AndreaBozzo/ceres-open-data-index huggingface dataset:
Data from: Depth Matters: Soil pH and Dilution Effects in the Northern Great Plains

<p dir="ltr">Near-surface soil acidification is becoming prevalent in dryland cropping systems throughout the northern Great Plains. To ensure management recommendations are optimized for crop production, soil sampling guidelines are needed that account for depth stratification of soil pH in surface horizons. Soil pH data from two long-term dryland cropping system experiments were evaluated to document outcomes from three depth increments: 0-7.6 cm, 0-15.2 cm, and 0-30.5 cm. The experiments were established in 1984 and 1993 on the Area IV Soil Conservation Districts Cooperative Research Farm near Mandan, North Dakota USA. Soil cores were collected from the surface 30.5-cm depth near the middle of each experimental plot using a hydraulic probe. Collected soil cores were carefully split into 0-7.6, 7.6-15.2, and 15.2-30.5-cm increments and composited by depth. Samples were dried, mechanically ground, and analyzed within 6 wk of collection. Soil pH was measured in a 1:1 soil/water mixture (by mass) with an ion-selective glass electrode. From the sampled depths, weighted averages were used to calculate soil pH at 0-15.2 and 0-30.5 cm. Data may be used to better understand depth effects on soil pH under dryland cropping systems within a semiarid continental climate. Applicable USDA soil types include Temvik, Wilton, Grassna, Linton, Mandan, and Williams.</p>

Tags: dryland-cropping-systems, nitrogen-fertilization, northern-great-plains, sampling-depth, soil-acidification, soil-ph
Organization: Department of Agriculture
FSIS SR - Antimicrobial Reports (Cecal)

Annual Sampling Reports for antimicrobial resistance, specifically in cecal and product. Cecal reports consists of data for Salmonella, Campylobacter, E. coli, and Enterococcus. Reports are updated annually. See the FSIS website for additional information.

Tags: antimicrobial, campylobacter, cecal, ecoli, enterococcus, fsis, salmonella, usda
Organization: Department of Agriculture
FSIS SR - Antimicrobial Reports (Product)

Annual Sampling Reports for antimicrobial resistance, specifically in cecal and product. Product reports consist of data for Salmonella, Campylobacter, and Shiga toxin-producing Escherichia coli (STEC). Reports are updated annually. See the FSIS website for additional information.

Tags: antimicrobial, campylobacter, fsis, product, salmonella, stec, usda
Organization: Department of Agriculture
Data from: Seed size has a major impact on fall seedling vigor in the cover crop hairy vetch (Vicia villosa Roth)

<p dir="ltr">This data is a subset of the Cover Crop Breeding Network's hairy vetch breeding program containing (1) maternal plants which have a seed size measurement and (2) their offspring.  Individuals were grown over multiple years at multiple sites in the eastern continental US.  Each row represents a plant and their ID code contains the site (using U.S. state acronym) and year (formatted 20XX).  For all individuals, visual fall and spring vigor scores are included, when available. Seed size is presented as two dimensional square millimeters based on a digital measurement from an image.  This dataset was used in a publication which concluded that seed size in hairy vetch is closely linked to seedling vigor, as measured by a visual fall vigor score.</p>

Tags: cover-crop-plants, legumes, plant-breeding
Organization: Department of Agriculture
<b>Data from: Soil Change Induced by Prairie Dogs Across Three Ecological Sites</b>

<p dir="ltr">Prairie dog influences on soil properties should be considered when implementing management recommendations to improve rangeland health. Unfortunately, few studies have addressed soil responses to prairie dog activity across a range of soil types and landscapes. A study was conducted in 2011 to quantify prairie dog effects on soil properties and infiltration rate within three ecological sites differing in landscape, soil, and vegetation characteristics in north central South Dakota, USA. Soil samples were collected from each ecological site in areas with and without prairie dog activity. Prairie dog mounds were sampled using two perpendicular transects over each mound, with samples collected 30, 60, and 120 cm from the mound center. Soil samples were collected from the 0-100cm depth in increments of 0-10, 10-20, 20-30, 30-60m, and 60-100 cm using a hydraulic probe with an inner tip diameter of 3.52 cm. Soil samples were evaluated for soil bulk density, soil pH, extractable nitrogen and phosphorus, and total carbon and nitrogen. Measurements of carbon and nitrogen were determined by dry combustion. Infiltration rate was measured using single-ring infiltrometers on active prairie dog mounds and in a control area without prairie dog activity. Data may be used to understand soil responses to prairie dog activity for rangeland in a semiarid continental climate. Rangeland with rolling landscapes (0-70% slope) and soils derived from soft clay shale or semi-consolidated loamy sedimentary beds closely align with conditions evaluated in this study. Applicable USDA soil types include Hurley, Cabba, and Wayden.</p>

Tags: bioturbation, ecological-sites, prairie-dog-colonies, rangeland, soil-change, south-dakota, water-infiltration-rate
Organization: Department of Agriculture
Data from: Draft genome sequences of eight streptogramin-resistant Enterococcus species isolates from animal and environmental sources in the United States

<p>Draft genome sequences of five <em>Enterococcus faecium</em>, two <em>Enterococcus hirae</em>, and one <em>Enterococcus gallinarum</em> from enviromental sources and chicken carcass rinsates.  Isolates were selected for their resistance to the streptogramin antibiotic, Quinupristin-Dalfopristin and were all collected in the United States between 2001 and 2004.  Antimicrobial resistance genes were identified conferring resistance to the macrolide-lincosamide-streptogramins, aminoglycosides, tetracycline, beta-lactams, and glycopeptides.   </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Streptogramin resistant Enterococcus.</p> <p>File Name: Web Page, url: <a href="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA398373">https://www.ncbi.nlm.nih.gov/bioproject/PRJNA398373</a> </p></li></ul><p></p>

Tags: antimicrobial-resistance-genes, ars, data-gov, dna-sequence, enterococcus, food-animals, np108
Organization: Department of Agriculture
Data from: Aerosol transmission from infected swine to ferrets of an H3N2 virus collected from an agricultural fair and associated with human variant infections

<p>A controlled influenza A virus transmission experiment was conducted in biosafety level 2 containment from January 23, 2018- February 13, 2018 assessing the respiratory droplet transmission efficiency of A(H3N2)/swine/Ohio/A01354299/2017 from experimentally inoculated pigs to naïve, contact ferrets.  This experimental setting models the human-swine interface at agricultural fairs, where human infection with influenza viruses of swine origin has been well documented.  Five pigs were housed in a standard enclosure and four ferrets were housed in isolators placed 7.5cm from the pig enclosure.  Nasal swab samples from pigs were collected on 0, 1, 3, and 5 days post infection and nasal wash samples from ferrets were collected 0, 2, 4, 6, 8, and 15 days post contact.  The whole genome sequences of 15 swine and 12 ferret virus isolates were obtained from respiratory samples cultured on Madin-Darby Canine Kidney cells.  Sequencing was performed on an Illumina MiSeq platform and consensus sequences for each gene segment were generated using in-house software at the USDA-APHIS National Veterinary Services Laboratory. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Swine and Ferret Consensus Sequences.</p> <p>File Name: Consensus_Sequences.txt</p><p>Resource Description: WGS consensus sequences of influenza virus from "Aerosol transmission from infected swine to ferrets of an H3N2 virus collected from an agricultural fair and associated with human variant infections".</p></li></ul><p></p>

Tags: ars, data-gov, ferret, influenza, np103, swine, transmission, variant
Organization: Department of Agriculture
Data from: Point Protection with Transfluthrin against <i>Musca domestica</i> L. in a Semi-Field Enclosure

<div>House flies are notoriously difficult to control, owing to their tendency to live in close relationships with humans and their livestock, and their rapid development of resistance to chemical controls. With this in mind, we explored an alternative chemical control, a spatial repellent to deter <em>Musca domestica </em>L. from points we wanted to protect (i.e., a baited trap [modified Captivator trap]) within a semifield enclosure located on the property of CMAVE (ARS Center for Medical, Agricultural, and Veterinary Entomology) in Gainesville, FL. Our results demonstrated that the synthetic spatial repellent, transfluthrin, is effective in preventing <em>M. domestica </em>adults from entering protected traps for both a susceptible strain (CAR21) and a field-acquired permethrin-resistant strain (WHF; 24 h LD<sub>50</sub> resistance ratio of 150), comprising 22% and 28% of the total number of flies collected, respectively. These results are promising and demonstrate that transfluthrin can be an effective spatial repellent to protect points of interest where needed.</div><p></p>

Tags: integrated-pest-and-disease-management, repellency-assays, spatial-repellents-transfluthrin, vector-control
Organization: Department of Agriculture
Data from: Groundwater surveillance of endemic swine pathogens on forty Iowa swine farms via dead-end ultrafiltration

<p dir="ltr">Groundwater samples were collected in an observational study design by dead-end ultrafiltration from private wells on 40 Iowa swine farms and analyzed by quantitative polymerase chain reaction (qPCR) to assess contamination by endemic swine pathogens and swine manure markers. These data facilitate investigation of groundwater as a biosecurity risk on swine farms. Each farm was sampled one time. Twenty farms were sampled in spring of 2024 (4/15/2024 – 5/29/2024) and twenty farms were sampled in fall of 2024 (9/16/2024 – 10/29/2024). Sample volumes were 639–853 L (mean = 759). Control samples were collected in the field for each field sample, and control samples were tested for all organisms if the corresponding field sample tested positive for any organism. Samples were shipped on ice to the laboratory where they were backflushed, underwent secondary concentration, and archived at -80 degrees Celsius. Secondary concentrates were subsampled for nucleic acid extraction using the QIAGEN QIAcube Connect system, and each nucleic acid extract was analyzed in duplicate by qPCR using a Roche LightCycler 480 II for the following microorganisms: <i>Cryptosporidium</i> spp., enteropathogenic <i>Escherichia coli</i>, porcine circovirus type 2, porcine epidemic diarrhea virus, porcine reproductive and respiratory syndrome virus, rotavirus group C, <i>Salmonella</i> spp., swine <i>Bacteroidales</i> (2 qPCR assays), and swine influenza virus. Negative and positive controls were included at lab steps for concentration, nucleic acid extraction, reverse transcription, and qPCR. PCR inhibition was assessed in each nucleic acid extract and mitigated by dilution if necessary. Data are expressed as genomic copies per liter of groundwater sampled unless otherwise indicated. Dataset consists of 1 spreadsheet file: Dataset 01102025_V4.csv. Variables in this file are described in the included data dictionary.</p>

Tags: biosecurity, groundwater, porcine-circovirus-2, porcine-influenza-a-virus, porcine-reproductive-and-respiratory-swine-virus, swine-pathogens
Organization: Department of Agriculture
Data from: Exposure of dengue-1 virus to Aedes aegypti and sensitivity to insecticides

<p dir="ltr">"PhD obj3 LD50 data submitted April 21 2025": applied to Table 1 of manuscript; used to calculate the lethal dose at which 25%, 50%, and 90% of the organisms (Aedes aegypti) die (LD25, LD50, LD90) using Probit software; PoloPlus - Leora Software. These data were generated by RLA under the supervision of KJL in July-August, 2021, at the USDA-ARS Center for Medical, Agricultural and Veterinary Entomology (USDA-ARS-CMAVE) facility in Gainesville, FL. using dilutions of technical malathion, technical permethrin, and rapeseed methyl ester. These values were generated in order to identify an LD50 dose to apply to 17d old female Ae. aegypti (7 days old prior to blood meal), 10 days after feeding on a blood meal containing dengue-1 virus. Ae. aegypti to determine the LD50 were blood fed at 7 d old, and aged 10 d after blood feeding, then exposed to the dilutions of technical malathion, technical permethrin, and rapeseed methyl ester.</p><p dir="ltr">"PhD Obj3 dengue mortality check submitted April 21 2025": used to populate the results for Table 2 and Table 3; describing the differences in mortality associated with exposure to a dengue-1 treated bloodmeal and LD50 pesticide/control treatment exposure in Aedes aegypti mosquitoes. Analysis was conducted using R. These data were generated by RLA under the supervision of BWA at the University of Florida - Florida Medical Entomology Laboratory (UF-FMEL) facility in Vero Beach, FL between September and November 2021. Ae. aegypti females were aged to 7 d, provided a dengue-1 tainted blood meal or sham blood meal, allowed to age for 10 d after blood feeding, then a topical LD50 dose of technical permethrin, technical malathion diluted in rapeseed methyl ester or neat rapeseed methyl ester as a control were applied and mortality was recorded at 24 h and 48 h. Following mortality checks, Ae. aegypti were frozen (-80 deg C) and checked for the presence of virus using RT-qPCR.</p>

Tags: insecticide-susceptibility-bioassay, malathion, permethrin-insecticide, topical-bioassay
Organization: Department of Agriculture
Data from: Hyperspectral reflectance and machine learning for multi-site monitoring of cotton growth

<p dir="ltr">Two field research projects focused on cotton were conducted at the El Reno, OK and Temple, TX USDA-ARS research stations. The study at the Southern Plains research station took place in 2019 where cotton cultivars included: FiberMax 1830 GLT, FiberMax 1888 GL, FiberMax 2498 GLT, Phytogen 300 W3FE, Phytogen 350 W3FE, and Phytogen 490 W3FE. The experiment took place on Norge silt loam soil. The experimental design included a randomized complete block design with three replications and four nitrogen treatments: unfertilized, cover crop (<i>Lathyrus sativus</i>) with 0, 30, or 60 kg/ha of inorganic nitrogen. The experiment was planted at a seeding rate of 12 seeds/m on May 28, 2019. </p><p dir="ltr">The study at the Texas Gulf station incorporated four cultivars: DP 1646 B2XF, DP 2012 B3XF, DP 2239 B3XF, and DP 1646 B2XF. The experiment took place on Houston Black clay soils. The experimental design included 6-row strip plots with 0.76 m row spacings and approximately 00.1 m plant spacing at a seeding rate of 13 seeds per meter. The experiment also included a multi-planting date design that included March 28, April 11, April 22, and May 11.</p><p dir="ltr">These two stations collected in-situ measurements of height, node count, leaf area index (LAI), canopy cover percentage, and chlorophyll content. LAI data were collected using the LAI-2200C Plant Canopy Analyzer (LI-COR, Lincoln, NE, USA). Canopy cover data were collected using the app “Canopeo” where a ratio of plant to ground pixels were calculated. Chlorophyll content data were collected using Chlorophyll Content Meter-300 (Opti-Sciences, Hudson, NH, USA) where the unit of measure was mg/m2. Directly following these measurements a spectroradiometer (FieldSpec Pro FR: Malvern Panalytical, Westborough, MA, USA) was utilized to collect hyperspectral data from 350nm to 2500nm. The locations of both the in-situ and hyperspectral data collections were chosen at random throughout the field projects and took place in 2019 (OK) and 2022 (TX) with specific dates of collection included in the database.</p>

Tags: biochemical, biophysical, cotton, hyperspectral, remote-sensing-and-field-data
Organization: Department of Agriculture
Western Bark Beetle Strategy: Point (Feature Layer)

Depicts the area of activities to implement the Western Bark Beetle Strategy. Activities were self-reported by field units, and center around three main objectives: increasing safety to ensure that people and community infrastructure are protected from the hazards of falling bark beetle-killed trees and elevated wildfire potential, facilitating recovery to re-establish forests damaged by bark beetles, and cultivating resiliency to prevent or mitigate future bark beetle impacts. <a href='https://data.fs.usda.gov/geodata/edw/edw_resources/meta/S_USA.Activity_WBBS_PT.xml' target='_blank' rel='nofollow ugc noopener noreferrer'>Metadata</a>

Tags: activities, beetle, environment, forest-management, fs, open-data, strategy, usfs, wbbs, western-bark
Organization: Department of Agriculture
Data from: No More Laborious Stem Counting: AI-powered Computer Vision Enables Identification and Quantification of Solid and Hollow Alfalfa Stems at the Pixel Level

<p dir="ltr">The data collected for the article "No More Laborious Stem Counting: AI-powered Computer Vision Enables Identification and Quantification of Solid and Hollow Alfalfa Stems at the Pixel Level" includes image data, labeled JSON data, and machine and deep learning model data. This data was gathered to develop and validate an AI-powered computer vision system designed to accurately identify and quantify solid and hollow alfalfa (<i>Medicago sativa</i> L.) stems at the pixel level. The images were captured under controlled conditions to ensure consistency and quality. The labeled JSON data provides detailed annotations for each image, which were used to train and evaluate the machine and deep learning models. These models were developed to automate the stem counting process, significantly reducing the manual labor involved and improving accuracy. By using this data and the provided models, researchers can reproduce the experiments and achieve the same results, facilitating further research and application in agricultural studies.</p>

Tags: hollowness, otsu_thresholding, otsus-method, phenotyping, solidness, stem, yolo, you-only-look-once
Organization: Department of Agriculture
Bat guano isotope systems (δ13C, δ15N, and δ2H) integrate environmental, climatic, and ecological signals

<p dir="ltr">Bat guano is an emergent paleoenvironmental archive and isotopic compositions of bat guano have been tied to climate, vegetation, and trophic processing in isolated studies. However, a comprehensive, multi-isotope assessment of bat guano has not been established, hindering the proliferation of guano-based paleoenvironmental research. In this study, we comprehensively examine isotopic compositions of a 12,000-year long bat guano core from Cave Springs Cave, Alabama as well as relevant isotopic data from other sources to improve our understanding of each isotope system (δ13C, δ15N, and δ2H), the source-to-sink components of guano isotope pathways, and the fractionation occurring along each multi-step isotopic pathway from sources (i.e., soil, atmosphere, rainfall) to guano formation. We find the δ13C values of guano from Cave Springs Cave primarily reflect local vegetation with a large shift that coincides with the onset of the Anthropocene (after 1950 C.E.). We also determine that the δ15N values of Cave Springs Cave guano were not associated with precipitation or any other climatic variable but instead reflect a change in bat diet and agricultural intensification during the past 600 years. Overall, these data adds to the existing body of bat guano research and supports bat guano as a reliable archive for paleoenvironmental reconstructions.</p>

Tags: bat-guano, holocene, isotope-fractionation, paleoclimatology, trophic-pathways
Organization: Department of Agriculture
Metadata for: Pilot-scale H2S and swine odor removal system using commercially available biochar

<p dir="ltr">This is digital research data corresponding to a published manuscript in "Pilot-scale H2S and swine odor removal system using commercially available biochar" Agronomy 2021, 11, 1611. Dataset may be assessed via the included link at the Dryad data repository.</p><p dir="ltr">Although biochars made in laboratory seem to remove H<sub>2</sub>S and odorous compounds effectively, very few studies are available for commercial biochars. This study evaluated the efficacy of a commercial biochar (CBC) for removing H<sub>2</sub>S.</p><p dir="ltr">Methods are described in the manuscript <a href="https://www.mdpi.com/2073-4395/11/8/1611" target="_blank">https://www.mdpi.com/2073-4395/11/8/1611</a>. Descriptions corresponding to each figure and table in the manuscript are placed on separate tabs to clarify abbreviations and summarize the data headings and units.</p><p dir="ltr">The data file, Table1-4Fig3-5.xslx is an Excel spreadsheet consisting of multiple sub-tabs which are associated with Tables 1, 2, 3, and 4, Figures 3, 4, and 5.</p><p dir="ltr">Tab “Table1” – raw data for physico-chemical characteristics of the commercial pine biochar for Table 1</p><p dir="ltr">Tab “Table2” – raw data for laboratory absorption column variables for Table 1. For dry or humid conditions, “Dry” or “Humid” is headed for each parameter name.</p><p dir="ltr">Tab “Table3” - analytical results for odorous volatile organic compounds for 21 days of operation for Table 3. To avoid the complexity, the single values are not repeated in the data. For the multiple raw data for influent and effluent concentrations of the organic compounds larger than the detection limits are presented in this worksheet.</p><p dir="ltr">Tab “Table4” – raw data (RH, influent and effluent concentrations) for adsorption of H2S using the pilot biochar system for Table 4. All effluent concentrations were below detection limit and not listed.</p><p dir="ltr">Tab “Fig 3”- raw data for observed pressure drops ratios predicted by Ergun and Classen equations, i.e.,(Ergon) /(Obs) or(Classen) /(Obs), for various gas velocities (U = 0.41, 0.025, 0.164, and 0.370 m/s) in Figure 3.</p><p dir="ltr">Tab “Fig4” – breakthrough sorption capacity data for two different inlet concentrations (25 and 100 ppm) used for Figure 4</p><p dir="ltr">Tab “Fig5” – raw data for daily sum of influent and effluent SCOAVs used for Figure 5</p>

Tags: commercial-biochar, hydrogen-sulfide, livestock-odor, odorous-volatile-organic-compounds, pilot-scale
Organization: Department of Agriculture