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

<p>AphID includes a key to the 66 most polyphagous and cosmopolitan aphid species. The key for slide-mounted specimens has 132 end points. The key does not include males, oviparae, or immatures. It may not work for all fundatrices or alatae and apterae from primary hosts (for those species with host alternation). AphID includes all 38 aphid species in the dichotomous keys to polyphagous aphids in the three seminal works by Roger Blackman & Victor Eastop (1994, 2000, 2006). The remaining aphids represent the 28 species most frequently intercepted at United States ports of entry that are not already represented on the Blackman & Eastop list. AphID offers users detailed descriptions of morphological features critical to identifying aphids along with annotated photographs to help illustrate each feature. Separate pages are devoted to suites of features, for example all features of the antenna are found on the same page. The morphology pages are crosslinked with a detailed glossary.</p>
<div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Aphidnet.</p> <p>File Name: Web Page, url: <a href="http://aphid.aphidnet.org/index.php" target="_blank">http://aphid.aphidnet.org/index.php</a> </p></li></ul>

Tags: ars, data-gov, np104, online-database
Organization: Department of Agriculture
iFarm Record Keeper

<p>The easy to use iFARM Field Record Keeper spreadsheet-based tool was designed to help farmers keep track of field operational records. The tool is designed to be farm specific allowing the user inputs to be specific to their operation. Drop down menus are created from user input including field names, crops, tillages, fertilizer, chemicals, landlords, and storage locations. This information needs only to be entered once. After initial setup each field will be saved as a file with the completed information. Up to four spray operations can be entered per field with the spray reports satisfying current Colorado Department of Agriculture and EPA requirements for Restricted Use Pesticide (RUP). The one page field report meets the fundamental requirements for the current Conservation Security Program (CSP) requirements for record keeping.  </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: iFarm Record Keeper.</p> <p>File Name: Web Page, url: <a href="https://www.ars.usda.gov/research/software/download/?softwareid=242&modecode=30-12-30-25">https://www.ars.usda.gov/research/software/download/?softwareid=242&modecode=30-12-30-25</a> </p><p>download page</p></li></ul><p></p>

Tags: colorado, conservation-security-program, crops, farmers, farms, fertilizers, information-needs, models, pesticides, plant-science-and-plant-products
Organization: Department of Agriculture
<b>Absorption of visible light by floral anthocyanins increases flower temperatures: implications for a warmer world</b>

<p dir="ltr">With rising global temperatures, understanding the mechanisms that influence plant thermal energy balance are critical to forecasting plant and pollinator responses. Flower temperatures impact visitation by insect pollinators, and several temperature-sensitive processes central to plant reproduction. Anthocyanin pigments absorb strongly in visible and ultraviolet wavebands, but clear support for a warming effect of pigments on flowers has remained elusive. We used infrared imaging to measure petal temperatures of horticultural varieties of plants differing in floral anthocyanin content. Excised sets of flowers were mounted perpendicularly to the sun, and exposed to direct ambient sunlight filtered either through Aclar (UV-transparent) or Courtguard (UV-opaque) under low-wind (< 1 m s-1) conditions. Petal temperatures were measured after one minute, and treatment order alternated between replicates. Results showed that pigmented flowers were consistently significantly warmer than white conspecifics (2.9°C warmer on average for lightly-pigmented varieties, 5.3°C warmer for darkly-pigmented). Most species showed no significant difference in petal temperatures under UV inclusion versus exclusion, indicating most warming by anthocyanins can be attributed to absorption of visible light. UV-enhanced warming was observed in some species, which could be due to the presence of side groups that enhance UV-absorption by the anthocyanin molecules. However, these differences were slight (always <1°C), and usually white varieties exhibited differences as well, suggesting other flavonoids too may contribute to floral warming. Additional experiments focusing on dark pink and white varieties of Impatiens x hybrida corroborated previous reports that the most dramatic warming effects occur under high-light, low-wind conditions. In the context of climate change, warmer temperatures could potentially drive the replacement of darkly-colored flowers with more lightly-colored morphs (or species), especially if flower temperatures exceed thermal maxima for fertilization and seed development. This pressure may be especially strong in species with floral morphologies conducive to heat trapping or in low-wind environments (e.g., growing in dense stands or close to the ground). Changes in flower color could also potentially induce shifts in pollinator communities, which could have community-scale effects.</p>

Tags: climate-change, flower-color, heat-stress, pollinators, temperature-stress
Organization: Department of Agriculture
Data from: Impact of larval food source on the stability of the <i>Bactrocera dorsalis </i>microbiome

<p dir="ltr">We conducted a fly rearing experiment to characterize diet-induced changes in the microbiome of female <i>Bactrocera dorsalis</i>. In order to explicitly investigate the impacts of larval diet on the microbiome, including potential stable bacterial constituents of <i>B. dorsalis</i>, we performed 16S rRNA sequencing on the gut tissues of teneral female flies reared from 4 different host fruits (guava, mango, papaya, and rose-apple) infested using a single cohort of wild <i>B. dorsalis</i> that emerged from tropical almond (mother flies). We provide processed data and R code for our analysis.</p><p dir="ltr">Raw data (.fastq files) for analysis are located at NCBI SRA under accession number PRJNA1061202</p>

Tags: 16s-amplicon-analysis-code, gut, insect, microbiome, reproduction
Organization: Department of Agriculture
Stewardship Contracting: Line (Feature Layer)

Depicts the linear activities within Stewardship Contracting Project Boundary. Activities are implemented through stewardship contracts or agreements and are self-reported by Forest Service Units through the FACTS database. <a href='https://data.fs.usda.gov/geodata/edw/edw_resources/meta/S_USA.Activity_StwrdshpCntrctng_LN.xml' target='_blank' rel='nofollow ugc noopener noreferrer'>Metadata</a>

Tags: activities, environment, forest-management, open-data, recovery, resiliency, safety, stewardship-contracting
Organization: Department of Agriculture
WeedCast Version 4

<p><strong>WeedCast Version 4</strong></p>
<p>The WeedCast Software Suite is a decision aid that currently includes the WeedCast and WheatScout models. These models were created by the USDA ARS and the University of Wisconsin. The software is written in Java and is free to download and use. The source code is released under the GPL.</p>
<p><strong>What is WeedCast?</strong></p>
<p>WeedCast is an easy to use software program that forecasts three types of weed growth: Emergence Potential, Emergence Timing, and Seedling Height. The forcasted data provides valuable information that can be used to aid in making weed management decisions. WeedCast is designed to function with a minimal amount of input.</p>
<p>Select the weed or weeds of interest and the following site properties using list boxes: Last Year's Crop, Tillage System, Soil Type, and Soil Water Content</p>
<p>Enter your local weather information using a simple spreadsheet editor.</p>
<p>Work in progress: Download your weather data!</p>
<p>Enter a date range and click view output to see your forcasts.</p>
<p>Resulting data is displayed in a spreadsheet form and may be graphed from within the program.</p>
<p>What is WheatScout?</p>
<p>WheatScout is a decision aid that predicts the effects of a variety of herbicides on green foxtail and wild oat in wheat crops. It requires similar information to Weedcast, but also requires some scouting information.</p>
<p>Download WeedCast 4.0 now.</p>
<p>In addition, you may be interested in viewing our:</p>
<ul>
<li>The GPL v2 (under which this software is licensed)</li>
<li>
<p>WeedCast Source Code will be coming soon</p>
<div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: WeedCast Version 4.</p> <p>File Name: Web Page, url: <a href="https://www.ars.usda.gov/research/software/download/?softwareid=112&modecode=50-60-05-00" target="_blank">https://www.ars.usda.gov/research/software/download/?softwareid=112&modecode=50-60-05-00</a> </p><p>download page</p></li></ul>
</li>
</ul>

Tags: ars, data-gov, np305
Organization: Department of Agriculture
Data from: Biomarkers associated with vaccine-associated enhanced respiratory disease following influenza A virus infection in swine

<p dir="ltr">The dataset contains measurements from a swine research study evaluating for biomarkers with influenza A vaccine associated enhanced respiratory disease. Hematology, plasma chemistry, serum antibody, and acute phase proteins in blood and viral titers in nasal swabs were evaluated over five days following infection. Additionally at 5 days post infection tissues were evaluated for lesions and bronchoalveolar lavage fluid collected for cytokine and viral assessment to develop a panel of potential biomarkers. </p>

Tags: biomarkers, influenza-a-viruses-iavs, influenza-vaccine, swine, vaccine-associated-enhanced-respiratory-disease-vaerd
Organization: Department of Agriculture
Data from: Hemipteran Species in Row Crops of the Brazos River Bottom in Central Texas

<p dir="ltr">Stink bug and plant bug species, commonly known as hemipterans, continue as major pests of cotton and other row crops in the U.S. Cotton Belt, but the composition of hemipterans has changed substantially over the past decade. Determining species composition is critical to understanding and managing these pests. Thus, a 2-year study was conducted to identify hemipteran species within corn, sorghum, cotton, and soybean in the Brazos River Bottom production area of Central Texas. Overall, 18 species of hemipterans were collected across all four crops. The brown stink bug and rice stink bug were the predominant species encountered in corn and sorghum, respectively, in both years of the study. The tarnished plant bug was the prevalent species in cotton during 2021, but the brown stink bug was predominant in 2022. Soybeans possessed the highest number of species, with the southern green stink bug as the prevalent species. Given that several of the hemipteran species were encountered in all four crops and are known to transmit disease-causing pathogens of row crops, our findings suggest the need for due diligence in monitoring these pest species in the major crops produced in Central Texas.</p>

Tags: corn, cotton, euschistus-servus, hemiptera, lygus-lineolaris, nezara-viridula, oebalus-pugnax, sorghum, soybeans, species-composition
Organization: Department of Agriculture
<b>Using calorimetry to measure metabolic heat in two dipteran species, </b><b><i>Tetanops myopaeformis</i></b><b> and </b><b><i>Drosophila melanogaster</i></b><b>, exposed to ecologically relevant low temperatures</b>

<p dir="ltr">This dataset contains the raw data (unsubstracted) and the machine normalized (subtracted) output files from calorimetry experiments measuring metabolic heat flow of the sugarbeet root maggot. Both isothermal and scanning calorimetry were employed in this project. The metabolism of the larvae was measured over an ecologically relevant temperature from 10 to -16°C. Quality control graphs are provided for each of the runs. The sugarbeet root maggots were examined with two different types of calorimeters, a model FDCS196 (Linkam Scientific, UK) and a model DSC7000X (Hitachi Global, Japan). The model FDCS196 calorimeter filmed the larvae during the runs, documenting the larvae’s ability to remain mobile down to temperatures just above their freezing point.</p><p dir="ltr">Despite their fundamentally different designs and algorithms, the two calorimeters gave congruent results. Both calorimeters unexpectedly revealed that the larvae’s metabolic heat flow increased as the temperature decreased. To confirm that our results were not due to equipment error or some misunderstanding on our part, we investigated a similar phenomenon in developing <i>Drosophila melanogaster</i> larvae on the model DSC7000X calorimeter. They gave the same result as the sugarbeet root maggots: increased metabolic heat flow at lower temperatures. This increase in heat flow occurs under both normoxic and anoxic conditions for both species.</p>

Tags: anoxia, calorimetry-dsc, diapause, dormancy, freeze-tolerant, metabolic-rate, normoxia, np305, overwintering, stress, sugarbeet-root-maggot, tetanops-myopaeformis
Organization: Department of Agriculture
US Federal LCA Commons Life Cycle Inventory Unit Process Template

<p>An excel template with data elements and conventions corresponding to the openLCA unit process data model. Includes LCA Commons data and metadata guidelines and definitions </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: READ ME - data dictionary.</p> <p>File Name: lcaCommonsSubmissionGuidelines_FINAL_2014-09-22.pdf</p></li><br><li><p>Resource Title: US Federal LCA Commons Life Cycle Inventory Unit Process Template.</p> <p>File Name: FedLCA_LCI_template_blank EK 7-30-2015.xlsx</p><p>Resource Description: Instructions: This template should be used for life cycle inventory (LCI) unit process development and is associated with an openLCA plugin to import these data into an openLCA database. See www.openLCA.org to download the latest release of openLCA for free, and to access available plugins.</p></li></ul><p></p>

Tags: ars, data-gov, earth-science-human-dimensions-environmental-governance-management-environmental-assessments, excel, nal-ksd
Organization: Department of Agriculture
Terrestrial Condition Assessment (TCA) Climate Exposure Precipitation Spring (Map Service)

The difference in Spring precipitation (in) between the reference time period of 1900-2014 and the current time period 2015-2019. Spring months include March, April, May. Data used are sourced from PRISM, Oregon State University. Data were summarized at the Subsection scale of the USFS National Hierarchy of Ecological Units and applied to the corresponding LTA.

Tags: gtac, open-data, precipitation, tca, usfs
Organization: Department of Agriculture
Data from: Characterizing Host microRNA: Virus Interactions of Orthoavulavirus javaense

<p dir="ltr">This dataset accompanies manuscript "Characterizing Host microRNA: Virus Interactions of Orthoavulavirus javaense" published in the journal Viruses on 11/07/2024. In this manuscript, the authors identified regions in the genome of Orthoavulavirus javaense, the causative of Newcastle disease that can modify function of host microRNAs. They postulate that viral sequences can either mimic host microRNA activity (viral seed mimics) or inhibit (viral seed sponges) it via sequence dependent sequestration. The data suggest that virulent "velogenic" strains of the virus harbor more viral seed mimics vs lentogenic viral genomes that harbor more sponges. The excel file contains tables showing the original BLASTN hits, the shortlisted viral seed mimics and seed sponges and individual tables for viral gene and intergenic region specific hits. The workbook also contains summaries of all the data finally graphed in the manuscript online as well as a list of all accession numbers used in the analysis. </p><p dir="ltr">The sequences used in these analyses were obtained from NCBI nucleotide and represent full length genomes corresponding to the different pathotypes of NDV. </p>

Tags: micrornas, orthoavulavirus-javaense, phosphoprotein, secondary-structure, viral-seed-mimics, viral-seed-sponges
Organization: Department of Agriculture
Stuttgart local weather data archive

<p>Weather data from two weather stations at Stuttgart Rice Research and Extension center are archived.  Current air temperature, relative humidity, wind speed, solar radiation and soil temperature data are provided by station and are displayed and archived either hourly or daily.  Historical weather data goes back to 2008. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Weather Station Data.</p> <p>File Name: Web Page, url: <a href="https://www.ars.usda.gov/southeast-area/stuttgart-ar/dale-bumpers-national-rice-research-center/docs/weather-station-data/">https://www.ars.usda.gov/southeast-area/stuttgart-ar/dale-bumpers-national-rice-research-center/docs/weather-station-data/</a> </p></li></ul><p></p>

Tags: air-temperature, ars, data-gov, relative-humidity, soil, solar-radiation, spreadsheet, stuttgart, temperature, weather, wind-speed
Organization: Department of Agriculture
NLEAP GIS 5.0

<p>NLEAP GIS 5.0 can help users identify hot spots across the landscape and identify management practices that can increase nitrogen use efficiency. A Nitrogen Trading Tool (NTT) analysis can be conducted to determine the potential benefits of implementing best management practices and the quantity of nitrogen savings that could potentially be traded in future air or water quality markets. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: NLEAP GIS 5.0.</p> <p>File Name: Web Page, url: <a href="https://www.ars.usda.gov/research/software/download/?softwareid=428&modecode=30-12-30-15">https://www.ars.usda.gov/research/software/download/?softwareid=428&modecode=30-12-30-15</a> </p><p>download page</p></li></ul><p></p>

Tags: air, best-management-practices, computer-software, landscapes, markets, natural-resources-earth-and-environmental-sciences, nutrient-use-efficiency, water-quality
Organization: Department of Agriculture
WeedSite

<p>Software for learning about the benefits of site-specific weed management compared to a uniform herbicide application. No GIS software is needed. The benefits are predicted from weed maps drawn by the user.</p>
<p>Herbicide use may be reduced 30 to 80% without impacting crop yield with site-specific weed management.  Herbicide use is varied within a field to match the variation in the weed population.  However, it is not always clear that the reduction in herbicide and other benefits of site-specific weed management will justify the cost and that future weed control will not be compromised.  The outcomes of site-specific weed management vary with the composition and spatial distribution of the weed population, possible herbicide treatments and the resolution of variable management. WeedSite software was developed for predicting the benefits of postemergence site-specific weed management in irrigated corn and how the benefits vary with the weed population and the approach for variable herbicide application. Georeferenced weed maps and GIS software are not needed. Net gain from site-specific weed management, area of the field not treated, herbicide use and cost, yield loss from weed competition, and weeds left in the field are all calculated from hand drawn weed maps. Results can be mapped. WeedSite is useful for educating growers, agricultural consultants and students about the potential benefits of postemergence site-specific weed management because predictions are consistent with what is known about the variation in the benefits of site-specific weed management. Also, users specify the distribution of weeds in a field, so the results may be more relevant to them than information from research studies.</p>
<p>The installation package includes a user's manual. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: WeedSite.</p> <p>File Name: Web Page, url: <a href="https://www.ars.usda.gov/research/software/download/?softwareid=181&modecode=30-12-30-20">https://www.ars.usda.gov/research/software/download/?softwareid=181&modecode=30-12-30-20</a> </p><p>download page</p></li></ul><p></p>

Tags: consultants, corn, crop-weed-competition, crop-yield, geographic-information-systems, georeferencing, growers, herbicides, irrigation, learning, models, pesticide-application, prediction, students, weed-control
Organization: Department of Agriculture
Data from: Putative neofunctionalization of a Poales-specific EXO70 clade

<p dir="ltr">EXO70s are uniquely expanded in land plants compared to all other eukaryotic lineages. The functional implications of this expansion and diversification on the conserved role of EXO70 as a subunit of the octameric exocyst complex have remained unresolved. We previously demonstrated barley (<i>Hordeum vulgare</i>) EXO70FX12, a member of the monocot-specific EXO70FX clade, is required for resistance to wheat stripe rust in conjunction with the leucine-rich repeat receptor kinase (LRR-RK) HvPUR1. Through phylogenetic analysis, we identified unique features of the EXO70FX clade, leading us to hypothesize that this clade experienced neofunctionalization. Using structural predictions and protein-protein interaction assays, we demonstrate that HvEXO70FX12 lost the ability to serve as a subunit within the exocyst complex. We predict that the EXO70FX clade has largely lost exocyst association and represents a novel acquisition that emerged during Poales diversification for immunity.</p><p dir="ltr">This data set contains data for Bergum et al. (2024) "Putative neofunctionalization of a Poales-specific EXO70 clade" that includes raw data, uncropped images, FASTA files, multiple sequence alignments, phylogenetic trees, and scripts used for data analysis and figure preparation. Folder organization is based on individual figures and tables.</p>

Tags: exo70, exocyst-complex, grass-evolution, green-plant-evolution
Organization: Department of Agriculture
Legume Information System

<p>The Legume Information System (<a href="https://legumeinfo.org">legumeinfo.org</a>) is the USDA-ARS genetics and genomics database for legume crops and relatives. Researchers can also submit their data directly. LIS houses data for more than a dozen species such as common bean and chickpea, peanut, and soybean, with genome sequences, genes and predicted functions, families of related genes, views of evolutionary relationships between genomic regions, genetic maps, markers, and links to germplasm resources. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Legume Information System.</p> <p>File Name: Web Page, url: <a href="https://legumeinfo.org">https://legumeinfo.org</a> </p><p>Website pointer for Legume Information System</p></li></ul><p></p>

Tags: adzuki-bean, ars, beans, chickpea, data-gov, legumes, lotus, lupin, medicago, mung-bean, np301, online-database, peanut, pigeonpea, red-clover, soybean
Organization: Department of Agriculture