AndreaBozzo/ceres-open-data-index huggingface dataset:
Data from: Bran data of total flavonoid and total phenolic contents, oxygen radical absorbance capacity, and profiles of proanthocyanidins and whole grain physical traits of 32 red and purple rice varieties

<p>Phytochemicals in red and purple bran rice have potential health benefit to humans. The phytochemicals in brans of 32 red and purple global rice varieties are determined. The description of the origin and physical traits of the whole grain (color, length, width, thickness and 100-kernel weight) of this germplasm collection are provided along with data of total flavonoid and total phenolic contents, oxygen radical absorbance capacity and total proanthocyanidin contents. The contents and proportions of individual oligomers, from degree of polymerization of monomers to 14-mers, and polymers in bran of these 32 rice (<em>Oryza sativa</em> L.) varieties are presented (DOI: <a href="http://dx.doi.org/10.1016/j.foodchem.2016.04.004">http://dx.doi.org/10.1016/j.foodchem.2016.04.004</a>)  </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Bran data of total flavonoid and total phenolic contents, oxygen radical absorbance capacity, and profiles of proanthocyanidins and whole grain physical traits of 32 red and purple rice varieties.</p> <p>File Name: Web Page, url: <a href="https://www.sciencedirect.com/science/article/pii/S235234091630289X">https://www.sciencedirect.com/science/article/pii/S235234091630289X</a> </p><p><em>Data in Brief</em> article providing the description of the origin and physical traits of the whole grain (color, length, width, thickness and 100-kernel weight) of this germplasm collection, along with data of total flavonoid and total phenolic contents, oxygen radical absorbance capacity, and total proanthocyanidin contents.</p></li></ul><p></p>

Tags: ars, data-gov, phytochemicals
Organization: Department of Agriculture
Hyalella azteca Official Gene Set v1.0

<p>The <em>Hyalella azteca</em> genome was recently sequenced and annotated as part of the i5k pilot project by the Baylor College of Medicine.  The <em>Hyalella azteca</em> research community has manually reviewed and curated the computational gene predictions and generated an official gene set, OGSv1.0. The OGS is an integration of automatic gene predictions from Maker with manual annotations by the research community (via the Apollo manual annotation software).</p>
<p>If you wish to use this dataset, please follow the Baylor College of Medicine's conditions for data use: <a href='\https://www.hgsc.bcm.edu/bcm-hgsc-conditions-use\"'>https://www.hgsc.bcm.edu/bcm-hgsc-conditions-use</a></p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Hyalella azteca Official Gene Set OGSv1.0.</p> <p>File Name: hyaazt_OGS_v1-0.tar.gz</p><p>Resource Description: </p><p>The attached tar.gz archive (hyaazt_OGS_v1-0.tar.gz) contains the following files:</p><p>hyaazt_OGSv1.0_cds.fa. CDS sequences of <em>Hyalella azteca</em> genome annotations OGSv1.0.</p><p>hyaazt_OGSv1.0_pep.fa. Amino acid sequences of <em>Hyalella azteca</em> genome annotations OGSv1.0.</p><p>hyaazt_OGSv1.0_trans.fa. cDNA sequences of <em>Hyalella azteca</em> genome annotations OGSv1.0.</p><p>hyaazt_OGSv1.0.gff. Gff3 of all gene predictions of <em>Hyalella azteca</em> genome annotations OGSv1.0</p><p>hyaazt_Manual2OGSv1.0_id_mapping.txt. A mapping file describing ID and name updates from dataset <em>Hyalella azteca</em> genome annotations v0.5.3.</p><p>readme.txt. This file briefly describes how the dataset Hyalella azteca Official Gene Set OGSv1.0 was generated.</p><p></p></li></ul>

Tags: ars, arthropods, data-gov, hyalella-azteca, i5k
Organization: Department of Agriculture
Hyalella azteca Official Gene Set v1.3

<p>This dataset presents the <em>Hyalella azteca</em> Official Gene Set OGSv1.3. This is an update to Official Gene Sets OGSv1.0 and OGSv1.2. Official Gene Set hyaazt_OGSv1.3 was generated by mapping hyaazt_OGSv1.2 (<a href="https://i5k.nal.usda.gov/bio_data/836772">https://i5k.nal.usda.gov/bio_data/836772</a>) to assembly GCF_000764305.2 using the program Liftoff v1.6.3 (<a href="https://github.com/agshumate/Liftoff">https://github.com/agshumate/Liftoff</a>).</p>

Tags: ars, arthropods, data-gov, hyalella-azteca, i5k
Organization: Department of Agriculture
Spatial Modeling for Resources Framework (SMRF)

<p>Spatial Modeling for Resources Framework (SMRF) was developed at the USDA Agricultural Research Service (ARS) in Boise, ID, and was designed to increase the flexibility of taking measured weather data and distributing the point measurements across a watershed. SMRF was developed to be used as an operational or research framework, where ease of use, efficiency, and ability to run in near real time are high priorities.</p>
<p>Highlights</p>
<ol>
<li>Robust meteorological spatial forcing data development for physically based models</li>
<li>The Python framework can be used for research or operational applications</li>
<li>Parallel processing and multi-threading allow for large modeling domains at high resolution</li>
<li>Real time and historical applications for water supply resourses</li>
</ol>
<p>Features
SMRF was developed as a modular framework to enable new modules to be easily intigrated and utilized.</p>
<ul>
<li>Load data into SMRF from MySQL database, CSV files, or gridded climate models (i.e. WRF)</li>
<li>Variables currently implemented: Air temperature; Vapor pressure; Precipitation mass, phase, density, and percent snow; Wind speed and direction; Solar radiation; Thermal radiation</li>
<li>Output variables to NetCDF files</li>
<li>Data queue for multithreaded application</li>
<li>Computation tasks implemented in C
<div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: SMRF GitHub repository.</p> <p>File Name: Web Page, url: <a href="https://github.com/USDA-ARS-NWRC/smrf" target="_blank">https://github.com/USDA-ARS-NWRC/smrf</a> </p><p>SMRF was designed to increase the flexibility of taking measured weather data, or atmospheric models, and distributing the data across a watershed.</p></li></ul></li>
</ul>

Tags: ars, data-gov, interpolation, netcdf, np211, smrf, spatial-modeling-for-resources-framework
Organization: Department of Agriculture
Microbial community structure is affected by cropping sequences and poultry litter under long-term no-tillage

<p>Soil microorganisms play essential roles in soil organic matter dynamics and nutrient cycling in agroecosystems and have been used as soil quality indicators. The response of soil microbial communities to land management is complex and the long-term impacts of cropping systems on soil microbes is largely unknown. Therefore, changes in soil bacterial community composition were assessed in response to cropping sequences and bio-covers at long-term no-tillage sites. Main effects of four different cropping sequences of corn (Zea mays L.), cotton (Gossypium hirsutum L.), and soybean (Glycine max L.) were rotated in four year phases for 12-yrs at two Tennessee Research and Education Centers in a randomized complete block design with split-block treatments of four winter bio-covers: hairy vetch (Vicia villosa L.), wheat (Triticum aestivum L.), poultry litter, and a fallow control. Using Illumina high-throughput sequencing of 16S rRNA genes, bacterial community composition was determined. Composition, diversity, and relative abundance of specific taxa were correlated per cropping system, bio-cover, and their interaction. We found that i) richness and diversity varied temporally and spatially, coinciding with soil carbon, pH, nutrient levels, and climatic variability; ii) community composition varied by cropping system, with continuous corn, soybean, and the corn-soybean rotation presenting a hybrid of the continuous corn and soybean communities; however, continuous cotton resulted in the most varied assemblage; iii) bio-covers asserted the greatest influence on microbial communities; specifically poultry litter treatments differed from cover crops (all of which received inorganic-N). Consequently, microbial diversity was greatest under nutrient rich bio-covers (poultry litter) and high residue producing, less pesticide-intensive cropping sequences (soybean and corn compared to cotton), suggesting a more dynamic soil ecology under these no-till cropping systems. This suggests that nutrient management (inorganic fertilizers vs. animal manure) and greater crop rotations (within 4-yr phases) may directly drive phylogenetic community structure and subsequent ecosystem services across agricultural landscapes. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Microbial diversity based on crop rotation, cover crop, and poultry litter after 14-years of managment .</p> <p>File Name: Ashworth microbial data by PLOT.xlsx</p></li><br><li><p>Resource Title: Microbial diversity based on crop rotation, cover crop, and poultry litter after 14-years of managment.</p> <p>File Name: Ashworth microbial data by PLOT.csv</p><p>Resource Description: CSV version of the data</p></li><br><li><p>Resource Title: Data Dictionary.</p> <p>File Name: Ashworth-PLOT-Jul2019-data-dictionary.csv</p><p>Resource Description: Defines variables, data type, accepted values, size, if required, etc. for the tabular data.</p></li></ul><p></p>

Tags: ars, data-gov, np212
Organization: Department of Agriculture
Data from: Metagenomic and near full-length 16S rRNA sequence data in support of the phylogenetic analysis of the rumen bacterial community in steers

<p>Amplicon sequencing utilizing next-generation platforms has significantly transformed how research is conducted, specifically microbial ecology. However, primer and sequencing platform biases can confound or change the way scientists interpret these data. The Pacific Biosciences RSII instrument may also preferentially load smaller fragments, which may also be a function of PCR product exhaustion during sequencing. To further examine theses biases, data is provided from 16S rRNA rumen community analyses. Specifically, data from the relative phylum-level abundances for the ruminal bacterial community are provided to determine between-sample variability. Direct sequencing of metagenomic DNA was conducted to circumvent primer-associated biases in 16S rRNA reads and rarefaction curves were generated to demonstrate adequate coverage of each amplicon. PCR products were also subjected to reduced amplification and pooling to reduce the likelihood of PCR product exhaustion during sequencing on the Pacific Biosciences platform. The taxonomic profiles for the relative phylum-level and genus-level abundance of rumen microbiota as a function of PCR pooling for sequencing on the Pacific Biosciences RSII platform were provided.</p>
<p>Data is within this article and raw ruminal MiSeq sequence data is available from the NCBI Sequence Read Archive (SRA Accession SRP047292). Additional descriptive information is associated with NCBI BioProject PRJNA261425. <a href="http://www.ncbi.nlm.nih.gov/bioproject/PRJNA261425/">http://www.ncbi.nlm.nih.gov/bioproject/PRJNA261425/</a> </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: NCBI Sequence Read Archive (SRA Accession SRP047292).</p> <p>File Name: Web Page, url: <a href="https://www.ncbi.nlm.nih.gov/sra/SRX704260">https://www.ncbi.nlm.nih.gov/sra/SRX704260</a> </p><p>1 ILLUMINA (Illumina MiSeq) run: 978,195 spots, 532.9M bases, 311.6Mb downloads.</p></li></ul><p></p>

Tags: 16s-rrna-gene, 16s-rrna-sequence-data, ars, bos-taurus, data-gov, miseq, pacific-biosciences
Organization: Department of Agriculture
Data from: Identification and functional characterization of immunity-suppressing, candidate effector proteins in the parasitic weed Phelipanche aegyptiaca

<p>All source data from the referenced paper (Figures 1b and Table 1). 22 Excel files of data from each experimental block of the reactive oxygen species assay, 1 Excel file of the combined data from the bacterial growth enhancement assay, 1 Excel file of the RT-qPCR data.</p>
<p>Parasitic plants are the primary biotic constraint in many crop production systems. The most agriculturally devastating parasitic plants, including witchweeds (<em>Striga spp.</em>) and broomrapes (<em>Phelipanche and Orobanche spp.</em>), are in the <em>Orobanchaceae</em> family. <em>Phelipanche aegyptiaca</em> is an obligate holoparasite that lacks the capacity for photosynthesis and therefore relies on host parasitization for acquisition of all nutrients. <em>P. aegyptiaca</em> is a broad host range pathogen with the ability to parasitize diverse dicot hosts through attachment and development of a feeding structure known as a haustorium. The mechanisms <em>P. aegyptiaca</em> and other parasitic plants employ to avoid host plant immunity and form successful haustorial attachments are unknown. Here, we demonstrate that <em>P. aegyptiaca</em> actively suppresses salicylic acid-mediated immunity of the host plant <em>Arabidopsis thaliana</em>. We hypothesized that parasitic plants may deploy immunity-suppressing effector proteins through the haustorial interface to subvert host plant immune responses. We devised a pipeline to select and clone 27 candidate secreted effector proteins in <em>P. aegyptiaca</em> and tested these proteins for the potential to suppress known plant immunity pathways. Five candidate effectors suppressed flg22-elicited production of reactive oxygen species when transiently expressed in <em>Nicotiana benthamiana</em>. We propose that two of these candidate effectors function through interfering with pattern triggered immunity using molecular mimicry. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Data from Identification and functional characterization of immunity-suppressing, candidate effector proteins in the parasitic weed Phelipanche aegyptiaca.</p> <p>File Name: AllSourceDataPaegEffectorPaper.zip</p><p>Resource Description: All source data from the referenced paper.</p></li></ul><p></p>

Tags: ars, data-gov, np303
Organization: Department of Agriculture
Economic Model of Deficit Irrigation

<p>This spreadsheet is a model of the economics of deficit irrigation that is described in detail in:  Trout, T.J. and D.T. Manning.  2019.  An economic and biophysical model of deficit irrigation.  Agron. J. 111:1–12.  doi:10.2134/agronj2019.03.0209 . </p>
<p>The model calculates net income from a crop on a unit of land based on a quadratic crop water production function, amount of effective precipitation, irrigation efficiency, cost of the irrigation water supply, crop production costs, and revenue from selling the crop.  The model includes potential income from leasing out saved irrigation water.  All biophysical variables are defined in terms of the relative evapotranspiration.  Net income is maximized by optimizing the amount of water consumed by the crop.</p>
<p>The spreadsheet progressively presents biophysical and economic models of deficit irrigation with water leasing.  Economic and biophysical parameters are input into the highlighted cells of each worksheet.  Parameters from previous worksheets are copied to following worksheets.  Relationships are graphed.  Output is the net income (NI) for a set of biophysical and economic parameters and level of deficit irrigation that maximizes net income.</p>
<div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Economic Model of Deficit Irrigation (spreadsheet).</p> <p>File Name: WPF Econ Model V2.xlsx</p></li><br><li><p>Resource Title: Description of the Model.</p> <p>File Name: Description of the Deficit Irrigation Economics Model.pdf</p><p>Resource Description: Description of the Model inputs and operation.</p></li></ul>

Tags: agricultural-economics, ars, data-gov, deficit-irrigation, economic-model, irrigation-and-water-use, np211
Organization: Department of Agriculture
Data 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>
<p><strong>Content</strong></p>
<p><br></p>
<p>Frost tolerance of 44 Linum lewisii accessions collected from western North America.</p>

Tags: frost-hardiness, linum-lewisii, perennial-grains
Organization: Department of Agriculture
Data from: Investigation of Stormwater Runoff at the Sleepy Hollow Neighborhood, Fort Irwin, California

<p dir="ltr">In arid and semi-arid region, low precipitation can lead to reliance on groundwater for our needs. A study was conducted in cooperation with the Environmental Protection Agency and the Agriculture Research Service (ARS) in Riverside, California in the residential area the Ft. Irwin Army base in southern California. The base only receives an average annual precipitation of 4 inches. An objective of the study was to see if enough runoff was generated in the residential neighborhood to enhance the recharge of groundwater. Rainfall, runoff, and characteristics of the watershed draining to a detention that in turn, drains into a dry well that is designed to enhance deep infiltration to groundwater. Three storm events with all instrumentation working properly were observed. The respective percentage of the rainfall that runoff was 9, 5 and 11 percent. These events were modeled with the uncalibrated ARS KINEROS2 watershed model using urban overland flow model elements. For EV1 and EV3 the precent difference between simulated and observed runoff was -9.7 and -14.1 percent, respectively. For EV2 the model overpredicted the observed runoff by 80.2 percent. However, EV2 was a very small runoff event where the measuring resolution of the rain gauges (0.25 mm) translated into 57% of the observed volume. To generate substantial volumes of runoff for groundwater recharge would require a much larger developed area than the one studied herein. In addition, a larger sample size of events, with all instruments in proper working order, would lend greater weight to overall character of rainfall-runoff processes at Ft. Irwin.</p>

Tags: ft-irwin, rainfall, recharge, runoff
Organization: Department of Agriculture
Data from: Mosquito mutations F290V and F331W expressed in acetylcholinesterase of the sand fly Phlebotomus papatasi (Scopoli): Biochemical properties and inhibitor sensitivity

<p dir="ltr"><b>Background:</b> The Old-World sand fly, <i>Phlebotomus papatasi</i> (Scopoli), a vector of zoonotic cutaneous leishmaniasis, is usually controlled by insecticides, including anticholinesterases. Previous studies revealed 85% amino acid sequence identity of recombinant <i>P. papatasi</i> acetylcholinesterase (r<i>Pp</i>AChE1) to mosquito AChE and identified synthetic carbamates that selectively inhibited r<i>Pp</i>AChE1 and circumvented the G119S mutation responsible for high level resistance to anticholinesterases. This study reports the construction, baculovirus expression, and biochemical properties of r<i>Pp</i>AChE1 containing the F290V and F331W orthologous mutations from mosquitoes.</p><p dir="ltr"><b>Methods: </b>Recombinant <i>Pp</i>AChE1 enzymes with or without the F290V, F331W, and G119S orthologous mosquito mutations were expressed in <i>Sf</i>21cells utilizing the baculoviral system. Ellman assays determined changes in catalytic properties and inhibitor sensitivity resulting from wild type and mutant r<i>Pp</i>AChE1 containing single or combinations of orthologous mosquito mutations.</p><p dir="ltr"><b>Results: </b>Each of the orthologous mutations (F290V, F331W, and G119S) from mosquito AChE significantly reduced inhibition sensitivity to organophosphate or carbamate pesticides, and catalytic activity was lost when they were expressed in combination. Novel synthetic carbamates were identified that significantly inhibited the r<i>Pp</i>AChEs expressing each of the single orthologous mosquito mutations.</p><p dir="ltr"><b>Conclusions: </b>These novel carbamates could be developed as efficacious insecticides with improved specificity and safety for use in sand fly or mosquito populations expressing the mutant AChEs.</p>

Tags: acetylcholinesterase-inhibition-acetylcholinesterase, carbamate, cattle-tick-rhipicephalus, f290v-mutation, f331w-mutation, g119s-mutation, mosquito-resistance, organophosphate-resistance, tacrine-dimers
Organization: Department of Agriculture
Terrestrial Condition Assessment (TCA) Ozone Chronic Exposure (Map Service)

The average of W126 which is a weighted measure of chronic (lower level) ozone exposure within a landscape analysis unit. Updated through 2018. Data used are sourced from the EPA's Air Quality System Data Mart: https://aqs.epa.gov/aqsweb/airdata/download_files.html

Tags: chronic, gtac, open-data, ozone, tca, usfs
Organization: Department of Agriculture