AndreaBozzo/ceres-open-data-index huggingface dataset:
Data from: Detection of live Shiga toxin-producing Escherichia coli with long-read sequencing

<p dir="ltr">A requirement of any foodborne pathogen testing method is that it only detects live bacteria. Ethidium monoazide (EMA) and propidium monoazide (PMA) are dyes that penetrate the membranes of dead cells and form cross-linkages in the DNA, which prevents its amplification in PCR. This study investigated whether treatment with EMA or PMA would inhibit sequencing of DNA from dead <i>Escherichia coli</i>. Range finding experiments with qPCR were conducted to determine the optimal concentrations of EMA and PMA needed to inhibit amplification of DNA from dead cells while not influencing live cells. An EMA concentration that differentiated between live and dead cells could not be established. However, a PMA concentration of 25 µM effectively prevented qPCR amplification of DNA from dead <i>E. coli</i> while not impacting the amplification of live <i>E. coli</i> DNA. Sequencing experiments were conducted with PMA-treated live, untreated live, PMA-treated dead, and untreated dead <i>E. coli</i>. There were no significant differences in the detection of virulence genes of interest between the PMA-treated live, untreated live, and untreated dead <i>E. coli</i>. However, no DNA sequencing data was obtained from the PMA-treated dead <i>E. coli</i>. These results suggest that PMA could be incorporated into sample preparation methods prior to sequencing to selectively detect live cells of foodborne pathogens.</p>

Tags: ethidium-monoazide, foodborne-pathogens, long-read-sequencing, method-development, propidium-monoazide
Organization: Department of Agriculture
Data from: Honey bee immune response to trace concentrations of clothianidin goes beyond the macronutrients found in artificial diets

<p dir="ltr">Honey bees (<i>Apis mellifera</i>) often encounter a variety of stressors in their environment, including poor nutrition and pesticides. These stressors interact and can be exacerbated in large-scale agroecosystems. We investigated how diets varying in macronutrient ratios can affect nurse bee susceptibility to pesticide stressors. Nurse bees were fed trace concentrations of clothianidin (CLO), a neonicotinoid insecticide known to have sublethal and lethal effects on honey bees, after newly emerged bees were given diets varying in proteins and lipids, a natural pollen diet, or sucrose solution diet. Bees given pollen had improved longevity, physiology, enzyme activity, and gene expression related to pesticide detoxification. The artificial diets helped improve bee health and physiology but did little to promote bee detoxification enzymes and genes. There was no effect of the trace CLO treatments on its own, but there was an interactive effect between our higher CLO treatment and poor nutrition on bee longevity and vitellogenin expression. Our results suggest that 1.) exposure to even trace concentrations of CLO can interact with poor nutrition to undermine adult bee health and 2.) macronutrients in artificial diets can help promote bee physiology, but other nutrients in pollen, such as potentially phytochemicals, are more directly linked honey bee tolerance to pesticide stress.</p><p><br></p><p dir="ltr">This work was supported by United States Department of Agriculture, Agricultural Research Service, Research Project No. 6066-21000-001-000-D, Ecological Assessment and Mitigation Strategies to Reduce the Risks of Bees to Stressors in Southern Crop Ecosystems.</p>

Tags: clothianidin, honey-bee, immunity, lipids, neonicotinoids, nutrition, pesticide, phytochemicals, proteins
Organization: Department of Agriculture
National Wilderness Areas: Legal Status (Feature Layer)

The Land Status view of National Forest System land parcels that have legal descriptions such as National Wilderness Area, Primitive Area, or Wilderness Study Area. Areas designated by Congress as a part of the National Wilderness Preservation System, with related details including the date of the designation, status of the final boundary description, authority, and land status case and document. <a href='https://data.fs.usda.gov/geodata/edw/edw_resources/meta/S_USA.WildernessStatus.xml' target='_blank' rel='nofollow ugc noopener noreferrer'>Metadata</a>

Tags: alp-land-dataset, land-status, lands-and-realty, legal-status, nfs-lands, open-data, wilderness-name
Organization: Department of Agriculture
Wheat Phenotypic Response to Hessian fly

<p dir="ltr">Hessian fly (<i>Mayetiola destructor</i>) is a destructive pest of wheat causing severe damage to wheat (<i>Triticum aestivum</i>) production globally. New and novel sources of Hessian fly resistant cultivars are needed that can be used for native resistance and in breeding programs to develop robust insect-resistant wheat lines. In the current study, a total of 374 wheat cultivars from different regions within the United States were evaluated for resistance to Hessian fly. Three pasta wheat cultivars, one originating from North Dakota and 2 others from Minnesota showed resistance to multiple forms (technically called as ‘biotypes’) of Hessian fly when tested at 20°C. Although at higher temperatures of 30°C these three cultivars are unable to maintain their resistance to Hessian fly and are not suitable in regions with higher environmental temperatures, these three wheat lines can offer breeders additional sources of Hessian fly resistance for developing elite Hessian fly-resistant cultivars.</p>

Tags: ars, biotypes, data-gov, hessian-fly, insect-resistance, phenotypic-response, tetraploids, wheat
Organization: Department of Agriculture
Data from: Characterizing Brown Marmorated Stink Bug, <i>Halyomorpha halys</i> Stål (Hemiptera: Pentatomidae), Host Plant Usage and Acceptability: Methodological Strengths and Shortcomings

<p dir="ltr">We assessed brown marmorated stink bug, <i>Halyomorpha halys </i>(Stål), seasonal patterns of host use and/or preference using three diverse approaches. We compared <i>H. halys </i>captures in small pyramid traps baited with <i>H. halys </i>aggregation pheromone and deployed in the mid-canopy of individual host trees during discrete intervals over two seasons. While captures were greatest in the late season, there was no significant effect of host tree species on captures, with the presence of pheromone lures likely confounding results. Harmonic radar was used to measure retention duration of tagged <i>H. halys</i> on potted trees including <i>Ailanthus altissima,</i> <i>Robinia pseudoacacia, </i><i>Celtis occidentalis, </i><i>Morus rubra, </i><i>Prunus persica</i>, and <i>Malus domestica,</i> as a proxy for host acceptability. Season-long, adults were retained significantly longer on <i>P. persica</i> and pheromone-baited <i>M. domestica</i> (positive control) compared with non-host grass treatment (negative control). For nymphs, significantly longer retention was recorded on nearly all hosts compared with non-host grass treatment. We also evaluated results of molecular gut content analysis of adults collected in the early and late season. Plant DNA from 22 genera across 18 families was detected. Commonly detected early season hosts included <i>Betula, Diospyros, Juglans, Liriodendron, Prunus, Rubus</i>, and <i>Sisymbrium</i> and late season hosts included <i>Ailanthus, Chenopodium, Juglans, Persicaria, </i>and<i> Prunus</i>. Overall, harmonic radar provided context for seasonal changes in host acceptability, and gut content results provided confirmation of specific host usage at different points in the season. Combining these two methods could provide a more comprehensive approach for defining host use patterns of this polyphagous pest.</p>

Tags: brown-marmorated-stink-bug, gut-content-analysis, harmonic-radar-tracking, host-plant-use, invasive-pest, non-crop-host-plants
Organization: Department of Agriculture
Data from: Timing of recovery of <i>Tribolium castaneum </i>(Coleoptera: Tenebrionidae) after contact insecticide exposure in different environmental and diet conditions

<p>Insects that infest postharvest commodities can cause significant damage or destruction, costing billions of dollars in lost product yearly. Insecticide treatments applied to surfaces as contact insecticides have been shown to be effective in managing populations of these insects. However, recovery after exposure to these insecticides, due to sublethal exposure periods, is significantly increased if there is food present in non-treated, recovery areas, which can lead to insect recovery and an ineffective treatment leading to further infestations. In addition, environmental variation in temperature and humidity could also play a significant role in recovery after a sublethal insecticide exposure. Here we assess the recovery of <em>Tribolium castaneum </em>Herbst, red flour beetle, after exposure to a contact insecticide with and without food at different temperatures, relative humidity (RH) levels, differing amounts of food, and particle presence with no nutrition. The dataset provides details on the number of insects knocked down or running every 15 minutes for a 3 hour (h) exposure to deltamethrin contact insecticide and knocked down and running insects 24 h, 48 h, and 168 h post-exposure at varying recovery parameters. All insects were exposed at the same environmental conditions. Each assay was conducted independently with all controls repeated each time. Diet, temperature, and RH were all varied during recovery only. Each treatment was done 5 times for each block; three total blocks were completed.</p>

Tags: contact-insecticide, grain-storage-facilities, insecticide-resistance, stored-product-insect, thermal-variation
Organization: Department of Agriculture
Data from: ECB-WQ: A Long-Term Agroecosystem Research (LTAR) - Eastern Corn Belt node field-scale water quality dataset

<p dir="ltr">The ECB-WQ database is comprised of hydrology and water quality data from three privately owned farms in Northwest Ohio and Northeast Indiana (USA). Specifically, the dataset includes information on site characteristics (drainage area, soil type), field management (fertilizer application, planting rate, yield), and daily discharge and measured nutrient concentrations from surface and subsurface tile drainage outlets.</p>

Tags: edge-of-field, gulf-of-mexico, lake-erie, nitrogen, phosphorus
Organization: Department of Agriculture
Data from: Detection and differentiation of low virulence and virulent Orthoavulavirus javaense using a molecular beacon with RT-LAMP

<p>This dataset accompanies the manuscript <a href="https://www.nature.com/articles/s41598-024-68816-7" target="_blank">Detection and differentiation of low virulence and virulent Orthoavulavirus javaense using a molecular beacon with RT-LAMP | Scientific Reports (nature.com)</a> published on 08/05/2024. The Orthoavulavirus javaense also called as Newcastle Disease virus is the causative of Newcastle disease a significant problem for the poultry industry. Virulent strains of this virus can cause extensive mortality and economic loss to the poultry industry. Current diagnostic methods rely on polymerase chain reaction targeting the fusion gene of this virus and this method is not only expensive and time consuming, but is also not field applicable. The dataset reported here and the manuscript published describe an assay that can be applied to field diagnosis of NDV via a colorimetric and fluorometric assay. The MB-RT-LAMP assay enables rapid detection of viruses from field samples without the need for RNA isolation and also enable rapid differentiation of virulent vs low virulence viruses. The data provided here demonstrate the sequence analysis undertaken to develop the MB-RT-LAMP primers and probes, the supporting data show the conditions tested to identify optimal parameters.</p>

Tags: diagnostic-assay, loop-mediated-isothermal-amplification, newcastle-disease-virus
Organization: Department of Agriculture
Data from: Acceptance of fire ant baits by nontarget ants in Florida and California

<p dir="ltr">Invasive red imported fire ant, <i>Solenopsis invicta</i>, infestations can be cleared from areas with baits, but these areas are often reinfested. To facilitate biotic resistance strategies to reinfestation, acceptance of commercial fire ant baits by nontarget ants was determined in Alachua County Florida and in Riverside County California. Presented are counts of four ant species that accepted baits among eight baits containing seven active ingredients in Florida. Also included are counts of four ant species in California that accepted baits among five of the fire ant baits. Tests were conducted in the field at nests or on actively trailing ants, for all species except for <i>Monomorium floricola</i>, which were from laboratory reared colonies. Zero or low counts of ants for a particular bait implies non-acceptance of that bait. Non-acceptance of a bait by several nontarget ant species would indicate which bait(s) exhibited more specificity to fire ants. None of the fire ant bait products tested exhibited non-acceptance by all the nontarget ant species evaluated. To conserve nontarget ants, fire ant bait selection will need to consider the nontarget ants present at individual sites and specific bait(s), that are least accepted by these ants.</p>

Tags: ant-baits, biotic-resistance, control, integrated-pest-management, invasive-ant, red-imported-fire-ant
Organization: Department of Agriculture
Data from: Predicted range expansion of the larger grain borer, <i>Prostephanus truncatus </i>(Coleoptera: Bostrichidae), under projected climate change scenarios

<p dir="ltr">The larger grain borer (<i>Prostephanus truncatus</i> [Horn] [Coleoptera: Bostrichidae]) is a wood-boring insect native to Central America but has adapted to stored maize and cassava. It was accidentally introduced to Tanzania and became a pest across central Africa. Unlike many grain pests, <i>P. truncatus </i>populations can establish and move within forested habitats. Consequently, novel infestations can occur without human influence. The objectives of our study were to (1) develop an updated current suitability projection for <i>P. truncatus</i> (2) assess its potential future distribution under different climate change scenarios, and (3) identify climate variables that best inform the model. We used WALLACE and MaxEnt to predict potential global distribution by incorporating bioclimatic variables and occurrence records. Future models were projected to 2050 and 2070 with Representative Concentration Pathways (RCP) 2.6 (low warming) and 8.5 (high warming). Distribution was most limited by high precipitation and cold temperatures. Globally, highly suitable areas (>75%) primarily occurred along coastal and equatorial regions with novel areas in northern South America, India, southeastern Asia, Indonesia, and the Philippines, totaling 7% under current conditions. Highly suitable areas at RCP 2.6 and 8.5 are estimated to increase to 12 and 15%, respectively, by 2050 and increase to 19% in 2070 under RCP 8.5. Centroids of highly suitable areas show the distribution centers move more inshore and away from the equator. Notably, the result is a range expansion, not shift. These results can be used to decrease biosecurity risks through more spatially explicit and timely surveillance programs for targeting the exclusion of this pest.</p>

Tags: ecological-niche-model-enm, grain-pest-species, invasive-species, movement, risk-prediction-modeling, species-distribution-modeling-technique-maxent, stored-product-insect
Organization: Department of Agriculture
Ranger District Boundaries (Feature Layer)

A depiction of the boundary that encompasses a Ranger District. <a href='https://data.fs.usda.gov/geodata/edw/edw_resources/meta/S_USA.RangerDistrict.xml' target='_blank' rel='nofollow ugc noopener noreferrer'>Metadata</a>

Tags: administrative-boundaries, alp-land-dataset, district-name, district-number, forest-name, land-status, lands-and-realty, national-forest-system-lands, open-data, ranger-districts, us-forest-service
Organization: Department of Agriculture
FS National Forests Dataset (US Forest Service Proclaimed Forests)

The FS National Forests Dataset (US Forest Service Proclaimed Forests) is a depiction of the boundaries encompassing the National Forest System (NFS) lands within the original proclaimed National Forests, along with subsequent Executive Orders, Proclamations, Public Laws, Public Land Orders, Secretary of Agriculture Orders, and Secretary of Interior Orders creating modifications thereto, along with lands added to the NFS which have taken on the status of 'reserved from the public domain' under the General Exchange Act. The following area types are included: National Forest, Experimental Area, Experimental Forest, Experimental Range, Land Utilization Project, National Grassland, Purchase Unit, and Special Management Area.<div><br /></div><div><a href='https://data.fs.usda.gov/geodata/edw/datasets.php?xmlKeyword=Original+Proclaimed+National+Forests' target='_blank' rel='nofollow ugc noopener noreferrer'>Metadata and Downloads</a> - https://data.fs.usda.gov/geodata/edw/datasets.php?xmlKeyword=Original+Proclaimed+National+Forests</div>

Tags: alp-land-dataset, boundaries, forest-name, land-status, land-use-land-cover, national-geospatial-data-asset, nfs-lands, ngda, open-data, planningcadastre, proclaimed-forest, usda-forest-service
Organization: Department of Agriculture
Forest Administrative Boundaries (Feature Layer)

An area encompassing all the National Forest System lands administered by an administrative unit. The area encompasses private lands, other governmental agency lands, and may contain National Forest System lands within the proclaimed boundaries of another administrative unit. All National Forest System lands fall within one and only one Administrative Forest Area. Click this link for full metadata description: <a href='https://data.fs.usda.gov/geodata/edw/edw_resources/meta/S_USA.AdministrativeForest.xml' target='_blank' rel='nofollow ugc noopener noreferrer'>Metadata</a>

Tags: administrative-boundaries, alp-land-dataset, land-status, lands-and-realty, national-forest-system-lands, open-data, us-forest-service
Organization: Department of Agriculture
EDW HFRA EmergencySituationDetermination 01

<div style="text-align:Left;"><div><p><span>Emergency Situation Determination (ESD) lands, per the Secretary's Memo 1078-006: Increasing Timber Production and Designating an Emergency Situation on National Forest System Lands, have been designated by either being at risk from insect and diseases under the Healthy Forest Restoration Act, or have a high or very high wildfire hazard potential. Only Forest Service owned lands are included in this feature. https://data.fs.usda.gov/geodata/edw/edw_resources/meta/BdyDesg_HFRA_EmergencySituationDetermination.xml</span></p></div></div>

Tags: ecology, ecosystems, environment, environment-and-people, fire, fire-detection, fire-ecology, fire-effects-on-environment, fire-suppressionpre-suppression, forest-management, landscape-management, prescribed-fire
Organization: Department of Agriculture
PADUS FS Proclaimed NF and National Grassland Boundaries (Feature Layer)

An area depicting designated land boundaries which are designated by proclamation. This data is intended for read-only use. The PAD-US feature classes were developed by the Forest Service for submission to the Protected Areas Database of the United States (PAD-US). It is the official inventory of public parks and other protected open space. With more than 3 billion acres in 150,000 holdings, the spatial data in PAD-US represents public lands held in trust by thousands of national, State and regional/local governments, as well as non-profit conservation organizations. PAD-US is published by the U.S. Geological Survey Gap Analysis Program (GAP). GAP produces data and tools that help meet critical national challenges such as biodiversity, conservation, recreation, public health, climate change adaptation, and infrastructure investment. <a href='https://data.fs.usda.gov/geodata/edw/edw_resources/meta/S_USA.PADUS_Proc.xml' target='_blank' rel='nofollow ugc noopener noreferrer'>Metadata</a>

Tags: alp-land-dataset, designation, easement, fee, land-status, nfs-lands, open-data, padus, proclamation, protected-areas-database, usda-forest-service
Organization: Department of Agriculture
Surface Ownership Parcels (Feature Layer)

An area depicted as surface ownership parcels dissolved on the same ownership classification.  <a href='https://data.fs.usda.gov/geodata/edw/edw_resources/meta/S_USA.BasicOwnership.xml' target='_blank' rel='nofollow ugc noopener noreferrer'>Metadata</a>

Tags: alp-land-dataset, basic-ownership, estate, land-status, lands-and-realty, nfs-lands, open-data, owner-name, parcels, planning-cadastre, usda-forest-service
Organization: Department of Agriculture
Other Surface Right (Feature Layer)

An area depicting a right to a surface resource, excluding rights of way. <a href='https://data.fs.usda.gov/geodata/edw/edw_resources/meta/S_USA.OtherSurfaceRight.xml' target='_blank' rel='nofollow ugc noopener noreferrer'>Metadata</a>

Tags: alp-land-dataset, estate, land-status, lands-and-realty, nfs-lands, open-data, other-surface-right, parcels, planning-cadastre, usda-forest-service
Organization: Department of Agriculture
Surface Ownership Parcels, detailed (Feature Layer)

An area depicting ownership parcels of the surface estate. Each surface ownership parcel is tied to a particular legal transaction. The same individual or organization may currently own many parcels that may or may not have been acquired through the same legal transaction. Therefore, they are captured as separate entities rather than merged together. This is in contrast to Basic Ownership, in which the surface ownership parcels having the same owner are merged together. Basic Ownership provides the general user with the Forest Service versus non-Forest Service view of land ownership within National Forest boundaries. Surface Ownership provides the land status user with a current snapshot of ownership within National Forest boundaries. <a href='https://data.fs.usda.gov/geodata/edw/edw_resources/meta/S_USA.SurfaceOwnership.xml' target='_blank' rel='nofollow ugc noopener noreferrer'>Metadata</a>

Tags: alp-land-dataset, basic-ownership, estate, land-status, lands-and-realty, nfs-lands, open-data, owner-name, parcels, planning-cadastre, usda-forest-service
Organization: Department of Agriculture
Other Sub Surface Right (Feature Layer)

An area depicting ownership parcels of the subsurface estate, excluding mineral rights; it is collected only if the subsurface estate is different than the overlying surface estate. <a href='https://data.fs.usda.gov/geodata/edw/edw_resources/meta/S_USA.OtherSubSurfaceRight.xml' target='_blank' rel='nofollow ugc noopener noreferrer'>Metadata</a>

Tags: alp-land-dataset, estate, land-status, lands-and-realty, nfs-lands, open-data, other-sub-surface-right, parcels, planning-cadastre, usda-forest-service
Organization: Department of Agriculture
Survey parcels described by metes and bounds (Feature Layer)

A depiction of a survey parcel described by a metes and bounds description. Examples include: land lots, housing subdivision lots, mineral surveys, and homestead entry surveys. <a href='https://data.fs.usda.gov/geodata/edw/edw_resources/meta/S_USA.Tract.xml' target='_blank' rel='nofollow ugc noopener noreferrer'>Metadata</a>

Tags: alp, alp-land-dataset, estate, forest-service, fs, land, land-status, lands-and-realty, legal-description, nfs-lands, open-data, parcels, planning-cadastre, tracts, usda-forest-service, usfs
Organization: Department of Agriculture