AndreaBozzo/ceres-open-data-index huggingface dataset:
Data from: Carbon and water dynamics of Old World Bluestem in the U.S. Southern Great Plains

<p dir="ltr">The dataset includes daily fluxes of net ecosystem CO2 exchange (NEE, g C m-2 d-1), gross primary production (GPP, g C m-2 d-1), ecosystem respiration (ER, g C m-2 d-1), and evapotranspiration (ET, mm d-1) from 2021 to 2024 for an Old World Bluestem pasture at the USDA-ARS, El Reno, Oklahoma.</p><p dir="ltr">The study site, Old World Bluestem (OWB) pasture (~63 ha), was established in the 1980s on a native tallgrass prairie site. It is located at the United States Department of Agriculture – Agricultural Research Service (USDA-ARS), Oklahoma and Central Plains Agricultural Research Center, El Reno (35.5467º N, 98.0452º W, and 435 masl), Oklahoma.</p><p dir="ltr">The eddy covariance (EC) tower was equipped with an open-path infrared gas analyzer (LI-7500 RS, LI-COR Biosciences, Lincoln, NE, USA) integrated with a three-dimensional sonic anemometer (CSAT3, Campbell Scientific Inc., Logan, UT, USA). These sensors were mounted at a height of ~2.8 m above the ground surface. The tower had enough fetch extending several hundred meters in all directions to ensure representative flux measurements from the OWB pasture.</p><p dir="ltr">Raw high-frequency EC data were processed using EddyPro software (version 7.0.6, LI-COR Biosciences, Lincoln, NE, USA) in its Express configuration to compute half-hourly (30-min) fluxes. Gap-filling of half-hourly eddy fluxes and meteorological variables, as well as the partitioning of NEE (using nighttime partitioning) into its component fluxes (GPP and ER), was conducted using the REddyProc (https://www.bgc-jena.mpg.de/REddyProc/ui/REddyProc.php).</p>

Tags: ecosystem-respiration-er, eddy-covariance, evapotranspiration, gross-primary-production-gpp, net-ecosystem-exchange-nee, old-world-bluestem
Organization: Department of Agriculture
Data from: Chromosome-level haplotype-resolved genome assemblies and annotations of Apios americana and Apios priceana

<p dir="ltr">The data in this collection comprise gene annotations for Apios americana and Apios priceana. Annotations were carried out using the BRAKER3 pipeline (Gabriel et al., 2024). Apios americana produces starchy, high-protein tubers that were used by indigenous Native Americans. Apios americana is found throughout eastern and central North America, from Louisiana in the south to Quebec in the north. Apios priceana is a rare legume species, found scattered locations in the North American Southeast (Alabama, Mississippi, Kentucky, and Tennessee). The plant is federally listed as a threatened species. It has a vining habit and produces an edible, thickened storage root.</p>

Tags: apios-americana, apios-priceana, potato-bean, prices-potato-bean
Organization: Department of Agriculture
Data from: Laboratory evaluation of two insecticide-incorporated nets for the management of <i>Prostephanus truncatus</i>

<p dir="ltr"><i>Insects</i></p><p dir="ltr">Adult <i>P. truncatus </i>were obtained from insect colonies kept in the Laboratory of Entomology and Agricultural Zoology (LEAZ), at the Department of Agriculture, Crop Production and Rural Environment, University of Thessaly, Greece, on whole maize kernels, at 26°C and 55% relative humidity (RH) and continuous darkness.</p><p dir="ltr"><i>Insecticide-Incorporated Netting</i></p><p dir="ltr">The experiments were carried out in plastic petri dishes 90 mm in diameter (50.4 cm<sup>2 </sup>bottom surface). The inside of each petri dish was covered with two types of LLIN (0.4% deltamethrin, D-Terrence, Vestergaard INC., Lausanne Switzerland; and 0.34% alpha-cypermethrin, Carifend, BASF Ag, Ludwigshafen, Germany) and a polytetraflurorethylene preparation (Fluon, 60 wt% dispersion in water, Sigma-Aldrich Chemie GmbH, Steinheim, Germany) to prevent insects from escaping. An additional series of dishes with physically identical control netting were prepared without an insecticide treatment to serve as the control. Twenty <i>P. truncatus</i> were then exposed on the insecticide-treated netting in petri dishes for 60, 90, 120, 240 min, 1, 3, and 5 days.</p><p dir="ltr"><i>Mortality and Recovery</i></p><p dir="ltr">After exposure, insects were evaluated for mortality and individual <i>P. truncatus</i> that remained alive or knocked down (not dead) were then place into clean Petri dish arenas with a small amount of clean cracked maize kernels and evaluated for delayed mortality after 7 days. Using a stereomicroscope (SMZ-18, Nikon Inc., Tokyo, Japan) under 60× magnification, <i>P. truncatus</i> were classified as alive (moving normally, is able to right itself when flipped over, no twitching), affected (moving sluggishly or erratically, unable to right itself, twitching of antennae or legs may be present), or dead (completely immobile even after prodding) according to prior published definitions. There were three 3 replicates for each time treatment and netting type and 3 subreplicates for a total of 9 replicates for each treatment combination.</p><p dir="ltr"><i>Explanation of files</i></p><p dir="ltr">The file "Greece Net Data 2023_All" includes the raw mortality ratings, whereas "Greece Net Data 2023_Recovery" includes calculated recovery values by <i>P. truncatus</i>, where recovery was calculated to "alive" from the initial reading (0 d) in "Greece Net Data 2023_All".</p>

Tags: carifend, cgahr, d-terrence, delayed-mortality, greece, insecticide-netting, integrated-pest-management, laboratory, larger-grain-borer, llin-utilization, long-lasting-insecticide-nets, prostephanus-truncatus, recovery, toxicology, university-of-thessaly, usda-ars, volos
Organization: Department of Agriculture
Whole genome sequences of bacteria isolated from Oil fly (<i>Helaeomyia petrolei</i>) larvae

<p dir="ltr">Larvae from the petroleum oil fly, Helaeomyia petrolei, live in the asphaltene and polyaromatic hydrocarbon rich asphalt seeps of Rancho La Brea, Los Angeles, California. These larvae pass high amounts of viscous asphalt through their digestive system, and their gut microbiota is exposed to these extreme conditions. Environmental stress response mechanisms can co-select for antibiotic resistance, and in the current study we used 16S rRNA and genomic sequencing along with the Comprehensive Antibiotic Resistance Database (CARD) tools to characterize antibiotic resistance profiles from six bacteria previously isolated from the oil fly larval intestinal tract, linking phenotypic and genotypic resistance profiles. The isolates contain a core set of antibiotic resistance determinants along with determinants that are rarely found in these species. Comparing these oil fly isolates to the phenotypic prevalence data generated by the CARD Resistance Gene Identifier revealed sixteen instances where the oil fly bacteria appeared to carry a resistance not seen in related taxa in the database, suggesting a novel suite of resistance families in the oil fly isolates compared to other members of the same taxa. Results highlight the functional duality of genes that code for antibiotic resistance and expand our understanding of the ecological and evolutionary role of antibiotic resistance genes in environmental habitats.</p>

Tags: antibiotic-resistance, bacteria, extreme-environments-microbiology, helaeomyia-petrolei, oil-fly
Organization: Department of Agriculture
Soybean aphid,<i> Aphis glycines</i>, field abundance from field collection and corresponding vgsc-h1 genotypes

<p dir="ltr">Data collected for soybean aphid, <i>Aphis glycines</i>, on soybean, <i>Glycine max</i>, in field efficacy trials conducted at the Iowa State University Northwest Research Farm, Sutherland, IA in 2023. Comprised of field aphid abundance (counts) from 10 sampled plants before and after insecticidal treatments, and corresponding genotypes of aphids at the voltage-gated sodium channel subunit h1 gene (<i>vgsc-h1</i>) encoding amino acid changes from a methionine at the <i>vgsc-h1</i> protein position 918 to either isoleucine (M918I) or leucine (M918L), a  leucine to methionine substitution at the 925<sup> </sup>position (L925M), and leucine to phenylalanine change at position 1014 (L1014F).</p>

Tags: insecticide-resistance, mutation, pyrethroid-insecticides, soybean-aphid, voltage-gated-sodium-channel
Organization: Department of Agriculture
Data from: Bringing cross-validation into the real world to evaluate transferability of satellite-based vegetation models

<p dir="ltr">This tabular dataset supports findings reported in "Bringing cross-validation into the real world to evaluate transferability of satellite-based vegetation models" published in <i>Scientific Reports</i>. Data are from the Central Plains Experimental Range (CPER), near Nunn, Colorado, and contains nearly 10,000 ground samples collected from 2014 to 2023. Data are aggregated to the plot level (n=2,322), of which there are 4-6 in each pasture and also provided at the transect level (n=9,647), of which there are 4 in each plot. Data were used to train progressively more complex Machine learning algorithms (MLAs) to predict standing aboveground herbaceous biomass in grazinglands, such as those found at CPER. These data support an investigation of whether (1) do simpler geospatial MLAs have better transferability to ‘unseen’ conditions and ‘worst-case’ performance (i.e., under extreme conditions) compared to more complex MLAs and (2) are they more consistent when re-trained with new data. Data include (1) unique identifiers and blocking co-variates (2) in-situ ground-sampled herbaceous standing biomass estimated using visual obstruction (VO) methods, along with the VO readings themselves (3) geographic polygon bounding coordinates of each plot/transect (WKT format), and (4) satellite-derived indices and bands from the Harmonized Landsat Sentinel (HLS) data product. All in situ values and satellite derived indices are means for the respective plot and transect areas.</p><p dir="ltr">This research used resources provided by the SCINet project and/or the AI Center of Excellence of the USDA Agricultural Research Service, ARS project numbers 0201-88888-003-000D and 0201-88888-002-000D.</p>

Tags: biomass, grasslands, machine-learning, rangelands, satellite-remote-sensing
Organization: Department of Agriculture
Data from: Genetic mapping and QTL analysis for peanut smut resistance

<p>This collection contains supplementary information for the manuscript “Genetic mapping and QTL analysis for peanut smut resistance”, which reports the genetic map and quantitative trait loci associated with resistance to peanut smut, a disease caused by the fungus <em>Thecaphora frezii</em>. The information includes genotyping data of a 103 recombinant inbred line (RIL) population {susceptible <em>Arachis hypogaea</em> subsp.<em>hypogaea</em> × resistant synthetic amphidiploid [(<em>A. correntina</em> × <em>A. cardenasii</em>) × <em>A. batizocoi</em>]⁴ˣ}  and parental lines, generated with the Axiom_Arachis2 SNP array. </p>
<p><br></p>
<p>For more information about this dataset contact: Renee Arias: Renee.Arias@usda.gov or Alicia Massa: Alicia.Massa@usda.gov </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: RILs of the mapping population.</p> <p>File Name: RIL_population.JPG</p></li><br><li><p>Resource Title: Data Dictionary.</p> <p>File Name: readme.txt</p></li><br><li><p>Resource Title: Supplementary Data 1: SNP genotypes as called by the Axiom Analysis Suite File name: SD01_RILs_SNPs_whole_Axiom_Arachis2.txt .</p> <p>File Name: SD01_RILs_SNPs_whole_Axiom_Arachis2.txt.zip</p><p>Resource Description: Supplementary Data 1: SNP genotypes as called by the Axiom Analysis Suite
File name: SD01_RILs_SNPs_whole_Axiom_Arachis2.txt
Single nucleotide polymorphism genotyping of a 103 RIL population and parental lines generated with the Arachis_Axiom2 SNP array.
</p><p>Resource Software Recommended: Axiom_Arachis2,url: <a href="https://www.thermofisher.com/us/en/home/life-science/microarray-analysis/microarray-analysis-instruments-software-services/microarray-analysis-software/axiom-analysis-suite.html">https://www.thermofisher.com/us/en/home/life-science/microarray-analysis/microarray-analysis-instruments-software-services/microarray-analysis-software/axiom-analysis-suite.html</a> </p></li><br><li><p>Resource Title: Supplementary Data 2: Genotyping calls in VCF format File name: SD02_RILs_SNPs_whole_Axiom_Arachis2.vcf.</p> <p>File Name: SD02_core_RILs_SNPs_Axiom<em>Arachis2.vcf</em>.zip</p><p>Resource Description: Supplementary Data 2: Genotyping calls in VCF format
File name: SD02_RILs_SNPs_whole_Axiom_Arachis2.vcf
Core SNP set used to characterize the RIL population and progenitors. </p></li></ul><p></p>

Tags: arachis, arachis-hypogaea, arachis_axiom2-snp-array, ars, data-gov, np301, np303, peanut, peanut-smut, smut-resistance, snp
Organization: Department of Agriculture
Data from: Application of visual soil evaluations in a semiarid region

<p dir="ltr">A half-day workshop exploring visual soil evaluation methods was developed for land managers by the USDA-ARS Northern Great Plains Research Laboratory, Mandan, ND USA. Outcomes from workshops held between 2018 and 2023 found that attendees were able to quickly acquire skills necessary to effectively apply the Visual Evaluation of Soil Structure (VESS) assessment method under conditions unique to the workshop. Annual measurements of soil properties and crop yield were conducted on five cropping systems with different management but common soil type and compared to VESS assessments. Soil measurements included soil bulk density, sorptivity, soil pH, soil organic matter, soluble C, soluble N, and C mineralization, while crop measurements included spring wheat grain and straw yield. Field measurements of sorptivity were conducted at the same time soil samples were collected from the 0-10 cm depth for laboratory analyses. Soil pH was estimated from a 1:1 soil-water mixture, soil organic matter by loss-on-ignition, soluble C and N from water extracts, and C mineralization using a 24-hr incubation. Spring wheat grain and straw yield were measured using standard methods for hand sampling and biomass processing. Visual Evaluation of Soil Structure assessments were conducted by workshop attendees and the instructor. Data may be used to understand how visual soil evaluations conducted by land managers compare with traditional soil and crop measurements. Data are generally applicable to cropland under a semiarid to sub-humid continental climate for the following USDA soil types: Grassna, Linton, Mandan, Temvik, Williams, and Wilton.</p>

Tags: land-managers, northern-plains, rainfed-cropping-systems, soil-health, visual-evaluation-of-soil-structure
Organization: Department of Agriculture
Data from: A scalable, low-cost phenotyping strategy to assess tuber size, shape, and the colorimetric features of tuber skin and flesh in potato breeding populations

<p>This data set contains images of potato tubers from clones in the A08241 F1 breeding population grown in Aberdeen, Idaho during the 2019 field season. Each clone was grown as 8-hill plots and replicated twice. Five tubers per sample were imaged. Each face of the tuber was imaged on two different backgrounds. The five tubers were also halved lengthwise and one of side was imaged using a flatbed scanner. </p>
<p>Resources in this dataset:</p>
<ul>
<li>
<p>Resource Title: A08241_scanner_images
File Name: tubers.zip
Resource description: These are images of halved potato tubers collected from clones in the A08241 breeding population using a Hewlett Packard HP ColorJet 6200C flatbed scanner. No color correction was performed on these images.</p>
</li>
<li>
<p>Resource Title: A08241_lightbox_images
File Name: box.zip
Resource description: These are images of potato tubers from the A08241 breeding population captured on a lightbox background using a Nikon D7100 camera. No color correction was performed on these images.</p>
</li>
<li>
<p>Resource Title: A08241_black_background_images
File Name: std.zip
Resource description: These are images of potato tubers from the A08241 breeding population captured on a black background using a Nikon D7100 camera. No color correction was performed on these images.</p>
</li>
<li>
<p>Resource Title: A08241_lightbox_color_corrected_images
File Name: lightbox_color_corrected.zip
Resource description: These are images of potato tubers from the A08241 breeding population captured on a lightbox background using a Nikon D7100 camera. Color correction was performed in MATLAB by Nathan Miller.</p>
</li>
<li>
<p>Resource Title: A08241_black_background_color_corrected_images
File Name: blackbackground_color_corrected.zip
Resource description: These are images of potato tubers from the A08241 breeding population captured on a non-reflective black background using a Nikon D7100 camera. Color correction was performed in MATLAB by Nathan Miller.</p>
</li>
</ul><p></p>

Tags: ars, data-gov, np301, potato
Organization: Department of Agriculture
Data from: Multiscale climatological albedo look-up maps derived from moderate resolution imaging spectroradiometer BRDF/albedo products

<p dir="ltr">Surface albedo determines radiative forcing and is a key parameter for driving Earth’s climate. Better characterization of surface albedo for individual land cover types can reduce the uncertainty in estimating changes to Earth’s radiation balance due to land cover change. The dataset includes albedo look-up maps (LUMs) using a multiscale hierarchical approach based on moderate resolution imaging spectroradiometer (MODIS) bidirectional reflectance distribution function (BRDF)/albedo products and Landsat imagery. Ten years (2001 to 2011) of MODIS BRDF/albedo products were used to generate global albedo climatology. Albedo LUMs of land cover classes defined by the International Geosphere-Biosphere Programme (IGBP) at multiple spatial resolutions were generated. The albedo LUMs included monthly statistics of white-sky (diffuse) and black-sky (direct) albedo for each IGBP class for visible, near-infrared, and shortwave broadband under both snow-free and snow-covered conditions. The LUMs provide high temporal and spatial resolution global albedo statistics without gaps for investigating albedo variations under different land cover scenarios and could be used for land surface modeling.</p><p dir="ltr">Resources in this dataset:</p><p dir="ltr">Resource Title: Multiscale climatological albedo look-up maps (LUMS).</p><p dir="ltr">The albedo look-up maps (LUMs) were built on moderate resolution imaging spectroradiometer (MODIS) bidirectional reflectance distribution function (BRDF)/albedo products and Landsat imagery. Ten years (2001 to 2011) of MODIS BRDF/albedo products were used to generate global albedo climatology. Albedo LUMs of land cover classes defined by the International Geosphere-Biosphere Programme (IGBP) at multiple spatial resolutions were generated. The albedo LUMs included monthly statistics of white-sky (diffuse) and black-sky (direct) albedo for each IGBP class for visible, near-infrared, and shortwave broadband under both snow-free and snow-covered conditions.The zipped file includes:</p><ul><li>readme.docx snow_covered_hierarchical.v3.tar</li><li>snow_covered_LUM.v3.tar snow_free_hierarchical.v3.tar</li><li>snow_free_LUM.v3.tar</li></ul><p dir="ltr"><br></p>

Tags: albedo, ars, brdf, climate-change, data-gov, look-up-map, modis, radiative-forcing
Organization: Department of Agriculture
UAS imagery protocols to map vegetation are transferable between dryland sites across an elevational gradient

<p dir="ltr">This dataset consists of UAS flight images from three sites along an elevation and precipitation gradient within Reynolds Creek Experimental Watershed collected between June 4 and July 9, 2019. The lowest elevation site ('wbs1', 1,425 m) was vegetated by shrub steppe dominated Wyoming big sage (<i>Artemisia tridentata</i> ssp. <i>wyomingensis</i>). Vegetation at the middle elevation site ('los1', 1,680 m) was shrub steppe dominated by low sage (<i>Artemisia arbuscula</i>). Shrub steppe at the highest elevation site ('mbs1', 2,110 m) was dominated by mountain big sage (<i>Artemisia tridentata</i> ssp. <i>vaseyana</i>) and Utah snowberry (<i>Symphoricarpos oreophilus utahensis</i>). A MicaSense RedEdge 3 sensor mounted on a DJI Matrice 600 Pro UAS platform was used to collect multispectral imagery of each site. The drone was flown by a Federal Aviation Administration (FAA) Part 107 certified remote pilot between June 5 and July 9 2019. All flights were completed within two hours of solar noon. The RedEdge is a broadband multispectral sensor: blue (475nm), green (560nm), red (668nm), red edge (717nm), and near-infrared (840nm). The RedEdge sensor was radiometrically calibrated using a reflectance panel before and after each flight. A DJI Phantom 4 with the stock FC330 Red Green Blue (sRGB) camera was flown over each site to collect imagery at a finer spatial resolution to assist with training and test data for vegetation type classification.</p><p dir="ltr">Resources in this dataset:</p><p dir="ltr">Folder containing imagery (.zip) and location (.csv) data. The .zip files contain unprocessed visual (RGB) imagery in<i> </i>.jpg format acquired with a 12-MP DJI (Sony) FC330 camera and unprocessed multispectral, 5-band imagery in <i>.</i>tif format acquired with a MicaSense RedEdge-M sensor. Camera settings and EXIF information are embedded in the imagery files. The .csv files contain ground control point (GCP) labels and coordinate information recorded with an RTK instrument for GCP target (black/white cross) locations at the relevant study areas.</p><p><br></p>

Tags: ars, basal-cover, canopy-cover, data-gov, drone, infrared, leaf-area-index, multispectral-imagery, near-infrared, np215, point-frame, remote-sensing, reynolds-creek-experimental-watershed, sagebrush, uas
Organization: Department of Agriculture