AndreaBozzo/ceres-open-data-index huggingface dataset:
Data from: Evaluation of alternative-design cotton gin lint cleaning machines on fiber length uniformity index

<p dir="ltr">This is USDA-ARS data from the publication: "Evaluation of Alternative-Design Cotton Gin Lint Cleaning Machines on Fiber Length Uniformity Index". The study was conducted in 2018 & 2019 with continued sample and data analysis through August 2023. Developing cotton ginning methods that improve fiber length uniformity index to levels that are compatible with the newer and more efficient spinning technologies would expand market share and increase the demand for cotton products and give U.S. cotton a competitive edge to synthetic fibers. Older studies on lint cleaning machines showed that the most widely used feed mechanism that places fiber on the cleaning cylinder damages fiber and reduces uniformity. The present study evaluates how conventional and experimental feed mechanisms affect uniformity. The lint cleaners were used with both saw and roller gin stands. Four diverse cotton cultivars from the Far West, Southwest, and Mid-South were used in the test. The data included gining process variables, raw seed cotton characteristics, raw lint High Volume Instrument (HVI), Advanced Fiber Information System (AFIS), and micro-dust and trash analyzer (MDTA3) measurements.</p>

Tags: cotton, lint, lint-cleaning, quality, roller-ginning, saw-ginning
Organization: Department of Agriculture
Data from: Establishment of the wasp Tetramesa romana for biological control of Arundo donax in northern California and the role of release plot manipulation

<p dir="ltr"><i>Arundo donax</i> is a non-native, invasive large-statured grass of riparian systems in the southwestern U.S.A., including the Sacramento and San Joaquin River watersheds of northern California and the Sacramento-San Joaquin Delta. In 2017, the shoot tip-galling wasp <i>Tetramesa romana</i> was released at nine sites, three in each region. Shoots in some release plots were manipulated prior to release by cutting to ground or pruning to 1 m height, while others were left uncut. One year later, exit holes made by emerging adult wasps were found at two of nine sites. Exit hole density per main shoot length was 16-fold higher on regrowth shoots in ground-cut plots than in uncut plots. An additional plot manipulation study at two other sites found that exit hole density per shoot length was 19-fold higher in plots that were double-cut (cut to ground and regrowth pruned) than in single-cut plots. By 2023, <i>T. romana</i> was established at eight sites spanning both river watersheds and their Delta with dispersal up to 6.4 km, based on dissection of shoots, multi-year counts of exit holes and galls, and trapping of adult <i>T. romana</i> with sticky traps. The abundance of <i>T. romana</i> may be limited in northern California by low annual heat unit accumulation. The results show that physical manipulation of host plants improves short-term establishment and demonstrate the importance of using multiple monitoring methods to determine long-term establishment.</p>

Tags: agent-density, agent-establishment, arundo, arundo-donax, augmentative-biological-control, biological-control, biological-control-insects, biological-control-weeds, conservation-biological-control, entomology, galling-wasp, giant-reed, integrated-weed-management, mechanical-control
Organization: Department of Agriculture
Data from: Cover cropping history affects cotton boll distribution, lint yields, and fiber quality

<p>This is digital research data corresponding to a published manuscript, Cover cropping history affects cotton boll distribution, lint yields, and fiber quality, in Crop Science, Vol. 63 p. 1209–1220. </p>
<p>There has been limited introduction of new cover crop species into cotton (Gossypium hirsutum L.) production within the last 30 years. Mounting evidence shows that traditional cover cropping species may be detrimental to cotton production, either by depleting soil fertility with crop removal, immobilizing minerals from high carbon residue, or excessive quantity of residue remaining at planting. The objective of this study was to determine the effects of growing a novel cover crop species, carinata (Brassica carinata A. Braun), as a winter annual cover crop for cotton rotation in the southeastern Coastal Plain. Over a 2-year period, carinata, winter wheat (Triticum aestivum L.), and fallow covers were maintained over winter months, then rotated into cotton. Each year, seedcotton and lint yields were collected, along with subsamples for ginning and subsequent fiber quality analyses. Additionally, end-of-season plant mapping was conducted on plants from 1-m of row per plot to determine cover crop effects on boll formation, retention, and distribution, as well as canopy architecture.</p>

Tags: ars, brassica-carinata, coastal-plain, cotton, cover-crops, data-gov, np301, winter-wheat
Organization: Department of Agriculture
<b>Data from: Soil CO2 Efflux Dynamics in an Integrated Crop-Livestock System</b>

<p dir="ltr">Integrated crop-livestock (ICL) systems combine crop and livestock production and have been found to improve soil health. However, there is limited understanding of how ICL systems affect soil carbon (C) dynamics, especially in semi-arid regions. To better understand C responses to ICL systems, a 3-yr study was conducted near Mandan, ND, USA. Carbon dioxide efflux, aboveground biomass, and soil C measurements were made in grazed and ungrazed ICL system crop rotations and grass pasture. Treatments were replicated four times. Measurements of CO<sub>2</sub> efflux were made using static chamber methodology 93 times over the study period (14 Oct 2016 – 16 Oct 2019). Aboveground biomass, soil organic matter, water-soluble C and N, and C mineralization were measured annually following standard protocols. Aboveground biomass was expressed as mass units of C per unit area assuming a plant tissue C concentration of 45%. Data may be used to understand CO<sub>2</sub> efflux, aboveground biomass, and soil C dynamics in ICL production systems. Data are generally applicable to cropland under a semiarid continental climate for the following soil types: Grassna, Linton, Mandan, Temvik, Williams, and Wilton.</p>

Tags: aboveground-biomass-carbon, carbon-dioxide, integrated-agricultural-systems, northern-plains, soil-organic-carbon
Organization: Department of Agriculture
Data From: Influence of cold temperature and exposure time on egg overwintering survival in the white-whiskered grasshopper (Orthoptera: Acrididae)

<p>Data are from a laboratory experiment conducted to examine the effects of cold temperatures on egg survival of Ageneotettix deorum, the white-whiskered grasshopper which is a common rangeland pest species in the Northern Great Plains region. </p>
<p>Abstract from published manuscript:<br>
The effect of cold temperatures and exposure time on egg survival and hatching success were examined in the white-whiskered grasshopper, Ageneotettix deorum. Temperature treatments ranged from 4°C to -35°C, with treatment times ranging from 48 to 240 hours. Both decreasing temperatures and exposure time negatively affected egg survival, with a temperature below -25°C being lethal. Similar lethal temperatures are known for several North American grasshopper species. The relatively shallow location of A. deorum egg pods would result in increased vulnerability of eggs to cold temperatures in the absence of snow.</p>
<p>Resources in this dataset:</p>
<ul>
<li>
<p>Resource title: Column descriptions for Winter Egg Survival and Daily Hatch
File name: Column Heading Winter Egg Survival and Hatch Count.xlsx</p>
</li>
<li>
<p>Resource title: Ageneotettix deorum hatch survival
File name: Winter Egg Survival.xlsx
Resource description: The data are total numbers of hatched and unhatched eggs at 3 significant temperatures (4, -20, and -25 degrees Celsius).</p>
</li>
<li>
<p>Resource title: Daily Hatch
File name: Hatch Count.xlsx
Resource description: The data are the daily hatch count for egg pods held at the various time and temperature parameters.</p>
</li>
</ul>

Tags: acrididae, ageneotettix, ars, data-gov, egg-pods, hatching-success, lethal-temperature, np304
Organization: Department of Agriculture
NLET - National Load Estimating Tool

<p><a href="https://nlet.brc.tamus.edu/Home/Index">NLET (National Load Estimating Tool)</a>, a component of the <a href="https://soilandwaterhub.brc.tamus.edu/Home/Index">USDA/ARS Soil and Water Hub</a>, is a web-based tool for estimating pollutant loads in watersheds across the contiguous United States. This tool helps visualize the effects of land use patterns, cultivated crops, and conservation practices through graphical representation. Visualizations illustrate baseline and scenario land-use, crops, conservation, runoff, sediment, nitrogen, and phosphorus, and load differences at 50th percentile.</p>
<p>NLET implements an export coefficient approach for predicting the pollutant loads. NLET also addresses the need for a user-friendly, reliable and cost-effective watershed modeling tool. </p>
<p>NLET utilizes the D3.js library for creating an open-source JavaScript and data-driven charts, as well as Mapbox and OpenStreetMap for the Leaflet library, another open-source JavaScript library used for displaying the locations of Hydrologic Unit Catalog (HUC). </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Website Pointer to NLET - National Load Estimating Tool .</p> <p>File Name: Web Page, url: <a href="https://nlet.brc.tamus.edu/">https://nlet.brc.tamus.edu/</a> </p><p>The web dashboard interface for estimating pollutant loads in watersheds across the contiguous United States.</p></li></ul><p></p>

Tags: ars, data-gov, national-load-estimating-tool, nlet, np211, np212, np215
Organization: Department of Agriculture
Data from: Switchgrass cultivar, yield, and nutrient removal responses to harvest timing

<p>Finite nutrients, such as P and K are assumedly remobilized post-senescence in herbaceous feedstocks like switchgrass (<em>Panicum virgatum</em> L.) as a function of environmental signaling and genotype. Harvesting early during the maturation phase may result in yield reductions and higher nutrient removal in biomass depending on ecotype. Therefore, it is necessary to target harvest dates that optimize yield while minimizing nutrient removal per cultivar. Consequently, objectives were to compare yields from 2010–2011 on eight widely used and experimental upland and lowland genotype (whole plot) at two locations in Tennessee, to determine: (i) which harvest timing (split-plot) provides maximum yield; (ii) effects of harvest timing (mid-September, October, November, and late October) on overall total P and K removal; and, (iii) how results are affected by cultivar. Among all post-senescence harvests, yields peaked early November (13.2 Mg ha–1), which was greater than all other harvests (P < 0.05), with mid-October and late October not differing from one another. Because yields peaked in early November, P and K removal did not vary across harvest dates (despite both P and K concentrations declining mid-October). Lowland cultivars yielded 3.9 Mg ha–1 more biomass annually than upland entries, suggesting lowland cultivars are better suited to environments in the Southeast. Due to lower yields, P and K removals were lower for upland (Blackwell and C62), compared with lowland cultivars. Consequently, switchgrass can be harvested as early as mid-September without removing greater amounts of P and K, although variations within upland and lowland cultivars will likely occur. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Switchgrass variety nutrient removal.</p> <p>File Name: variety removal.csv</p><p>Resource Description: Switchgrass variety P and K tissue (leaves and stems) removal for fall harvest periods (mid-September, October, November, and late October), at East Tennessee and Highland Rim Research and Education Centers from 2010–2011.</p></li><br><li><p>Resource Title: Data Dictionary.</p> <p>File Name: switchgrass-variety-nutrient-removal-data-dictionary.csv</p><p>Resource Description: Defines variables, units, and data types for the tabular data.</p></li></ul><p></p>

Tags: ars, data-gov, feedstocks, np212, nutrient-remobilization, post-senescence
Organization: Department of Agriculture
Data from: Plasmopara echinaceae, a new species of downy mildew affecting cone flowers (Echinacea purpurea) in the United States

<p>A new species of downy mildew (Oomycota, Peronosporales) is reported. This dataset contains alignments of DNA sequences (cox2 and LSU) markers, alignment of cox2 marker to be used in species identification and resulting phylogenetic trees.</p>
<p>Resources in this dataset:</p>
<ul>
<li>
<p>Resource Title: Alignment Cox2 dataset
File Name: Cox2_EchDM_final_alignment.fasta
Resource Description: Alignment of Cox2 DNA sequences.</p>
</li>
<li>
<p>Resource Title: Alignment LSU dataset
File Name: LSU_EchDM_final_alignment.fasta
Resource Description: Alignment of LSU DNA sequences.</p>
</li>
<li>
<p>Resource Title: Alignment Cox2 dataset Barcoding
File Name: Cox2_EchDM_Genetic_differences_alignment.fasta
Resource Description:  Alignment of cox2 marker to be used in species identification and resulting phylogenetic trees.</p>
</li>
</ul>

Tags: alignments, ars, cox2, data-gov, downy-mildew, lsu, new-species, np303, oomycete-pathogen, peronosporales, phylogenetic-analysis, phylogenetic-trees, plasmopara
Organization: Department of Agriculture
Data from: Evaluating plant biodiversity measurements and exotic species detection in National Resources Inventory Sampling protocols using examples from the Northern Great Plains of the USA

<p>Plant biodiversity data and associated soils, ecological site, and livestock management data that were collected at the USDA-ARS Northern Great Plains Research Laboratory in 2011 and 2013. Data were collected using the modified Whittaker technique. The unique design of the Whitaker method reduces autocorrelation among subplots, which is common in standard transect methods (Goslee, 2006). Grassland scientists worldwide use this standard technique to quantify and monitor plant diversity on, for example, Serengeti grasslands (Anderson et al., 2006), South African serpentine grasslands (Reddy et al., 2009), and rangelands in Turkey (Firinciglu et al., 2007) among many other environments. In addition, Sanderson at the NGPRL and Goslee at ARS University Park have developed a large database on plant species diversity of grazing lands in the U.S. (nearly 300 sites sampled using the Whitaker plot method). The use of the standardized Whitaker plot method allows us to combine data from the northern Great Plains with other databases worldwide for larger-scale meta-analyses. The multiscale technique also enables comparison of vegetation dynamics at multiple scales.</p>
<p>Resources in this dataset:</p>
<ul>
<li>
<p>Resource Title: NGPRL modified Whittaker data
File Name: NGPRL_ModWhit.csv</p>
</li>
<li>
<p>Resource Title:  Ancillary data for NGPRL modified Whittaker plots
File Name: NGPRL_ModWhit_Ancillary data.csv</p>
</li>
<li>
<p>Resource Title: Data dictionary for NGPRL modified Whittaker data
File Name: Modified Whittaker dataset dictionary.csv</p>
</li>
<li>
<p>Methods for NGPRL modified Whittaker data
File Name: modWhit methods and metadata.docx</p>
</li>
</ul>

Tags: ars, biodiversity, data-gov, np215, species-richness
Organization: Department of Agriculture
Landscape Data Commons

<p>The Landscape Data Commons is an inter-agency monitoring data repository and portal, led by the USDA-ARS at the Jornada Experimental Range, that connects standardized monitoring data to analysis tools to support land management and research. The Landscape Data Commons aggregates and harmonizes core methods data collected across agencies and monitoring programs (e.g., Bureau of Land Management Assessment, Inventory and Monitoring Program, the Natural Resources Conservation Service National Resources Inventory Grazing land On-Site program, the National Wind Erosion Research Network, smaller research and monitoring efforts). With these aggregated data, the Landscape Data Commons supports natural-resource management, modeling, and research.</p>

Tags: aeolian, agricultural-monitoring, agroecosystems-environment, ars, basal-cover, canopy, climatologymeteorologyatmosphere, composition, core-methods, cover, data-gov, dry-deposition, dust-deposition, dust-emission, gap-intercept, geoscientificinformation, herbaceous, line-point-intercept, np216, plant-height, plant-species, soil-stability, species-inventory, surface-stability, wet-deposition, wind-erosion, woody-plants
Organization: Department of Agriculture
Evaluating accuracy of DNA pool construction based on white blood cell counts

<p>Pooling individual samples prior to DNA extraction can mitigate the cost of DNA extraction and genotyping; however, these methods need to accurately generate equal representation of individuals within pools. This data set was generated to determine accuracy of pool construction based on white blood cell counts compared to two common DNA quantification methods. Fifty individual bovine blood samples were collected, and then pooled with all individuals represented in each pool. Pools were constructed with the target of equal representation of each individual animal based on number of white blood cells, spectrophotometric readings, spectrofluorometric readings and whole blood volume with 9 pools per method and a total of 36 pools. Pools and individual samples that comprised the pools were genotyped using a commercially available genotyping array. ASReml was used to estimate variance components for individual animal contribution to pools. The correlation between animal contributions between two pools was estimated using bivariate analysis with starting values set to the result of a univariate analysis.</p>
<p>The dataset includes:
1) pooling allele frequencies (PAF) for all pools and individual animals computed from normalized intensities for red (X) and green (Y); PAF = X/(X+Y).
2) Genotypes or number of copies of B(green) allele (0,1,2).
3) Definitions for each sample.</p>
<div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Pooling Allele Frequencies (paf) for all pools and individual animals.</p> <p>File Name: pafAnimal.csv.gz</p><p>Resource Description: Pooling Allele Frequencies (paf) for all pools and individual animals computed from normalized intensities for red (X) and green (Y); paf = X / (X + Y)</p></li><br><li><p>Resource Title: Genotypes for individuals within pools.</p> <p>File Name: g.csv.gz</p><p>Resource Description: Genotypes (number of copies of the B (green) allele (0,1,2)) for individual bovine animals within pools.</p></li><br><li><p>Resource Title: Sample Definitions .</p> <p>File Name: XY Data Key.xlsx</p><p>Resource Description: Definitions for each sample (both pools and individual animals).</p></li></ul>

Tags: alleles, ars, blood, blood-volume, data-gov, gene-frequency, genotype, genotyping, np101, sample-pooling, spectrophotometers, white-blood-cell-count, white-blood-cells
Organization: Department of Agriculture
Data from: Soil hydrological attributes of an integrated crop-livestock agroecosystem: Increased adaptation through resistance to soil change

<p dir="ltr">Integrated crop-livestock systems can have positive agronomic and environmental benefits compared to specialized, single-enterprise production systems. However, concerns exist regarding the effect of livestock in integrated systems to cause soil compaction and decrease water infiltration rates. A study was conducted to evaluate the effects of residue management, frequency of hoof traffic, season, and production system (e.g., integrated annual cropping vs. perennial grass) on infiltration rates in central North Dakota. Infiltration measurements were made using single-ring infiltrometers by inserting a 15 cm (inner diameter) aluminum ring into the soil and applying two separate applications of water within the enclosed space of the ring. The volume of water for each application was equivalent to a 2.54 cm depth (1 inch) within the ring. The time necessary for each application of water to infiltrate into the soil was recorded, and only data from the second water application was used for analysis. Data may be used to understand integrated crop-livestock system impacts on water infiltration. Data are generally applicable to cropland under a semiarid continental climate for the following soil types: Grassna, Linton, Mandan, Temvik, Williams, and Wilton.</p>

Tags: integrated-crop-livestock-system, northern-great-plains, soil-compaction, water-infiltration
Organization: Department of Agriculture
Data from: Variations in Phytochemical Content and Composition in Distillers Corn Oil from 30 U.S. Ethanol Plants

<p>The data is in csv format. It contains the plant averages for all data presented in the published manuscript 'Variations in Phytochemical Content and Composition in Distillers Corn Oil from 30 U.S. Ethanol Plants'. The analytical replications vary by test type, and are specified in the published paper.  </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: dataset from: Variations in Phytochemical Content and Composition in Distillers Corn Oil from 30 U.S. Ethanol Plants .</p> <p>File Name: DCO oil analysis.csv</p><p>Resource Description: this is the csv file </p></li></ul><p></p>

Tags: ars, carotenoids, data-gov, distillers-corn-oil, distillers-dried-grains, np306, oxidative-stability, tocopherols
Organization: Department of Agriculture
Data from: Phased Genotyping-by-Sequencing Enhances Analysis of Genetic Diversity and Reveals Divergent Copy Number Variants in Maize

<p>High-throughput sequencing (HTS) of reduced representation genomic libraries has ushered in an era of genotyping-by-sequencing (GBS), where genome-wide genotype data can be obtained for nearly any species. However, there remains a need for imputation-free GBS methods for genotyping large samples taken from heterogeneous populations of heterozygous individuals. This requires that a number of issues encountered with GBS be considered, including the sequencing of nonoverlapping sets of loci across multiple GBS libraries, a common missing data problem that results in low call rates for markers per individual, and a tendency for applicability only in inbred line samples with sufficient linkage disequilibrium for accurate imputation. We addressed these issues while developing and validating a new, comprehensive platform for GBS. This study supports the notion that GBS can be tailored to particular aims, and using <em>Zea mays</em> our results indicate that large samples of unknown pedigree can be genotyped to obtain complete and accurate GBS data. Optimizing size selection to sequence a high proportion of shared loci among individuals in different libraries and using simple in silico filters, a GBS procedure was established that produces high call rates per marker (>85%) with accuracy exceeding 99.4%. Furthermore, by capitalizing on the sequence-read structure of GBS data (stacks of reads), a new tool for resolving local haplotypes and scoring phased genotypes was developed, a feature that is not available in many GBS pipelines. Using local haplotypes reduces the marker dimensionality of the genotype matrix while increasing the informativeness of the data. Phased GBS in maize also revealed the existence of reproducibly inaccurate (apparent accuracy) genotypes that were due to divergent copy number variants (CNVs) unobservable in the underlying single nucleotide polymorphism (SNP) data. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Supplementary Data.</p> <p>File Name: Web Page, url: <a href="https://academic.oup.com/g3journal/article/7/7/2161/6053605#supplementary-data">https://academic.oup.com/g3journal/article/7/7/2161/6053605#supplementary-data</a> </p></li></ul><p></p>

Tags: ars, data-gov, genome, genotypes, genotyping-by-sequencing, high-throughput-sequencing, zea-mays
Organization: Department of Agriculture