AndreaBozzo/ceres-open-data-index huggingface dataset:
Data from: Association mapping of resistance to tan spot in the Global Durum Panel

<div>Phenotypic data: A total of 510 lines from the global durum panel (GDP) were evaluated for reaction to five isolates of the fungal pathogen <em>Pyrenophora tritici-repentis</em>. The five isolates were Pti2 (race 1), 86-124 (race 2), 331-9 (race 3), L13-192 (race 4), and DW5 (race 5). The GDP lines were inoculated in a greenhouse when plants were at the two- or three-leaf stage. Plants were grown in a randomized complete block design consisting of one replicate per experiment, and each experiment was repeated three times. Following inoculation, the plants were placed in misting chambers with 100% relative humidity at 21 °C for 24 h, and then placed in a growth chamber under a 12-h photoperiod at 21 °C. Disease reactions were scored 7 days after inoculation following the 1–5 scale where 1 was highly resistant and 5 was highly susceptible.</div>
<p>Seedlings of the GDP were also infiltrated with cultures containing the necrotrophic effectors (NEs) Ptr ToxA and Ptr ToxB. Approximately 20 μl of NE-containing culture filtrate (CF) was infiltrated into two plants (1 leaf per plant) in each cone using a needleless 1-ml syringe. The infiltrated area (~3 cm) was marked with permanent marker on the leaves, and the plants were placed in a growth chamber (21 °C, 12-h photoperiod) for 5 days. The reactions were scored using a 0–3 scale where 0 indicated no reaction and 3 indicated severe necrosis or chlorosis. The expansion of chlorosis beyond the boundaries of Ptr ToxB infiltration to the distal end of the leaf was scored separately using 0 or 1 meaning the absence or presence of the symptom, respectively. This trait is noted as ‘ToxB_Spread’ in the data file.</p>
<p>Genotypic data: The GDP lines were genotyped using the Illumina iSelect 90K SNP array. Markers were filtered using previously published genetic maps, and marker sequences were aligned to the Svevo.v1 reference genome. SNP imputation was performed, and the redundant markers were pruned based on genome wide linkage disequilibrium, which resulted in a data set with no missing SNP calls. The hapmap information of 855 genotypes and 13,373 SNPs developed by M. Maccaferri is located on the GrainGenes website (<a href="https://wheat.pw.usda.gov/GG3/global_durum_genomic_resources" target="_blank">https://wheat.pw.usda.gov/GG3/global_durum_genomic_resources</a>). The haplotype map of the 855 genotypes was reduced to 510 genotypes that were selected for phenotypic tests. The SNP data set was selected according to the set filtering for minor allele frequency (MAF) > 5% that resulted in a marker set containing 12,222 SNPs.</p>

Tags: ars, data-gov, disease, gwas, np301, tan-spot, triticum-turgidum-subsp-durum
Organization: Department of Agriculture
Data from: Field Estimates of Attraction of Ceratitis capitata to Trimedlure and Bactrocera dorsalis (Diptera: Tephritidae) to Methyl Eugenol in Varying Environments

<p dir="ltr">This package includes the data from field experiments to measure the range of attraction of two "male lures" on two different pest fruit fly species via Mark-Release-Recapture (MRR). These values will be of importance to those seeking to optimize fruit fly detection networks or other networks of traps. Methyl eugenol is found to be more attractive to <i>Bactrocera dorsalis</i> compared with trimedlure to <i>Ceratitis capitata</i>. Data consists of number released, proportion responsive, quality control assay results, and recaptures in traps set in a grid pattern after the release.</p><p dir="ltr">Resources in this dataset:</p><ul><li>Resource Title: Trap positions File Name: coords_grids.csv Resource Description: Lat/long data for each of the traps in the three grids used for MRR experiments.</li><li>Resource Title: Temperature and Humidity data for experimental dates in each site File Name: all_weather_data.csv Resource Description: Mean and min/max values of temp and humidity for "Island Princess" and "Puuwaawaa" sites on the dates of experiments.</li><li>Resource Title: All trap capture data File Name: all_recapture_data.csv Resource Description: Each row is the number of marked male flies released on a particular date and recaptured in a given trap on a subsequent date.</li><li>Resource Title: Metadata File Name: metadata.pdf Resource Description: From a previous package, EML metadata. Useful for reference.</li></ul><p></p>

Tags: ars, attraction-range, data-gov, mark-release-recapture, np304, pheromone-lure, tephritidae
Organization: Department of Agriculture
NWISRL South Farm Study for Greenhouse gas Reduction through Agricultural Carbon Enhancement network in Kimberly, Idaho

<p>NWISRL South Farm Study for Greenhouse gas Reduction through Agricultural Carbon Enhancement network in Kimberly, Idaho
We report N2O emissions along with CO2 and CH4 from a silage corn (2013)–barley (2014)–alfalfa (2015) rotation under conventional tillage and sprinkler irrigation. The main study objectives were to evaluate the effectiveness of an enhanced-efficiency fertilizer (SuperU; stabilized granular urea with urease and nitrification inhibitors) to reduce N2O emissions when compared to granular urea, and determine GHG emissions from fall-applied dairy manure or composted dairy manure and spring-applied dairy manure. Nitrogen treatments were only applied during the first two years of the study. Compared to urea, SuperU plots emitted 53% less N2O during the monitoring period with corn, while no N2O emission reductions occurred in 2014 with barley. The N2O-N emission losses as a percentage of total N applied were 0.21% and 0.04% for urea and SuperU in 2013, respectively, with losses of 0.05% from both urea fertilizers in 2014. On average, N2O fluxes from fall and spring manure were statistically similar and greater than the other N treatments in 2014, and there was a lasting manure treatment effect on emissions when under alfalfa. Carbon dioxide fluxes, on average, were greatest from fall- and spring-applied manure during the first two years of study. Methane fluxes were negative on average, indicating microbial oxidation, and no differences occurred among the N treatments. Silage corn, barley grain, and alfalfa yields were statistically similar among all N treatments. This work demonstrates that SuperU can potentially reduce N2O emissions from irrigated cropping systems in the semiarid western United States while not affecting crop yields.</p> <div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Kimberly, ID NWISRL South Farm Study (IDKM) CSV data.</p> <p>File Name: IDKM_csv_data.zip</p><p>Resource Description: CSV format data on Experimental Units, Field Sites, Greenhouse Gas Flux, Residue Management, Soil Chemistry, Soil Physics, Amendments, Growth Stages, Planting, Tillage, Persons, Treatments, Weather Daily, Weather Station.</p></li></ul>

Tags: ars, data-gov, environment, farming, gracenet, np211, np212
Organization: Department of Agriculture
Elderberry syrup buffer modeling data

<p dir="ltr">Data for the article: "Modeling the Formulation pH of Elderberry Syrup with multiple weak acids", <a href="https://doi.org/10.1111/1750-3841.16664">https://doi.org/10.1111/1750-3841.16664</a>. To develop methods to assess the influence of the ingredients of an acidified elderberry syrup on product pH., a total of 16 model syrup formulations containing elderberry juice with mixed acids (malic, acetic, and ascorbic) and having pH values between 3 and 4 were prepared. The pH values of the formulations were compared to predicted values from combined buffer models of the individual ingredients. Regression analysis indicated an excellent fit of the observed and predicted pH data, with a root mean square error of 0.076 pH units. The results indicated that buffer models may be useful for in silico estimates of how the ingredients in acid and acidified foods may influence pH, thus aiding in product development and safety assessments.</p><p dir="ltr">Resources in this dataset:</p><ul><li>Resource Title: Elderberry syrup buffer modeling data File Name: Tables S1 and S2 Buffer modeling data.xlsx Resource Description: The concentration and pK values for each buffer of a mixture of elderberry syrup ingredients. The formulation mixtures are described in the article "Modeling the Formulation pH of Elderberry Syrup with multiple weak acids" <a href="https://doi.org/10.1111/1750-3841.16664">https://doi.org/10.1111/1750-3841.16664</a>.<br></li></ul><p></p>

Tags: ars, buffer-modeling, data-gov, elderberry, np108, ph, product-development, weak-acid
Organization: Department of Agriculture
Data from: Quantifying wildfire risk to the built environment in rangelands of the US Interior West

<p dir="ltr"><b>Overview</b></p><p dir="ltr">Fire increasingly conflicts with the built environment. The Wildland-Urban Interface (WUI) describes areas where vegetation near the built environment increases wildfire hazard. In the United States, attention concentrates on WUI in forested areas, but human populations are extending into rangelands. The combination of WUI expansion and woody plant encroachment might present novel challenges to wildfire management, especially given the rural nature of rangelands in the US, which extends the response time of emergency services. We use publicly available data to describe the abundance, distribution, type, and overall wildfire risk in rural rangelands. Most of the WUI in the US Interior West (54%) occurs in rangeland: The majority of the US Interior West is rangeland and 4.3% of that—over 1 million km<sup>2</sup> —is WUI. Most WUI is rural: 59% is further than 10 km from town and Tribal areas are even more remote. Rangeland WUI is approximately twice as likely to be degraded by woody encroachment than non-WUI rangeland, suggesting that conventional fire suppression tactics for rangeland fuels might be insufficient or unsafe. Greater awareness of rural rangeland WUI might help leverage community-level adaptive capacity against the novel challenges of protecting lives and property beyond urban/peri-urban zones.</p><p dir="ltr"><b>Files included</b></p><p dir="ltr">These files include summarized data and R script used to create the analysis described above.</p>

Tags: landscape-ecology, rural-capacity, wildfire-risk, wildland-urban-interface
Organization: Department of Agriculture
Nitrogen Source Study for Greenhouse gas Reduction through Agricultural Carbon Enhancement network in Fort Collins, Colorado

<p>Nitrogen Source Study for Greenhouse gas Reduction through Agricultural Carbon Enhancement network in Fort Collins, Colorado
Nitrogen fertilization is essential for optimizing crop yields; however, it increases N2O emissions. The study objective was to compare N2O emissions resulting from application of commercially available enhanced-effi ciency N fertilizers with emissions from conventional dry granular urea in irrigated cropping systems. These emissions were monitored from several irrigated cropping systems receiving N fertilizer rates ranging from 0-246 kg/ha from years 2007-2008 with intermediate rates of 157 kg/ha applied to the barley crop in corn-barley rotation and 56 kg/ha applied to the dry bens in the corn-dry bean rotation. Cropping systems included conventional-till continuous corn (CT-CC), no-till continuous corn (NT-CC), no-till corn–dry bean (NT-CDb), and no-till corn–barley (NT-CB). Nitrous oxide fluxes were measured during ten growing seasons using static, vented chambers and a gas chromatograph analyzer.  This work shows that the use of no-till and enhanced-effi ciency N fertilizers can potentially reduce N2O emissions from irrigated systems.</p> <div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: GeoData catalog record.</p> <p>File Name: Web Page, url: <a href="https://geodata.nal.usda.gov/geonetwork/srv/eng/catalog.search;jsessionid=6BDC7D66926FA0429979C09A9A3B0601?node=srv#/metadata/11aec7d7-2a2a-4b52-ae96-990001c7d994" target="_blank">https://geodata.nal.usda.gov/geonetwork/srv/eng/catalog.search;jsessionid=6BDC7D66926FA0429979C09A9A3B0601?node=srv#/metadata/11aec7d7-2a2a-4b52-ae96-990001c7d994</a> </p></li></ul>

Tags: ars, barley, carbon-dioxide, corn, cropping-systems, crops, data-gov, emissions, environment, farming, fertilizer, greenhouse-gas-emissions, herbicides, irrigation, methane, nitrous-oxide, np211, np212, soil, tillage, water
Organization: Department of Agriculture
PhenoCam images from ARSLTARMDCR site, Caroline County, Maryland, USA since 2017

<p>This data set consists of repeat digital imagery from a tower-mounted digital camera (hereafter, PhenoCam) maintained by the USDA-ARS Hydrology Remote Sensing Laboratory (HRSL) in the Lower Chesapeake Bay (LCB) watershed. HRSL is a member of the PhenoCam network, which has as its mission to serve as a long-term, continental-scale, phenological observatory. Imagery is uploaded to the PhenoCam server every 30 minutes. The archived images provide a permanent record that can be visually-inspected to determine the phenological state of the vegetation at any point in time. Vegetation greenness metrics (e.g., GCC) derived from the ratio of the green color band to sum of red, green, and blue color bands serve as proxies for vegetation greenness. Greenness metrics can be extracted from the images using simple image processing methods in 1-day or 3-day increments.</p>
<p>This dataset is available to the public and may be freely downloaded. Please keep the designated Contact person informed of any plans to use the dataset. Consultation or collaboration with the original investigators is strongly encouraged. Publications and data products that make use of the dataset must include proper acknowledgement.</p>
<p>The development of PhenoCam has been supported by multiple entities. Those include the Northeastern States Research Cooperative, NSF’s Macrosystems Biology program (award EF-1065029), DOE’s Regional and Global Climate Modeling program (award DE-SC0016011), the US National Park Service Inventory and Monitoring Program, the USA National Phenology Network (grant number G10AP00129 from the United States Geological Survey), and is currently supported by the Department of Agriculture (USDA) Agricultural Research Service.</p>
<p>This research was a contribution from the Long-Term Agroecosystem Research (LTAR) network. LTAR is supported by the United States Department of Agriculture (USDA) Agricultural Research Service.</p>

Tags: ars, choptank-river, corn-soybean-rotation, data-gov, long-term-monitoring-sites, ltar, np211, np212, phenocam, phenology, primary-productivity
Organization: Department of Agriculture
Carbon Crops Study for Greenhouse gas Reduction through Agricultural Carbon Enhancement network and Resilient Economic Agricultural Practices in Morris, Minnesota

<p>Carbon Crops Study for Greenhouse gas Reduction through Agricultural Carbon Enhancement network and Resilient Economic Agricultural Practices in Morris, Minnesota
The overall goal of the Carbon Crop study, established in 2000, was to assess strategies for increasing soil C sequestration including converting to no till systems and including perennial grasses (e.g., switchgrass and big bluestem) Overall, the goal of the study has remained constant, although individual treatments were changed after an incremental soil sampling, in response to new hypotheses and questions. Soil sampling is conducted as treatment changes are implemented. In 2012, two of the perennial grass systems (spring harvest of Switchgrass and Big Bluestem) were changed to corn/soybean rotations, beginning with a soybean entry point, to determine if the SOC accrued under the perennial system was lost by converting to a short annual rotation managed without tillage. The second change made was to compare the productivity between recent and traditional switchgrass cultivars. The final change was conversion of autumn harvest of Big Bluestem treatment replaced with an annual biomass crop – Sorghum-Sudan grass. Soil samples were taken to 1 m in 2000, 2006, 2011, and 2016. Nitrous oxide and carbon dioxide fluxes from the soil were measured from June 2009 through March 2012.</p> <div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: GeoData catalog record.</p> <p>File Name: Web Page, url: <a href="https://geodata.nal.usda.gov/geonetwork/srv/eng/catalog.search#/metadata/21d6ff3b-de69-44ff-a2b6-980a9c972a35" target="_blank">https://geodata.nal.usda.gov/geonetwork/srv/eng/catalog.search#/metadata/21d6ff3b-de69-44ff-a2b6-980a9c972a35</a> </p></li></ul>

Tags: andropogon-gerardii, ars, autumn, carbon, carbon-dioxide, carbon-nitrogen-ratio, carbon-sequestration, clay, cultivars, data-gov, energy-crops, environment, experimental-design, farming, gracenet, grasses, growing-season, harvesting, lakes, morris-mn-cc, natural-resources-and-genomics, nitrous-oxide, no-tillage, np211, np212, on-farm-research, outreach, panicum-virgatum, perennials, ph, reap, snow, soil, soil-conservation, soil-organic-carbon, soil-sampling, sorghum-bicolor-subsp-drummondii, soybeans, spring, temperature, tillage, winter
Organization: Department of Agriculture
Data from: Woody perennial polycultures increase ant diversity and ant-mediated ecosystem services compared to conventional corn-soybean rotations

<p dir="ltr">Data files for manuscript titled "Woody perennial polycultures increase ant diversity and ant-mediated ecosystem services compared to conventional corn-soybean rotations".</p><p dir="ltr">Excel file with 4 tabs: Metadata, abundance and richness, community composition, and sentinel prey consumption.</p><p dir="ltr">Abstract from paper: The role plant diversity has played in regulating insect communities has been of interest for decades. Recent syntheses from agroecosystems suggest increasing plant diversity can positively affect beneficial insects like predators, reducing pest pressure and increasing yield. However, the agricultural landscape of the Midwestern United States is dominated by just two crops - corn and soybean - which cover approximately 180 million acres of arable land yearly. New ideas to conserve wildlife that additionally provide economic opportunities for farmers must be developed in order to promote sustainable and resilient ecosystems. Here we tested the capacity of an alternative cropping system to support more diverse insect populations than conventional cropping systems. We quantified differences in the diversity of an insect taxon, ants (Hymenoptera: Formicidae), over an annual cycle using pitfall traps in thirty-two 2-m<sup>2</sup> plots of either woody perennial polycultures that contained apples, chestnuts, currants, hazelnuts, and raspberries or conventional corn-soybean rotations. In doing so, we found that woody perennial polycultures supported 2.4-fold more ant species and maintained a unique fauna of specialist and predatory ants. The observed differences in diversity were linked to higher levels of predation as 18.2-fold more sentinel prey were consumed during each month of the growing season. Combined, our results suggest that agricultural landscapes in the Midwestern United States can be modified to support important beneficial insects like ants while still producing commodities that can be economically beneficial to farmers.</p>

Tags: agriculture, agroforestry, biodiversity, biological-control, natural-enemy, sentinel-prey
Organization: Department of Agriculture
Data from: Scale Insect (Hemiptera: Coccomorpha) Morphology is Transformed Under Trophobiosis

<p>Supplementary raw data, R scripts, and results underpinning analyses of geometric morphometric and linear data derived from scale insects; includes source code for all analyses, raw data for ostiole, leg, and body shape analyses, and alpha tables for body size analysis and ostioles analyses. Abbreviations are defined in the R script file.  See README for list of resources.</p>

Tags: acropyga, ars, coccoidea, coccomorpha, data-gov, morphometrics, mutualism, np304, root-mealybug
Organization: Department of Agriculture
Nitrogen Rate Study for Greenhouse gas Reduction through Agricultural Carbon Enhancement network in Fort Collins, Colorado

<p>Nitrogen Rate Study for Greenhouse gas Reduction through Agricultural Carbon Enhancement network in Fort Collins, Colorado
Nitrogen fertilization is essential for optimizing crop yields; however, it increases N2O emissions. These emissions were monitored from several irrigated cropping systems receiving N fertilizer rates ranging from 0-246 kg/ha from years 2002-2006. Cropping systems included conventional-till continuous corn and no-till continuous corn at varying N rates. Nitrous oxide fluxes were measured during four growing seasons using static, vented chambers and a gas chromatograph analyzer.  This work shows that the use of no-till can potentially reduce N2O emissions from irrigated systems and increase soil carbon storage.</p> <div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Fort Collins, CO Nitrogen Rate Study (COFOARD1) CSV data.</p> <p>File Name: COFOARD1_csv_data.zip</p><p>Resource Description: CSV format data on Experimental Units, Field Sites, Greenhouse Gas Flux, Soil Chemistry, Soil Physics, Yield Nutrient Uptake, Amendments, Planting, Tillage, Persons, Treatments, Weather Daily, Weather Station. </p></li></ul>

Tags: ars, corn, cropping-systems, data-gov, emissions, environment, farming, fertilizer, greenhouse-gas-emissions, herbicides, methane, nitrous-oxide, np211, np212, soil, tillage
Organization: Department of Agriculture
Data and code from: A high throughput approach for measuring soil slaking index

<p>This dataset includes soil wet aggregate stability measurements from the Upper Mississippi River Basin LTAR site in Ames, Iowa. Samples were collected in 2021 from this long-term tillage and cover crop trial in a corn-based agroecosystem.</p>
<p>We measured wet aggregate stability using digital photography to quantify disintegration (slaking) of submerged aggregates over time, similar to the technique described by Fajardo et al. (2016) and Rieke et al. (2021). However, we adapted the technique to larger sample numbers by using a multi-well tray to submerge 20-36 aggregates simultaneously. We used this approach to measure slaking index of 160 soil samples (2120 aggregates).</p>
<p>This dataset includes slaking index calculated for each aggregates, and also summarized by samples. There were usually 10-12 aggregates measured per sample.</p>
<p>We focused primarily on methodological issues, assessing the statistical power of slaking index, needed replication, sensitivity to cultural practices, and sensitivity to sample collection date. We found that small numbers of highly unstable aggregates lead to skewed distributions for slaking index. We concluded at least 20 aggregates per sample were preferred to provide confidence in measurement precision. However, the experiment had high statistical power with only 10-12 replicates per sample. Slaking index was not sensitive to the initial size of dry aggregates (3 to 10 mm diameter); therefore, pre-sieving soils was not necessary. The field trial showed greater aggregate stability under no-till than chisel plow practice, and changing stability over a growing season. These results will be useful to researchers and agricultural practitioners who want a simple, fast, low-cost method for measuring wet aggregate stability on many samples.</p>

Tags: cover-crops, image-analysis-routines, no-tillage-farming, soil-health-management, wet-aggregate-stability
Organization: Department of Agriculture