AndreaBozzo/ceres-open-data-index huggingface dataset:
USLE Project

<p>The USLE_1981-4 project data (Universal Soil Loss Equation) was collected from of (9) sites at (4) locations. A Swanson rotating boom simulator with (30) V-Jet 80100 nozzles applied rainfall at two different intensities, 60 or 130 mm/hour depending on how many nozzles were turned on.  Specially designed flumes used with the FW-1 automatic water level recorder were used to obtain continuous runoff flow measurements. The sites in this data set followed a standardized rainfall simulator protocol which future studies by multiple investigators would continue to use. The data set contains rainfall simulator hydrologic and erosion data as well as vegetation and ground data collected in spring and fall from 1981 to 1984.</p>
<p>All sites had (3) treatments with (2) replications.  The vegetative plot manipulation treatments were: clipped, all vegetation clipped at ground surface and removed, bare, vegetation clipped and removed with all rocks larger than 5 mm removed, natural, vegetation left natural, tilled, all vegetation removed and soil tilled. Dataset data was published in Proceedings of the Rainfall Simulator Workshop 1985 Tucson, AZ in table format appendices.  There is also (8) supporting data files with related site data.  The raw data for the New Mexico site is not currently available. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: USLE Project.</p> <p>File Name: USLE Study.ZIP</p><p>Resource Description: USLE_81-4_Read Me file describes: general information, unresolved issues, data set contents, and list of references  and Journal papers.
USLE_81-4_AllData.xls includes: runoff data, foliar cover, and ground cover data.</p></li></ul><p></p>

Tags: autumn, data-collection, hydrology, nozzles, rain, runoff, spring, standard-operating-procedures, vegetation
Organization: Department of Agriculture
Code from: Survival analysis of freezing stress in the North American native perennial flax, Linum lewisii Pursh.

<p><strong>Abstract</strong></p>
<p><br></p>
<p>The expansive range of Lewis flax (Linum lewisii Pursh.), an herbaceous perennial, exposes the species to a diversity of climatic conditions. As interest in the domestication and adoption of perennial crop alternatives grows and interest in this species for natural area restoration continues, the assurance of a commercial plant variety’s ability to endure the full range of possible climatic extremes is paramount. This study examines the freezing tolerance of a geographically representative sampling of 44 Lewis flax accessions at winter temperature extremes experienced in the northern Great Plains of the United States. Survival analysis models were adapted to include temperature exposure, in replacement of ordinal time typically used in such models, to produce statistics evaluating reactions to extreme temperatures that Lewis flax would encounter in our field environments. Our results revealed Lewis flax is more freezing tolerant than previously reported, and revealed four accessions with significantly superior genetic freezing tolerance than the released ‘Maple Grove’ cultivar. Furthermore, regrowth analyses indicate variation among accessions not associated with survival, which could lead to improving regrowth rate and survival simultaneously. These findings and their methodology expand the understanding of Lewis flax adaptation for winter hardiness and offer an efficient, new model that can be used to evaluate freezing tolerance at ordinal temperatures without requiring extensive prior physiological knowledge for a species.</p>
<p><br></p>
<div><strong>Content</strong></div>
<p>GitHub for Gossweiler et al., 2024. Contains R code used for figure generation and SAS code for statistical analyses.</p>

Tags: frost-hardiness, linum-lewisii, perennial-grains
Organization: Department of Agriculture
Climate Shield Cutthroat Trout (50% Brook Trout), 2040 (Feature Layer)

This feature class represents the mid-century (2030-2059) scenario for cutthroat 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 CT_0BRK - CT_100BRK indicate the probabilities of cutthroat 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, climate-change, climate-shield, climatologymeteorologyatmosphere, crowd-sourcing, cutthroat-trout, ectotherm, environment, geostatistics, health, inlandwaters, invasive-species, models, open-data, refugia, salmonid, species-distribution, stream-temperature, trout, usfs
Organization: Department of Agriculture
The RHEM Web Tool

<p>The RHEM Web Tool is a web-based interface for the Rangeland Hydrology and Erosion Model (RHEM). The interface allows users to input commonly known rangeland characteristics and use parameter estimation equations to construct model input files and run the RHEM model.</p>
<p>RHEM is designed to provide sound, science-based technology to model and predict runoff and erosion rates on rangelands and to assist in assessing rangeland conservation practice effects. RHEM is a newly conceptualized, process-based erosion prediction tool specific for rangeland application, based on fundamentals of infiltration, hydrology, plant science, hydraulics and erosion mechanics.</p>
<p>This web application was built with the following goals in mind:</p>
<ul>
<li>Simplify the use of RHEM</li>
<li>Manage user sessions</li>
<li>Centralize scenario results (model runs)</li>
<li>Compare scenario results</li>
<li>Risk assessment</li>
<li>
<p>Provide tabular and graphical reports</p>
<div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: The RHEM Web Tool.</p> <p>File Name: Web Page, url: <a href="https://dss.tucson.ars.ag.gov/rhem/" target="_blank">https://dss.tucson.ars.ag.gov/rhem/</a> </p><p>Main tool web site</p></li></ul>
</li>
</ul>

Tags: ars, data-gov, np211, np215
Organization: Department of Agriculture
Data from: Proteomics analysis reveals novel host molecular mechanisms associated with thermotherapy of 'Ca. Liberibacter asiaticus'-infected citrus plants

<p>Background
Citrus Huanglongbing (HLB), which is linked to the bacterial <em>Candidatus</em> pathogen '<em>Ca.</em> Liberibacter asiaticus' (Las), is the most devastating disease of citrus plants, and longer-term control measures via breeding or genetic engineering have been unwieldy because all cultivated citrus species are susceptible to the disease. However, the degree of susceptibility varies among citrus species, which has prompted efforts to identify potential Las resistance/tolerance-related genes in citrus plants for application in breeding or genetic engineering programs. Plant exposure to one form of stress has been shown to serendipitously induce innate resistance to other forms of stress and a recent study showed that continuous heat treatment (40 to 42 °C) reduced Las titer and HLB-associated symptoms in citrus seedlings. The goal of the present study was to apply comparative proteomics analysis via 2-DE and mass spectrometry to elucidate the molecular processes associated with heat-induced mitigation of HLB in citrus plants. Healthy or Las-infected citrus grapefruit plants were exposed to room temperature or to continuous heat treatment of 40 °C for 6 days.</p>
<p>Results
An exhaustive total protein extraction process facilitated the identification of 107 differentially-expressed proteins in response to Las and/or heat treatment, which included a strong up-regulation of chaperones including small (23.6, 18.5 and 17.9 kDa) heat shock proteins, a HSP70-like protein and a ribulose-1,5-bisphosphate carboxylase oxygenase (RuBisCO)-binding 60 kDa chaperonin, particularly in response to heat treatment. Other proteins that were generally down-regulated due to Las infection but up-regulated in response to heat treatment include RuBisCO activase, chlorophyll a/b binding protein, glucosidase II beta subunit-like protein, a putative lipoxygenase protein, a ferritin-like protein, and a glutathione S-transferase.</p>
<p>Conclusions
The differentially-expressed proteins identified in this study highlights a premier characterization of the molecular mechanisms potentially involved in the reversal of Las-induced pathogenicity processes in citrus plants and are hence proposed targets for application towards the development of cisgenic Las-resistant/tolerant citrus plants. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Appendix 1. Mascot match results and peptide sequences of the 130 differentially-expressed spots - Download Excel.</p> <p>File Name: 12870_2016_942_MOESM1_ESM.xlsx, url: <a href="https://static-content.springer.com/esm/art:10.1186/s12870-016-0942-x/MediaObjects/12870_2016_942_MOESM1_ESM.xlsx">https://static-content.springer.com/esm/art:10.1186/s12870-016-0942-x/MediaObjects/12870_2016_942_MOESM1_ESM.xlsx</a> </p></li></ul><p></p>

Tags: ars, citrus-huanglongbing, data-gov, hlb, las
Organization: Department of Agriculture
Data from: Detection of Vesicular Stomatitis Virus Indiana from Insects Collected during the 2020 Outbreak in Kansas, USA

<p>Vesicular stomatitis (VS) is a reportable viral disease which affects horses, cattle, and pigs in the Americas. Outbreaks of vesicular stomatitis virus New Jersey serotype (VSV-NJ) in the United States typically occur on a 5–10-year cycle, usually affecting western and southwestern states.</p>
<p><br></p>
<p>In 2019–2020, an outbreak of VSV Indiana serotype (VSV-IN) extended eastward into the states of Kansas and Missouri for the first time in several decades, leading to 101 confirmed premises in Kansas and 37 confirmed premises in Missouri. In order to investigate which vector species contributed to the outbreak in Kansas, we conducted insect surveillance at two farms that experienced confirmed VSV-positive cases, one each in Riley County and Franklin County. Centers for Disease Control and Prevention miniature light traps were used to collect biting flies on the premises. Two genera of known VSV vectors, Culicoides biting midges and Simulium black flies, were identified to species, pooled by species, sex, reproductive status, and collection site, and tested for the presence of VSVIN RNA by RT-qPCR. </p>
<p><br></p>
<p>In total, eight positive pools were detected from Culicoides sonorensis (1), Culicoides stellifer (3), Culicoides variipennis (1), and Simulium meridionale (3). The C. sonorensis- and C. variipennis-positive pools were from nulliparous individuals, possibly indicating transovarial or venereal transmission as the source of virus. This is the first report of VSV-IN in field caught C. stellifer and the first report of either serotype in S. meridionale near outbreak premises. These results improve our understanding of the role midges and black flies play in VSV epidemiology in the United States and broadens the scope of vector species for targeted surveillance and control.</p>

Tags: culicoides, indiana, kansas, rhabdoviridae, simulium, vesicular-stomatitis-virus, vesiculovirus, vsv-in
Organization: Department of Agriculture
Climate Shield Cutthroat Trout (50% Brook Trout), 1980 (Feature Layer)

This feature class represents the historical (1970-1999) scenario for cutthroat 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 CT_0BRK - CT_100BRK indicate the probabilities of cutthroat 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, climate-change, climate-shield, climatologymeteorologyatmosphere, crowd-sourcing, cutthroat-trout, ectotherm, environment, geostatistics, health, inlandwaters, invasive-species, models, open-data, refugia, salmonid, species-distribution, stream-temperature, trout, usfs
Organization: Department of Agriculture
Conservation Practice Effectiveness (CoPE) Database

<p>The Conservation Practice Effectiveness Database compiles information on the effectiveness of a suite of conservation practices. This database presents a compilation of data on the effectiveness of innovative practices developed to treat contaminants in surface runoff and tile drainage water from agricultural landscapes. Traditional conservation practices such as no-tillage and conservation crop rotation are included in the database, as well as novel practices such as drainage water management, blind inlets, and denitrification bioreactors. This will be particularly useful to conservation planners seeking new approaches to water quality problems associated with dissolved constituents, such as nitrate or soluble reactive phosphorus (SRP), and for researchers seeking to understand the circumstances in which such practices are most effective. Another novel feature of the database is the presentation of information on how individual conservation practices impact multiple water quality concerns. This information will be critical to enabling conservationists and policy makers to avoid (or at least be aware of) undesirable tradeoffs, whereby great efforts are made to improve water quality related to one resource concern (e.g., sediment) but exacerbate problems related to other concerns (e.g., nitrate or SRP). Finally, we note that the Conservation Practice Effectiveness Database can serve as a source of the soft data needed to calibrate simulation models assessing the potential water quality tradeoffs of conservation practices, including those that are still being developed. This database is updated and refined annually. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: 2019 Conservation Practice Effectiveness (CoPE) Database.</p> <p>File Name: Conservation_Practice_Effectiveness_2019.xlsx</p><p>Resource Description: This version of the database was published in 2019.</p></li></ul><p></p>

Tags: ars, data-gov, np211
Organization: Department of Agriculture
Data from: Infestation ratings database for soybean aphid on early-maturity wild soybean lines

<p>Soybean aphid (<em>Aphis glycines</em> Matsumura; SA) is a major invasive pest of soybean [<em>Glycine max</em> (L.) Merr.] in northern production regions of North America. Although insecticides are currently the main method for controlling this pest, SA-resistant cultivars are being developed to sustainably manage SA in the future. The viability of SA-resistant cultivars may depend on identifying a diverse set of resistance genes from screening various germplasm sources, including wild soybean (<em>Glycine soja</em> Siebold and Zucc.), the progenitor of cultivated soybean. Data consisted of infestation ratings generated for a total of 337 distinct plant introduction lines of wild soybean that were exposed to avirulent SA biotype 1 for 14 d in 25 separate tests. Individual plants of the test lines were given a common rating by two researchers, based on a rating scale that progressed from 1=0 to 50, 2=51 to 100, 3=101 to 150, 4=151 to 200, 5=201 to 250, and 6 with >250 SA per test plant. Public dissemination of this dataset will allow for further analyses and evaluation of resistance among the test lines. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Infestation ratings for individual plants of various wild soybean lines.</p> <p>File Name: Web Page, url: <a href="https://ars.els-cdn.com/content/image/1-s2.0-S2352340917304432-mmc2.xlsx">https://ars.els-cdn.com/content/image/1-s2.0-S2352340917304432-mmc2.xlsx</a> </p><p>MS Excel spreadsheet showing infestation ratings for individual plants of 337 distinct plant introduction (PI) wild soybean lines following 14 d of exposure to SA.</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, crop-ancestors, data-gov, host-plant-resistance, resistance-screening
Organization: Department of Agriculture
Data from: Data on morphological features of mycosis induced by Colletotrichum nymphaeae and Lecanicillium longisporum on citrus orthezia scale

<p>Symptoms of mycosis induced by two native fungal entomopathogens of the citrus orthezia scale, <em>Praelongorthezia praelonga</em> (Hemiptera: Ortheziidae), an important pest of citrus orchards, are described. The data presented in this article are related to the article entitled "Seasonal prevalence of the insect pathogenic fungus <em>Colletotrichum nymphaeae</em> in Brazilian citrus groves under different chemical pesticide regimes". The endemic fungal pathogen, <em>C. nymphaeae</em>, emerges through the thin cuticular intersegmental regions of the citrus orthezia scale body revealing orange salmon-pigmented conidiophores bearing conidial masses, as well as producing rhizoid-like hyphae that extend over the citrus leaf. By contrast, nymphs or adult females of this scale insect infected with <em>Lecanicillium longisporum</em> exhibit profuse outgrowth of bright white-pigmented conidiophores with clusters of conidia emerging from the insect intersegmental membranes, and mycosed cadavers are commonly observed attached to the leaf surface by hyphal extensions. These morphological differences are important features to discriminate these fungal entomopathogens in citrus orthezia scales.</p>
<div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Data on morphological features of mycosis induced by Colletotrichum nymphaeae and Lecanicillium longisporum on citrus orthezia scale.</p> <p>File Name: Web Page, url: <a href="https://www.sciencedirect.com/science/article/pii/S2352340916302967" target="_blank">https://www.sciencedirect.com/science/article/pii/S2352340916302967</a> </p><p><em>Data in Brief</em> article with photographs and microphotographs portraying typical signs of mycosis of two fungal pathogens infecting the citrus orthezia scale.</p></li></ul>

Tags: ars, ascomycetous-fungi, citrus-orthezia-scale, colletotrichum-nymphaeae, data-gov, praelongorthezia-praelonga
Organization: Department of Agriculture
Data from: Genome Sequence of the Thermotolerant Foodborne Pathogen Salmonella enterica Serovar Senftenberg ATCC 43845 and Phylogenetic Analysis of Loci Encoding Increased Protein Quality Control Mechanisms

<p><em>Salmonella enterica</em> subsp. <em>enterica</em> bacteria are important foodborne pathogens with major economic impact. Some isolates exhibit increased heat tolerance, a concern for food safety. Analysis of a finished-quality genome sequence of an isolate commonly used in heat resistance studies, <em>S. enterica</em> subsp. <em>enterica</em> serovar Senftenberg 775W (ATCC 43845), demonstrated an interesting observation that this strain contains not just one, but two horizontally acquired thermotolerance locus homologs. These two loci reside on a large 341.3-kbp plasmid that is similar to the well-studied IncHI2 R478 plasmid but lacks any antibiotic resistance genes found on R478 or other IncHI2 plasmids. As this historical <em>Salmonella</em> isolate has been in use since 1941, comparative analysis of the plasmid and of the thermotolerance loci contained on the plasmid will provide insight into the evolution of heat resistance loci as well as acquisition of resistance determinants in IncHI2 plasmids. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Supplementary Material.</p> <p>File Name: "inline-supplementary-material-1.pdf", url: <a href="https://msystems.asm.org/content/msys/2/1/e00190-16/DC1/embed/inline-supplementary-material-1.pdf">https://msystems.asm.org/content/msys/2/1/e00190-16/DC1/embed/inline-supplementary-material-1.pdf</a> </p><p>The map of plasmid pSSE ATCC-43845 is shown, with the thermotolerance locus islands indicated as orange regions. Base modification signals generated by BaseModFunctions.v.2.1.R and Circos are overlaid on the plasmid map. Qmod values are height proportional to the interpulse distance ratio for each of the modified bases on the positive strand (red outmost track) and negative strand (red innermost track). Green hash marks correspond to the CAGAG motifs present on the plasmid. </p>
<p>The map of plasmid pSSE ATCC-43845 is shown, with the thermotolerance locus islands indicated as orange regions. Base modification signals generated by BaseModFunctions v2.1.R and Circos are overlaid on the plasmid map. Qmod values are height proportional to the interpulse distance ratio for each of the modified bases on the positive strand (red outmost track) and negative strand (red innermost track). Blue hash marks correspond to the GATC motifs present on the plasmid.</p></li></ul><p></p>

Tags: ars, data-gov, np108, phylogenetic-analysis, thermotolerance-loci, thermotolerant-foodborne-pathogen
Organization: Department of Agriculture
USDA Agricultural Research Service- Patented Crop Production and Crop Protection Technologies

<p>Recent USDA/ARS patented technologies on crop production and protection 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: Crop Production and Protection - Available Technologies, June 2018.</p> <p>File Name: Crop Production and Protection.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: Crop Production and Protection - June 2018.</p> <p>File Name: Crop_Production_and_Protection.csv</p><p>Resource Description: Listing of technologies for increased crop productivity, economically and environmentally sustainable methods of crop production, and protection from plant diseases and pests. 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: ars, attractants, bacterial, breeding, crops, data-gov, equipment, fungal, infection, insects, irrigation, pesticides, plants, repellant, soil, sorghum, strains, subsoil, trees, virus
Organization: Department of Agriculture