Gas Flux, Harvest Fraction, Nutrient Efficiency, Soil Chemistry, Soil Physics, Amendments, Planting, Persons, Treatments, Weather Daily, Weather Station.</p></li></ul>

Tags: ars, data-gov, environment, farming, fertilizer, greenhouse-gas-emissions, np211, np212
Organization: Department of Agriculture
U.S. National Fungus Collections

<p>The U.S. National Fungus Collections (BPI) are the “Smithsonian for fungi” and are the repository for over one million fungal specimens worldwide - the largest such collections in the world. The collection includes preserved organisms, their parts and products, and their associated data. Information associated with these specimens constitute an enormous data resource, especially about plant-associated fungi. The collections document fungi through time and space for the past 200 years.</p>
<p>Data from the labels of more than 750,000 of the specimens have been entered into a database. These labels have information on the host on which the fungus was found and the locality in which the specimen was collected. Sixty percent of these specimens are from the United States and thus represent a large body of information about the fungi in this country.  </p>
<p>Data entry has been completed for the Uredinales (rusts), the Ustilaginales (smuts), the Polyporales (polypores), the Deuteromycetes (imperfect fungi), the Ascomycetes, and the C.G. Lloyd collections. Recent progress has been made in the computerization of specimens of the agarics and the "lower" fungi including the Oomycetes and Chytridiomycetes. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Fungal databases - Specimens.</p> <p>File Name: Web Page, url: <a href="https://nt.ars-grin.gov/fungaldatabases/specimens/specimens.cfm">https://nt.ars-grin.gov/fungaldatabases/specimens/specimens.cfm</a> </p><p>The direct database form link</p></li></ul><p></p>

Tags: ars, ascomycota, chytridiomycetes, data-gov, deuteromycotina, fungi, microbiology, mycology, online-database, oomycetes, organisms, polyporales, pucciniales, specimens, ustilaginales
Organization: Department of Agriculture
Data and code from: Use of automated capillary immunoassay for quantification of antibodies in chicken sera against recombinant Salmonella enterica serotype Heidelberg proteins

<p>This entry contains all data and code required to reproduce the analysis of immune response data presented in the manuscript:</p>
<p>Yeh, H.-Y., J. G. Frye, C. R. Jackson, Q. D. Read, J. E. Line, and A. Hinton. 2023. Use of automated capillary immunoassay for quantification of antibodies in chicken sera against recombinant <em>Salmonella enterica</em> serotype Heidelberg proteins. <em>Journal of Microbiological Methods</em>. <a href="https://doi.org/10.1016/j.mimet.2023.106757">https://doi.org/10.1016/j.mimet.2023.106757</a></p>
<p>Files included are:</p>
<ul>
<li><code>chicken_salmonella_immunoassay_analysis.Rmd</code>: RMarkdown notebook with all analysis code and full supplementary results, figures, tables, and explanatory notes. The Excel file containing the data should be in the same dictionary as the .Rmd file when the notebook is rendered.</li>
<li><code>chicken_salmonella_immunoassay_analysis.html</code>: rendered output of notebook including full supplementary results, figures, and tables, and explanatory text.</li>
<li><code>Chicken Sera FliD FimA.xlsx</code>: Excel file with chicken immune response data in the form of chemiluminescence values (arbitrary units) that are a proxy for immunoglobulin concentration. Each row contains measurements from an individual bird, across two time points (bleedings); at each time point IgG chemiluminescence values in response to Salmonella FliD and FimA proteins are given, and IgM chemiluminescence as well. This results in a total of eight measurements per bird (2 bleedings x 2 types of immunoglobulin x 2 Salmonella proteins). The first ten rows are non-immunized control birds and the next ten rows are immunized birds.</li>
<li><code>concentration_chemiluminescence.xlsx</code>: Excel file with protein concentration and chemiluminescence data to verify relationship between them. There are three columns, one to identify the protein (FliD and FimA), one for known protein concentration, and one for chemiluminescence. This is used to verify that the chemiluminescence values are suitable proxies for protein concentration.</li>
</ul>
<p>This research is associated with USDA project 6040-32000-079-00D and falls under National Program NP108. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: RMarkdown document with immune response model fitting code.</p> <p>File Name: chicken_salmonella_immunoassay_analysis.Rmd</p></li><br><li><p>Resource Title: Rendered HTML version of notebook.</p> <p>File Name: chicken_salmonella_immunoassay_analysis.html</p></li><br><li><p>Resource Title: Immunoglobulin response data.</p> <p>File Name: Chicken Sera FliD FimA.xlsx</p></li><br><li><p>Resource Title: Concentration and chemiluminescence data.</p> <p>File Name: concentration_chemiluminescence.xlsx</p></li></ul><p></p>

Tags: ars, capillary-immunoassay, chickens, data-gov, immunoassay, immunoglobulin, np108, salmonella-enterica, salmonella-enterica-serotype-heidelberg
Organization: Department of Agriculture
The Cause of Increased Effectiveness of Water-In-Oil Emulsion over Water Application of Trichoderma ovalisporum on Therobroma cacao Pods

<p>Previous research conducted in Costa Rica determined that <em>Trichoderma ovalisporum</em>, when applied in a water-in-oil emulsion to <em>Theobroma cacao</em> pods, had  less <em>Moniliophthora roreri</em> (frosty pod rot) than in water.  The current research was conducted to determine why bio-control agents when applied to cacao pods were more effective in a water-in-oil emulsion than water for controlling frosty pod rot.  The experiments were conducted in Ecuador in 2011 and 2012.  Two formulations were used: water-in-oil emulsion and water.  Water-sensitive cards were attached to the lower branches of the cacao trees.  There were four trees per treatment and six cards per tree.  One hundred and eighty ml of formulation were applied to each tree with a Stihl SR 420 backpack mist-blower.  The cards underwent droplet analysis with the DepositScan software package. Droplet analysis determined that the increased efficacy of water-in-oil emulsion was the result of the micro-environment advantage of the water-in-oil emulsion. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Rc139MetaData.</p> <p>File Name: RC139MetaData.zip</p><p>Resource Description: RC139MetaData is composed of five files. (1)  RC139Readme: is a description of the files in the RC139MetaData.zip. (2)   RC139CodeBook: Is a description of the experiment, how it was conducted, what variables are in the RC139Data with their description. (3) & (5) SAS satistical program code for analysis of RC139data. (5) RC139Data: Dataset containing results of experiments.</p>
<p></p></li><br><li><p>Resource Title: RC139 Data Dictionary.</p> <p>File Name: RC139-data-dictionary.csv</p><p>Resource Description: Defines variables, origination, data type, etc. for each column in RC139Data.csv data. (NOTE: Also contained in the markdown Code book RC139CodeBook.md file within the RC139MetaData.zip.)</p></li></ul><p></p>

Tags: ars, backpack-mistblower, bio-control, data-gov, droplet-analysis, np303, theobroma-cacao, water-in-oil-emulsion, water-sensitive-cards
Organization: Department of Agriculture