AndreaBozzo/ceres-open-data-index huggingface dataset:
Data from: Site-specific management of cotton root rot using airborne and high resolution satellite imagery and variable rate technology

<p>Cotton root rot is a century-old cotton disease that now can be effectively controlled with Topguard Terra fungicide. Because this disease tends to occur in the same general areas within fields in recurring years, site-specific application of the fungicide only to infested areas can be as effective as and considerably more economical than uniform application. The overall objective of this research was to demonstrate how site-specific fungicide application could be implemented based on historical remote sensing imagery and using variable-rate technology. Procedures were developed for creating binary prescription maps from historical airborne and high-resolution satellite imagery. Two different variable-rate liquid control systems were adapted to two existing cotton planters, respectively, for site-specific fungicide application at planting. One system was used for site-specific application on multiple fields in 2015 and 2016 near Edroy, Texas, and the other system was used on multiple fields in both years near San Angelo, Texas. Airborne multispectral imagery taken during the two growing seasons was used to monitor the performance of the site-specific treatments. Results based on prescription maps derived from historical airborne and satellite imagery of two fields in 2015 and one field in 2016 are reported in this article. Two years of field experiments showed that the prescription maps and the variable-rate systems performed well and that site-specific fungicide treatments effectively controlled cotton root rot. Reduction in fungicide use was 41%, 43%, and 63% for the three fields, respectively. The methodologies and results of this research will provide cotton growers, crop consultants, and agricultural dealers with practical guidelines for implementing site-specific fungicide application using historical imagery and variable-rate technology for effective management of cotton root rot.</p>
<p>Resources in this dataset:</p>
<ul>
<li>
<p>Resource Title: A ground picture of cotton root rot
File Name: IMG_0124.JPG
Resource Description: A cotton root rot-infested area in a cotton field near Edroy, TX.</p>
</li>
<li>
<p>Resource Title: An aerial image of a cotton field
File Name: Color-infrared image of a field.jpg
Resource Description: Aerial color-infrared (CIR) image of a cotton field infested with cotton root rot.</p>
</li>
<li>
<p>Resource Title: As-applied fungicide application data
File Name: Jim Ermis-Farm 1-Field 11 Fungicide Application.csv
Resource Description: As-applied fungicide application rates for variable rate application of Topguard to a cotton field infested with cotton rot</p>
</li>
</ul>

Tags: airborne-imagery, cotton-root-rot, high-resolution-satellite-imagery, np304, np305, prescription-map, variable-rate-application
Organization: Department of Agriculture
Data from: Alternative fertilization practices lead to improvements in yield-scaled global warming potential in almond orchards

<p dir="ltr">This study investigates the impact of alternative fertilization practices on the yield-scaled global warming potential in almond orchards. Almond production contributes to greenhouse gas emissions due to fertilizer nitrogen (N) use. Field experiments were conducted in an almond orchard using three fertigation practices: Advance Grower Practice (AGP), Pump and Fertilizer (P&F) and High Frequency-Low Concentration (HFLC).</p><p dir="ltr">The study was conducted in a commercial almond orchard (16 ha, 2015 and 2016 growing seasons) in the San Joaquin Valley (Madera, California; 36◦ 49’ 15.85” N 120◦ 12’1.20 W, elevation 60 m). The trees (ca. 16 years, 73 trees per row) were spaced 5.5 m tree to tree within row and approximately 14.6 m between alternating rows of Nonpareil and Carmel cultivars. The soil type was the Cajon soil series (<i>Mixed, thermic Typic Torripsamments</i>), characterized by loose fine sand with low organic carbon content and low water holding capacity (Web Soil Survey, 2021). The orchard exists in a semiarid, Mediterranean-like climate. All samples were collected in the second and third year after fertigation treatments were initiated.</p><p dir="ltr">Urea Ammonium Nitrate [UAN; 32% nitrogen (N), composed of 50% urea-N, 25% NH<sub>4</sub><sup>+</sup>-N, and 25% NO<sub>3</sub><sup> -</sup>-N) was delivered through the irrigation system to all three irrigation treatments (i.e. fertigation). Generally, the fertilizer N content was similar across all Pump and Fertigate treatments but the frequency of application varied. Two treatments (, P&F; HFLC, High Frequency-Low Concentration) provided a similar total, annual N targeted to meet the demands for high yielding commercial almond production based on above- and below-ground growth. The third, AGP, applied approximately 30% more N fertilizer than P&F and HFLC because it represented the standard growing practice with respect to timing and quantity of fertilizer application for the local industry. P&F and HFLC reduced the amount of applied N fertilizer by accounting for groundwater N concentrations. Each fertigation treatment was composed of four tree rows, with each of the four replicates placed along one of the two center tree rows.</p><p dir="ltr">Greenhouse gas emissions from fertigation were sampled using an array of static chambers that were placed to cover the drip zone and within the tree row and alley. At the same time, soil water content, temperature and inorganic N pools were collected. During harvest, almond yields were measured to allow for calculation of yield-scaled global warming potential.</p>

Tags: almonds, california, fertigation, greenhouse-gas-emissions, nitrous-oxide
Organization: Department of Agriculture
Long-Term Agricultural Research (LTAR) network - Meteorological Station - Rock Springs - Upper Chesapeake Bay

<p>The USDA-ARS Pasture Systems and Watershed Management Research Unit established a meteorological station in 2015 as part of the Upper Chesapeake Bay (UCB) site in the Long-Term Agroecosystem Research (LTAR) network (est. 2012). Measurements include air temperature and humidity, shortwave (solar) irradiance, longwave (thermal) radiation, wind speed and direction, barometric pressure, and rainfall. Data are recorded at 15-minute intervals.</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/5beaa9db-5772-43b1-87ae-7148602d4619" target="_blank">https://geodata.nal.usda.gov/geonetwork/srv/eng/catalog.search#/metadata/5beaa9db-5772-43b1-87ae-7148602d4619</a> </p></li></ul>

Tags: air-pressure, air-temperature, ars, climate, data-gov, longwave-radiation, meteorological-data, np211, shortwave-radiation, weather, wind-speed
Organization: Department of Agriculture
Data from: Temperature influences lipid content in the red harvester ant, Pogonomyrmex barbatus

<p>Data files for manuscript titled "Temperature influences lipid content in the red harvester ant, <em>Pogonomyrmex barbatus</em>".</p>
<p>Excel file with 3 tabs: Metadata, Monthly Lipid Content, and 10 Day Lipid Content. Metadata is contained within Excel file that describes all variables for each tab.</p>
<p>Abstract from paper:
Temperature is one of the most important environmental conditions affecting physiological processes in ectothermic organisms like ants. Yet we often lack information on how certain physiological traits co-vary with temperature across time. Here, we test predictions on how one trait—lipid content—co-varies with temperature using a conspicuous, ground-dwelling harvester ant. We focus on lipid content as fat bodies are metabolically active tissues that are important for storing and releasing energy in response to demand, which could be vital for survival under variable temperatures. From March to November, we extracted lipids from surface workers of 14 colonies while simultaneously recording ground temperature. We first assessed if lipid content was highest during cooler temperatures when ants were less active and less metabolically stressed. In doing so, we found that lipid content of ants declined almost 70% from cool months (November lipid content = 14.6%) to hot months (August lipid content = 4.6%). We next assessed if lipid levels from a group of ants collected at a single time point could change by placing individuals into environmental chambers set at 10, 20, and 30°C (i.e. the approximate span of average temperatures from March to November). Temperature again had a significant impact such that after 10 days, lipid content of ants in the hottest chamber (30°C) had decreased more than 75%. While intraspecific variation in physiological traits often follows seasonal patterns, our results suggest fluctuations in temperature may account for a portion of the variance observed in traits like lipid content.</p>

Tags: ars, body-size, data-gov, fat-content, formicidae, np304, physiology, temperature
Organization: Department of Agriculture
Data from: Honeydew associated with four common crop aphid species increases longevity of the parasitoid wasp, Bracon cephi (Hymenoptera: Braconidae)

<p>Data are from a laboratory experiment conducted to examine the potential effects of honeydew from six different aphid species by crop species combinations on the longevity of Bracon cephi Gahan (Hymenoptera: Braconidae), the most important biological control of the wheat stem sawfly, Cephus cinctus Norton (Hymenoptera: Cephidae), a major pest of wheat in the northern Great Plains of North America. We quantified the number of days parasitoids lived on each honeydew type. </p>
<p>Abstract from published manuscript:
The absence of sugar resources can be an important factor in limiting the success of parasitoids as biological control agents. Restoring vegetation complexity within agricultural landscapes has thus become a major focus of conservation biological control efforts, with a traditional emphasis on nectar resources. Aphid honeydew is also an important source of sugars that is infrequently considered. We carried out a laboratory experiment to examine the potential effects of honeydew from six different aphid species by crop species combinations on the longevity of Bracon cephi Gahan (Hymenoptera: Braconidae), the most important biological control of the wheat stem sawfly, Cephus cinctus Norton (Hymenoptera: Cephidae), a major pest of wheat in the northern Great Plains of North America. The benefits of honeydew for parasitoid longevity varied significantly among different aphid and crop species, illustrating the complexity of these interactions. However, honeydew produced by four aphid species commonly found in wheat, pea, and canola crops significantly increased the longevity (by two- to threefold) of the parasitoid. The study suggests that honeydew provisioning could be an important mechanism underlying the benefits of crop diversification to support biological control that merits further research. </p>
<p>Resources in this dataset:</p>
<ul>
<li>
<p>Resource title: Data Directory
File name: Data Directory for Bc x Honeydew.xlsx
Resource description: Column descriptions for WSS BC X Honeydew longevity_ Ag Data Commons</p>
</li>
<li>
<p>Resource title: Parasitoid survival by honeydew treatment
File name: WSS BC X Honeydew longevity_ Ag Data Commons.xlsx
Resource description: The data are parasitoid survival in days on six different honeydew sugar resources.</p>
</li>
</ul>

Tags: ars, biological-control, bracon-cephi, data-gov, np304, nutiritional-ecology, sugar-resources, wheat-stem-sawfly
Organization: Department of Agriculture
Data from: Vegetative Buffer Strips for Reducing Herbicide Transport in Runoff: Effects of Buffer Width, Vegetation, and Season

<p>The effectiveness of vegetative buffer strips (VBS) for reducing herbicide transport has not been well documented for runoff prone soils. A multi‐year plot‐scale study was conducted on an eroded claypan soil with the following objectives: (1) assess the effects of buffer width, vegetation, and season on runoff transport of atrazine (ATR), metolachlor (MET), and glyphosate; (2) develop VBS design criteria for herbicides; and (3) compare differences in soil quality among vegetation treatments. Rainfall simulation was used to create uniform antecedent soil water content and to generate runoff. Vegetation treatment and buffer width impacted herbicide loads much more than season. Grass treatments reduced herbicide loads by 19‐28% and sediment loads by 67% compared to the control. Grass treatments increased retention of dissolved‐phase herbicides by both infiltration and adsorption, but adsorption accounted for the greatest proportion of retained herbicide load. This latter finding indicated VBS can be effective on poorly drained soils or when the source to buffer area ratio is high. Grass treatments modestly improved surface soil quality 8‐13 years after establishment, with significant increases in organic C, total N, and ATR and MET sorption compared to continuously tilled control. Herbicide loads as a function of buffer width were well described by first‐order decay models which indicated VBS can provide significant load reductions under anticipated field conditions. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Supplemental Material: Main factor interaction effects on runoff (flow depth), herbicide and sediment loads, and dissolved‐phase herbicide retention - Download docx.</p> <p>File Name: downloadSupplement, url: <a href="https://onlinelibrary.wiley.com/action/downloadSupplement?doi=10.1111/1752-1688.12526&file=jawr12526-sup-0001-Supinfo.docx">https://onlinelibrary.wiley.com/action/downloadSupplement?doi=10.1111/1752-1688.12526&file=jawr12526-sup-0001-Supinfo.docx</a> </p><p>Table S1. The effect of vegetation and buffer width on runoff depth.
Table S2. The effect of vegetation and buffer width on input normalized atrazine, metolachlor, glyphosate, and sediment loads.
Table S3. Vegetation by season interactions for input normalized atrazine and metolachlor loads.
Table S4. The effect of vegetation and buffer width on reductions in dissolved-phase herbicide loads by infiltration and adsorption.
Figure S1. Effect of vegetation treatment and buffer width on herbicide and sediment input normalized loads, illustrating the significant vegetation by width interaction for all four contaminants.
</p></li></ul><p></p>

Tags: ars, data-gov, grass-treatments, herbicide-load, vegetated-buffer-strips
Organization: Department of Agriculture
USDA Database for the Flavonoid Content of Selected Foods, Release 3.3 (March 2018)

<p>The database contains values for 506 food items for five subclasses of flavonoids:</p>
<ul>
<li>FLAVONOLS:Quercetin, Kaempferol, Myricetin, Isorhamnetin</li>
<li>FLAVONES:</li>
<li>Luteolin, Apigenin</li>
<li>FLAVANONES:</li>
<li>Hesperetin, Naringenin, Eriodictyol</li>
<li>FLAVAN-3-OLS:</li>
<li>(+)-Catechin, (+)-Gallocatechin, (-)-Epicatechin, (-)-Epigallocatechin, (-)-Epicatechin 3-gallate, (-)-Epigallocatechin 3-gallate, Theaflavin, Theaflavin 3-gallate, Theaflavin 3'-gallate, Theaflavin 3,3' digallate, Thearubigins</li>
<li>ANTHOCYANIDINS:</li>
<li>
<p>Cyanidin, Delphinidin, Malvidin, Pelargonidin, Peonidin, Petunidin </p>
<div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: USDA Database for the Flavonoid Content of Selected Foods, Release 3.3 (March 2018).</p> <p>File Name: Flav_R03-3.accdb</p><p>Resource Description: This file contains the Flavonoid Database imported into a MS Access database.  In addition to the summary values, a separate file containing the individual values used to calculate the summary values is included, along with all information on conversion factors used to calculate the individual aglycone values, analytical method, country of origin, etc.  It also includes relationships between files. You need MS Access 2007 or later to use this file. The file structure is the same as that of the USDA National Nutrient Database for Standard Reference. 
</p></li><br><li><p>Resource Title: USDA Database for the Flavonoid Content of Selected Foods Release 3.3 Documentation .</p> <p>File Name: Flav3.3.pdf</p></li></ul>
</li>
</ul>

Tags: anthocyanidins, ars, data-gov, egcg, flavan-3-ols, flavanones, flavones, flavonoids, quercetin
Organization: Department of Agriculture
GitHub repository for: Heritable genetic differences affect sunflower rhizosphere archaeal, bacterial, and fungal communities across all taxonomic levels

<p dir="ltr">A GitHub repository (<a href="https://github.com/KaneLab/SunflowerG" rel="noopener noreferrer" target="_blank">https://github.com/KaneLab/SunflowerG</a>) containing data, processing and analysis code, initial exploratory figures, final publication figures, and final publication tables was released through Zenodo with a stable DOI (<a href="https://doi.org/10.5281/zenodo.14523061" rel="noopener noreferrer" target="_blank">https://doi.org/10.5281/zenodo.14523061</a>)</p>

Tags: assembly, diversity, genotype, heritability, rhizosphere, sunflower
Organization: Department of Agriculture
Dataset from: Variation in patterns of production and water-use efficiency among agroecosystems across the LTAR Network

<p dir="ltr">Across agroecosystems, water is a key driver of primary production, and thus, the relationship between water and production (i.e., water-use efficiency; WUE) provides a relevant indicator for evaluating agroecosystem function. These data were used to characterize this relationship spanning diverse agroecosystems and climates represented by the USDA’s Long-Term Agroecosystem Research (LTAR) network. This dataset contains precipitation and aboveground net primary production (ANPP) across an extensive set of rainfed production systems and climate conditions, including rangelands, croplands, and pasturelands that span a precipitation gradient of 265-1347 mm yr<sup>-1</sup>. Data include long-term ANPP data from fifteen LTAR sites collected between 1983 and 2022, with record lengths ranging from 5 to 38 years, and corresponding annual precipitation amounts. These long-term data serve as an important resource for understanding how shifts in water availability with climate change may impact the ability of agricultural lands to produce the resources needed to support a growing human population.</p>

Tags: agroecosystem, climate-change, precipitation, production, water-use-efficiency-wue
Organization: Department of Agriculture
Data from: Modeling the Spread of a Livestock Disease With Semi-Supervised Spatiotemporal Deep Neural Networks

<p>This dataset contains the spatiotemporal data used to train the spatiotemporal deep neural networks described in "Modeling the Spread of a Livestock Disease With Semi-Supervised Spatiotemporal Deep Neural Networks". The dataset consists of two sets of NumPy arrays. The first set: <code>X_grid.npy</code> and <code>Y_grid.npy</code> were used to train the convolutional LSTM, while the second set: <code>X_graph.npy</code>, <code>Y_graph.npy</code>, and <code>edge_index.npy</code> were used to train the graph convolutional LSTM. The data consists of spatiotemporally varying environmental and anthropogenic variables along with case reports of vesicular stomatitis. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: NumPy Arrays of Spatiotemporal Features and VS Cases.</p> <p>File Name: vs_data.zip</p><p>Resource Description: This is a ZIP archive containing five NumPy arrays of spatiotemporal features and geotagged VS cases.</p><p>Resource Software Recommended: NumPy,url: <a href="https://numpy.org/">https://numpy.org/</a> </p></li></ul><p></p>

Tags: ars, data-gov, deep-learning, machine-learning, vesicular-stomatitis-virus
Organization: Department of Agriculture
Data and code from: Cover crop and crop rotation effects on tissue and soil population dynamics of Macrophomina phaseolina and yield in no-till system - V2

<p>[Note 2023-08-14 - Supersedes version 1, <a href="https://doi.org/10.15482/USDA.ADC/1528086">https://doi.org/10.15482/USDA.ADC/1528086</a> ]</p>
<p>This dataset contains all code and data necessary to reproduce the analyses in the manuscript:</p>
<p>Mengistu, A., Read, Q. D., Sykes, V. R., Kelly, H. M., Kharel, T., & Bellaloui, N. (2023). Cover crop and crop rotation effects on tissue and soil population dynamics of Macrophomina phaseolina and yield under no-till system. Plant Disease. <a href="https://doi.org/10.1094/pdis-03-23-0443-re">https://doi.org/10.1094/pdis-03-23-0443-re</a></p>
<p>The .zip archive <code>cropping-systems-1.0.zip</code> contains data and code files.</p>
<h2>Data</h2>
<ul>
<li><code>stem_soil_CFU_by_plant.csv</code>: Soil disease load (SoilCFUg) and stem tissue disease load (StemCFUg) for individual plants in CFU per gram, with columns indicating year, plot ID, replicate, row, plant ID, previous crop treatment, cover crop treatment, and comments. Missing data are indicated with <code>.</code></li>
<li><code>yield_CFU_by_plot.csv</code>: Yield data (YldKgHa) at the plot level in units of kg/ha, with columns indicating year, plot ID, replicate, and treatments, as well as means of soil and stem disease load at the plot level.</li>
</ul>
<h2>Code</h2>
<ul>
<li><code>cropping_system_analysis_v3.0.Rmd</code>: RMarkdown notebook with all data processing, analysis, and visualization code</li>
<li><code>equations.Rmd</code>: RMarkdown notebook with formatted equations</li>
<li><code>formatted_figs_revision.R</code>: R script to produce figures formatted exactly as they appear in the manuscript</li>
</ul>
<p>The Rproject file <code>cropping-systems.Rproj</code> is used to organize the RStudio project. Scripts and notebooks used in older versions of the analysis are found in the <code>testing/</code> subdirectory. Excel spreadsheets containing raw data from which the cleaned CSV files were created are found in the <code>raw_data</code> subdirectory.</p>

Tags: ars, charcoal-rot, cover-crops, crop-rotation, data-gov, glycine-max, macrophomina-phaseolina, np303, soybean, soybean-yield
Organization: Department of Agriculture
Data from: Genetic diversity and classification of <i>Colletotrichum sublineola</i> pathotypes using a standard set of sorghum differentials

<p dir="ltr">A total of 30 isolates of Colletotrichum sublineola, causal agent of sorghum anthracnose were collected from Georgia, North Carolina, Puerto Rico, and Texas. Data for their virulence patterns on 18 sorghum differentials, RTx2536, SC748-5, Martin (BTx398), TAM428, BTx430, Brandes, SC112-14, Theis, BTx378, SC326-6, SC283, BTx623, SC328C, SC414-12E, PI570841, PI570726, PI569979, and IS18760 were collected from greenhouse trials in College Station, Texas by Louis K. Prom, Ezekiel J. S. Ahn, Ramasamy Perumal, Hugo E. Cuevas, William L. Rooney, Thomas S. Isakeit, and Clint W. Magill between 2014 and 2018. As described by Prom et al. 2012 and 2024, plants were assessed for anthracnose infection twice, 30 days post-inoculation and a week later using disease rating scale 1-5, where 1 = no symptoms or chlorotic flecks on leaves; 2 = hypersensitive reaction (reddening or red spots) on inoculated leaves but no acervuli formation; 3 = lesions on inoculated and bottom leaves with acervuli in the center; 4 = necrotic lesions with acervuli observed on inoculated and bottom leaves with infection spreading to middle leaves, and not yet on the flag leaves; and 5 = most leaves dead due to infection with infection on the flag leaf containing abundant acervuli. The symptom types were then categorized into two reaction classes, resistant = rating 1 or 2; and susceptible = rating 3, 4, or 5. As noted in the dataset, R = resistant response and S = susceptible response.</p><p><br></p>

Tags: colletotrichum-sublineola, fungal-genetics, pathotypes, population-genetics, sorghum-anthracnose, sorghum-differentials, virulence-pattern
Organization: Department of Agriculture