AndreaBozzo/ceres-open-data-index huggingface dataset:
Data from: Host plant water deficit stress impairs reproduction and development of the galling fly (Parafreutreta regalis), a biological control agent of Cape-ivy (Delairea odorata)

<p>Data from choice and no-choice tests associated with the paper cited below. Drought leading to water deficit stress is known to reduce performance of galling insects. The shoot tip-galling fly <em>Parafreutreta regalis</em> has been released for biological control of Cape-ivy (<em>Delairea odorata</em>) in California. Lack of moisture during the dry season causes wilting of Cape-ivy shoots, and subsequent reduced host quantity and quality could influence the fly’s ability to multiply and establish. We imposed water deficit stress on potted Cape-ivy plants, then measured the plant’s and insect’s response to water deficit compared to fully-watered plants. Water deficit stress was imposed during female oviposition (short-term), gall development (long-term), or full insect life cycle (long-term). Plants subjected to long-term water deficit showed declines in shoot growth, leaf area, and total biomass. In choice tests, 72% fewer galls were found on water deficit stressed plants, but there was no difference in the numbers of insects per gall. In no-choice tests, long-term water deficit reduced the number and size of galls by up to 51% and 39%, respectively, and puparia inside the galls were up to 35% smaller. Long-term water deficit also increased the time required for the insect to complete its life cycle (egg to adult) by about 10 days, and up to 80% fewer adults emerged, decreasing the fly’s rate of increase by up to five-fold. Our study shows that <em>P. regalis</em> will oviposit and develop successfully on water deficit-stressed plants, but declines in female preference, insect development and abundance could inhibit fly field establishment and/or population growth under climatic drought conditions.  </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Data from: Host plant water deficit stress impairs reproduction and development of the galling fly (Parafreutreta regalis), a biological control agent of Cape-ivy (Delairea odorata).</p> <p>File Name: CI Fly Drought Stress Biological Control Data Archive.csv</p><p>Resource Description: Tabular data for all choice and no-choice experiments</p><p>Resource Software Recommended: MS Excel,url: <a href="https://www.microsoft.com/en-us/microsoft-365?ms.url=office365com&rtc=1">https://www.microsoft.com/en-us/microsoft-365?ms.url=office365com&rtc=1</a> </p></li><br><li><p>Resource Title: Data dictionary text file describing column headings in the csv data file..</p> <p>File Name: Data Dictionary for Archiving Feb17-2021.txt</p><p>Resource Description: Data dictionary text file describing column headings in the csv file</p><p>Resource Software Recommended: MS Word,url: <a href="https://www.microsoft.com/en-us/microsoft-365?ms.url=office365com&rtc=1">https://www.microsoft.com/en-us/microsoft-365?ms.url=office365com&rtc=1</a> </p></li></ul><p></p>

Tags: ars, biological-control, data-gov, diptera, drought-stress, np304, water-deficit-stress, weed-management
Organization: Department of Agriculture
Transmission from swine-to-ferret of antigenically drifted contemporary swine H3N2 influenza A virus as indications of zoonotic risk to humans

<p>The dataset comprises viral titrations collected from nasal swabs of swine and weight measurements and viral titration from nasal washes of ferrets.
Nasal swabs were collected from pigs at 0, 1, 3, 5, 7 9 and 11 days post infection (dpi). Weight of ferrets was measured daily from -4 to 5, then 7, 9, 11 and 12 days post contact (dpc). Nasal washes were collected at 0, 1, 3, 5, 7, 9, 11 and 12 dpi from ferrets. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Viral shedding of swine and viral shedding and weight measures of ferrets.</p> <p>File Name: FLU38B_H3 swine and ferret data.xlsx</p><p>Resource Description: The dataset comprises viral titrations collected from nasal swabs of swine and weight measurements and viral titration from nasal washes of ferrets.
Nasal swabs were collected from pigs at 0, 1, 3, 5, 7 9 and 11 days post infection (dpi). Ferret weight was measured daily from -4 to 5, then 7, 9, 11 and 12 days post contact (dpc). Nasal washes were collected at 0, 1, 3, 5, 7, 9, 11 and 12 dpi from ferrets. </p></li></ul><p></p>

Tags: ars, data-gov, ferret, influenza-a-virus, np103, pig, transmission, viral-shedding
Organization: Department of Agriculture
Data from: Characterization of Levilactobacillus brevis genotypes and phenotypes from industrial cucumber fermentation identifies the presence of 1,2-propanediol metabolosomes in the species

<p>Data collected from Phenotypic Microarray (PM) plates PM01 and PM02, using an Omnilog system for the characterization of four species of <em>Levilactobacillus brevis</em> autochthonous to commercial cucumber fermentations and two ATCC reference strains, ATCC14869 and ATCC367. Each PM plate was duplicated for each isolate and the cells were prepared as suggested by the manufacturer. Omnilog data is the result of a screening and phenotypes should be confirmed using conditions that mimic the habitat of interest. This dataset was generated for scientific research purpose only. The <em>Levilactobacillus brevis</em> isolates included in this dataset have publicly available genome sequences described in the Microbiology Resource Announcement peer reviewed journal. </p>
<p>Resources in this dataset:</p>
<ul>
<li>Resource Title: Data for PM01 and PM02 for Levilactobacillus brevis autochthonous to cucumber fermentation and two reference strains
File Name: Ag Data Commons Levilactobacillus brevis PM01 & PM02.xlsx
Description: This is an Microsoft Excel file with two tabs, one for the PM01 plates and the second for the PM02 plates. Date corresponds to four Levilactobacillus brevis isolates that originated from commercial cucumber fermentations and two ATCC reference strains. All plates were ran in duplicates.</li>
</ul>

Tags: ars, cucumber, data-gov, fermentation, levilactobacillus-brevis, np306, omnilog, phenotypic-microarray, phenotyping, sugar-utilization
Organization: Department of Agriculture
NVND Study for Greenhouse gas Reduction through Agricultural Carbon Enhancement network in Sidney, Montana

<p>NVND Study for Greenhouse gas Reduction through Agricultural Carbon Enhancement network in Sidney, Montana
Management practices, such as irrigation, tillage, cropping system, and N fertilization, may influence soil greenhouse gas (GHG) emissions. We quantified the effects of irrigation, tillage, crop rotation, and N fertilization on soil CO2, N2O, and CH4 emissions from March to November, 2008 to 2011 in a Lihen sandy loam in western North Dakota. Treatments were two irrigation practices (irrigated and non-irrigated) and five cropping systems (conventional-tilled malt barley [Hordeum vulgaris L.] with N fertilizer [CTBFN], conventional-tilled malt barley with no N fertilizer [CTBON], no-tilled malt barley-pea [Pisum sativum L.] with N fertilizer [NTB-PN], no-tilled malt barley with N fertilizer [NTBFN], and no-tilled malt barley with no N fertilizer [NTBON]). The GHG fluxes varied with date of sampling while peaking immediately after precipitation, irrigation, and/or N fertilization events during increased soil temperature. Both CO2 and N2O fluxes were greater in CTBFN under the irrigated condition but CH4 uptake was greater in NTB-PN under the non-irrigated condition than in other treatments. While tillage and N fertilization increased CO2 and N2O fluxes by 8 to 30%, N fertilization and monocropping reduced CH4 uptake by 39 to 40%. The NTB-PN, regardless of irrigation, might mitigate GHG emissions by reducing CO2 and N2O emissions and increasing CH4 uptake relative to other treatments. To account for global warming potential for such a practice, information on productions associated with CO2 emissions along with N2O and CH4 fluxes are needed.</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/686b4236-9997-4d32-93b6-1bb490d3fa13" target="_blank">https://geodata.nal.usda.gov/geonetwork/srv/eng/catalog.search#/metadata/686b4236-9997-4d32-93b6-1bb490d3fa13</a> </p></li></ul>

Tags: ars, biomass, carbon-dioxide, climate-change, crops, data-gov, environment, farming, fertilizers, grains, greenhouse-gas-emissions, herbicides, irrigation, methane, nitrogen, np211, np212, soil, temperature, tillage, water
Organization: Department of Agriculture
LTAR Upper Mississippi River Basin - Morris - Swan Lake Research Farm Phenocam

<p>The PhenoCam network is collecting color and near infrared images year-round using cameras in fixed positions on agricultural lands including a site located on the Swan Lake Research Farm. The network effort was initiated in 2015 at this long-term, plot-scale research site. The camera at the research farm on focused a plot-scale, replicated research study that was established in 1997 to assess the long-term impacts of various tillage management options on soil organic carbon. Initially the study included eight tillage treatments: no-tillage, moldboard + disk tillage, chisel tillage, and fall and spring residue management, with or without strip-tillage and strip-tillage + sub-soiling. In 2004, the number of treatments were reduced to no-tillage, moldboard tillage, and fall and spring residue management without strip-tillage. All tillage treatments also had an early or late planting date. In 2008, the strip-tillage plots were modified to explore alternative strategies for supporting cellulosic bioenergy feedstock production, including planting of cellulosic feedstock.  The modification included adding perennials grasses into an extended 6-year rotation, winter cereal rye cover crops in a corn-soybean rotation, and an alternative Sorghum-Sudan grass hybrid forage system. Detailed soil and crop properties data have been collected from this site.  This site is designated to be continued as part of the LTAR "common experiment" comparing agricultural and environmental results from "business as usual" and "aspirational best practices.</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/da7457b6-633e-4564-8bb0-2b7d5adbe35d" target="_blank">https://geodata.nal.usda.gov/geonetwork/srv/eng/catalog.search#/metadata/da7457b6-633e-4564-8bb0-2b7d5adbe35d</a> </p></li></ul>

Tags: ars, corn, cover-crops, data-gov, earth-science-agriculture-agricultural-plant-science, earth-science-biosphere-vegetation, earth-science-biosphere-vegetation-chlorophyll, earth-science-biosphere-vegetation-leaf-characteristics, earth-science-biosphere-vegetation-plant-phenology, np212, np305, soybeans
Organization: Department of Agriculture
TPAC Study for Greenhouse gas Reduction through Agricultural Carbon Enhancement network in West Lafayette, Indiana

<p>TPAC Study for Greenhouse gas Reduction through Agricultural Carbon Enhancement network in West Lafayette, Indiana
Recent efforts have attempted to establish emission estimates for greenhouse gases (GHG) from agricultural soils in the United States. This research project was conducted to assess the influence of cropping system management on non-carbon dioxide (non-CO2) GHG emissions from an eastern cornbelt alfisol. Corn (Zea mays L.) and soybean (Glycine max (L.) Merr.) rotation plots were established, as were plots in continuous management of native grasses or Sorghum/Sudan grass. GHG fluxes were monitored throughout each growing season from 2004 through 2007. Fluxes of N2O were significantly correlated with soil temperature (P < 0.001), and thus a Q10 correction was made (3.48 for N2O). Nitrous oxide emissions from corn were lowest from the precision tillage treatment (2.4 kg N ha-1 yr-1), significantly lower than the conventional tillage (4.9 kg N ha-1 yr-1) or cover crop corn treatments (5.0 kg N ha-1 yr-1). Corn-soybean and biomass-based cropping systems resulted in significantly greater N2O emissions than native grasses. There was a positive correlation between N fertilization rate and N2O emissions when comparing all treatments in this study. These soils were typically a sink for atmospheric CH4 for these cropping systems, and thus N2O is the primary non-CO2 GHG of concern. When evaluating the entire cropping system, native grasses resulted in the lowest N2O emissions, while corn-soybean rotation planted with precision tillage resulted in similar N2O emissions as bare soil and were significantly lower than emissions from the other cropping systems assessed.</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/87f505d7-9c43-4082-a2f2-329a838be6c9" target="_blank">https://geodata.nal.usda.gov/geonetwork/srv/eng/catalog.search#/metadata/87f505d7-9c43-4082-a2f2-329a838be6c9</a> </p></li></ul>

Tags: air-temperature, ars, carbon-dioxide, corn, data-gov, environment, farming, grasses, greenhouse-gas, methane, nitrous-oxide, np211, np212, soil-temperature, soil-water, soybeans, tillage, weather
Organization: Department of Agriculture
The Carbon Security Index: A novel approach to assessing how secure carbon is in sagebrush ecosystems within the Great Basin

<p dir="ltr">We created an index to look at carbon security in the sagebrush steppe across the Great Basin. Our index uses a fractional plant cover dataset from the Rangeland Analysis Platform (<a href="https://rangelands.app/" rel="noreferrer" target="_blank">https://rangelands.app/</a>), a fire probability model dataset created for the Great Basin (Smith et al., 2023), and the resistance and resilience categorical dataset created for the sagebrush steppe (Chambers et al., 2014, 2017). Our carbon security index (CSI) is made up of three parts as following:</p><p dir="ltr"><i>CSI = Preferred Rangeland Cover Index + Resistance & Resilience – P(Fire)</i></p><p dir="ltr"><i>The result is an index that spans from -2 to +2 and can be used to compare carbon security in different spatial.</i></p><p dir="ltr"><i>For greater detail of methods and rational please read the associated paper.</i></p>

Tags: carbon-security, sagebrush-conservation-design
Organization: Department of Agriculture
USDA Database for the Proanthocyanidin Content of Selected Foods, Release 2 (2015)

<p>The database contains values for 283 food items for the following proanthocyanidins groups:</p>
<ul>
<li>Dimers</li>
<li>Trimers</li>
<li>4-6 mers (tetramers, pentamers and hexamers)</li>
<li>7-10 mers (heptamers, octamers, nonamers and decamers</li>
<li>Polymers (DP>10)</li>
</ul>
<div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: READ ME - USDA Database for the Proanthocyanidin Content of Selected Foods.</p> <p>File Name: PA02.pdf</p><p>Resource Description: Information regarding the documentation, data sources, data management, data quality evaluation, aggregation and format, sources of data, and references cited.</p><p>Resource Software Recommended: Adobe Acrobat Reader,url: <a href="http://www.adobe.com/prodindex/acrobat/readstep.html" target="_blank">http://www.adobe.com/prodindex/acrobat/readstep.html</a> </p></li><br><li><p>Resource Title: Data Dictionary.</p> <p>File Name: PA02_DD.pdf</p></li><br><li><p>Resource Title: PA02.accdb.</p> <p>File Name: PA02.zip</p><p>Resource Description: This file contains the Proanthocyanidin Database imported into a MS Access database version 2007 or later. The file structure is the same as that of the USDA National Nutrient Database for Standard Reference.
</p></li></ul>

Tags: ars, data-gov, np107, proanthocyanidin
Organization: Department of Agriculture
Data from: Characterization of particle size distributions and water-soluble ions in particulate matter measured at a broiler farm

<p>This is USDA-ARS data from the publication, "Characterization of particle size distributions and water-soluble ions in particulate matter measured at a broiler farm." This study was conducted in June of 2018. Data included here are from several measurements:</p>
<ol>
<li>Gas-phase ammonia measurements measured by an electrochemical sensor (Cairpol) in part-per-billion (ppb) with 1 minute time interval.</li>
<li>Particle number concentration inside and outside the house measured by two optical particle counters (MetOne) in number per cubic centimeter (mg/cc) with 20 second interval. Particles were measured from 0.5-10 micrometers in 8 size bins.</li>
<li>Particle number concentration measured by a scanning mobility particle sizer (TSI) and given as the differential number per size bin over 80 bins from 10-500 nanometers with a 5 minute time interval.</li>
<li>Water-soluble ions in particulate matter measured by an ambient ion monitor (URG) measured in microgram per cubic meter with a 1 hour time interval.</li>
</ol>
<p>Resources in this dataset:</p>
<ul>
<li>
<p>Resource Title: Ammonia Sensor Measurements
File Name: SensorNH3.txt</p>
</li>
<li>
<p>Resource Title: Optical Particle Counter 1
File Name: OpticalParticleCounter1.txt</p>
</li>
<li>
<p>Resource Title: Optical Particle Counter 2
File Name: OpticalParticleCounter2.txt</p>
</li>
<li>
<p>Resource Title: Scanning Mobility Particle Sizer Data (Matrix)
File Name: SMPS Data.txt</p>
</li>
<li>
<p>Resource Title: Scanning Mobility Particle Sizer Axes
File Name: SMPS Axes.txt</p>
</li>
<li>
<p>Resource Title: AIM Particulate Chemical Composition
File Name: AIM Composition.txt</p>
</li>
</ul>

Tags: ammonia, ars, broiler, data-gov, np212, particulate-matter, poultry
Organization: Department of Agriculture
Agroecological classes | 2018

<p><a href="https://www.reacchpna.org/sites/default/files/AR3_1.2.pdf" target="_blank">https://www.reacchpna.org/sites/default/files/AR3_1.2.pdf</a>

Pixel classification:
Classification, Stable, Dynamic, Unstable
Urban, 1, 101, 202   
Rangeland, 3, 103, 203
Forest, 4, 104, 204
Water, 5, 105, 205
Wetlands, 6, 106, 206
Barren, 7, 107, 207
Wilderness, 9, 109, 209
Annual, 11, 111, 211
Transition, 12, 112, 212
Grain-fallow, 13, 113, 213
Irrigated, 14, 114, 214
Orchard, 15, 115, 215
Agriculture, 50, 150, 250
Water and Other, 51, 151, 251</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/83415cb1-f993-4f61-ac85-e0efcd360bb1" target="_blank">https://geodata.nal.usda.gov/geonetwork/srv/eng/catalog.search#/metadata/83415cb1-f993-4f61-ac85-e0efcd360bb1</a> </p></li></ul>

Tags: ars, data-gov, environment, farming, forests, irrigation, rangelands, wetlands, wilderness
Organization: Department of Agriculture
2014 Swine CAFO Study SE for Agricultural Antibiotic Resistance in Mississippi State, Mississippi

<p>2014 Swine CAFO Study SE for Agricultural Antibiotic Resistance in Mississippi State, Mississippi
The environmental influence of farm management in concentrated animal feeding operations (CAFO) can yield vast changes to the microbial biota and ecological structure of both the pig and waste manure lagoon wastewater.  While some of these changes may not be negative, it is possible that CAFOs can enrich antibiotic resistant bacteria or pathogens based on farm type, thereby influencing the impact imparted by the land application of its respective wastewater.  The purpose of this study was to measure the microbial constituents of swine-sow, -nursery, and -finisher farm manure lagoon wastewater and determine the changes induced by farm management.  A total of 37 farms were visited in the Mid-South USA and analyzed for the genes 16S rRNA, spaQ (Salmonella spp.), Camp-16S (Campylobacter spp.), tetA, tetB, ermF, ermA, mecA, and intI using quantitative PCR.  Additionally, 16S rRNA sequence libraries were created.  Overall, it appeared that finisher farms were significantly different from nursery and sow farms in nearly all genes measured and in 16S rRNA clone libraries.  Nearly all antibiotic resistance genes were detected in all farms.  Interestingly, the mecA resistance gene (e.g. methicillin resistant Staphylococcus aureus) was below detection limits on most farms, and decreased as the pigs aged.  Finisher farms generally had fewer antibiotic resistance genes, which corroborated previous phenotypic data; additionally, finisher farms produced a less diverse 16S rRNA sequence library.  Comparisons of Camp-16S and spaQ GU (genomic unit) values to previous culture data demonstrated ratios from 10 to 10,000:1 depending on farm type, indicating viable but not cultivatable bacteria were dominant.  The current study indicated that swine farm management schemes positively and negatively affect microbial and antibiotic resistant populations in CAFO wastewater which has future “downstream” implications from both an environmental and public health perspective.</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/651220ea-a65e-43a1-9c28-433c27464cae" target="_blank">https://geodata.nal.usda.gov/geonetwork/srv/eng/catalog.search#/metadata/651220ea-a65e-43a1-9c28-433c27464cae</a> </p></li></ul>

Tags: antibiotic-resistance, antibiotic-resistance-genes, ars, data-gov, environment, farming, np211, np212, pig, resistance
Organization: Department of Agriculture
Central Mississippi River Basin LTAR Dataset: NFARM, Inorganic N, & C Production, 2016-2018

<p>In situ denitrification rates in intact soil cores from the Central Mississippi River Basin (CMRB) LTAR site in MO quantified by directly measuring dinitrogen (N2) and nitrous oxide (N2O) production via the Nitrogen-Free Air Recirculation Method (N-FARM) from 2016-2018. 10-day laboratory incubations provided estimates of ancillary soil data, including microbial respiration and potential net N mineralization and nitrification. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Central Mississippi River Basin Data Dictionary.</p> <p>File Name: Central Mississippi River Basin Data Dictionary.csv</p><p>Resource Description: Data Dictionary for CMRB dataset.</p></li><br><li><p>Resource Title: Central Mississippi River Basin Metadata.</p> <p>File Name: Central Mississippi River Basin Metadata.csv</p><p>Resource Description: Metadata for CMRB dataset.</p></li><br><li><p>Resource Title: Central Mississippi River Basin Dataset.</p> <p>File Name: Central Mississippi River Basin Dataset.csv</p><p>Resource Description: CMRB Dataset.</p></li></ul><p></p>

Tags: ammonium, ars, carbon-dioxide, confining-soil-layer, data-gov, deep-soil, denitrification, dinitrogen, ecosystems, hot-moment, hot-spot, laboratory-incubation, ltar, mineralization, nitrate, nitrification, nitrogen, nitrous-oxide-flux, respiration, soil, soil-depths, surface-soil, usda-long-term-agricultural-research-ltar-network
Organization: Department of Agriculture