AndreaBozzo/ceres-open-data-index huggingface dataset:
Amplicon sequencing of pollen foraged by Bombus affinis for compositional analysis

This study generated genetic 'barcode' data using high-throughput sequencing to characterize pollen collected by the endangered rusty-patched bumblebee, Bombus affinis. Pollen samples were associated with a single Bombus affinis colony within a structure in Red Wing, Minnesota, USA, as previously described by Boone et al. (2022).  
This data release consists of two tab-delimited files:
1) sample.metadata.txt includes sample identifiers and accessions assigned by the National Center for Biotechnology Information (NCBI), the authoritative repository for publicly funded genetic data in the United States. These accessions can be used individually to obtain raw sequencing data or sample information at www.ncbi.nih.nlm.gov.  Alternatively, the BioProject accession PRJNA1045705 can be searched to retrieve the full set of data and sample accessions listed in the file. Entity and attribute metadata are provided for this file.
2) taxon.counts.txt includes the inferred counts, or number of sequences, attributable to each identified taxon in each sample. Taxa are in rows and sequencing libraries are in columns. Taxa are listed by scientific name and the taxonomic rank of that scientific name. A numeric taxonomic identifier used by NCBI for each taxon is also provided, as the taxonomic identifier is unique in the NCBI databases whereas scientific names may not be. Entity and attribute data are not provided for this file due to its size and repetitive content.

Tags: biota, conservation-genetics, genetics, invertebrate-zoology, usgs-65aff78bd34ef34c3506e376
Organization: Department of the Interior
Estimated high-frequency chloride concentrations

This data set includes estimated chloride concentrations for the 93 USGS water quality monitoring stations located across the eastern United States. Chloride concentrations were predicted using regression equations that established the relationship between simultaneous measurements of chloride and specific conductance (SC). Site-specific models were developed and applied when data were available, and regional regression models were used where there were insufficient data available to establish a site-specific regression model. These models were applied to high-frequency SC data sets to produce high-frequency predicted chloride concentrations at 2-minute to 1-hour intervals, depending on the frequency at which SC is measured at each site. Up to four chloride concentration estimations may be available for a particular site, depending on whether a simple linear regression was developed (SLR), a piecewise regression was developed (SEG), and whether or not site-specific models were developed and applied. The best-fitting regional regression model was applied to all 93 sites. Regions include the southeast, Mid-Atlantic, Mid-Atlantic carbonate (e.g., underlain with carbonate bedrock), and New England, and correspond to the regions included in Moore and others (in review). Each file is labeled by its short name.  Please see "Chloride_site_information.csv" for the corresponding site IDs and the USGS station numbers. 
Moore, J., R. Fanelli, and A. Sekellick. In review.  High-frequency data reveal deicing salts drive elevated conductivity and chloride along with pervasive and frequent exceedances of the EPA aquatic life criteria for chloride in urban streams. Submitted to Environmental Science and Technology.

Tags: chloride, deicers, environment, road-salt, specific-conductance, urbanization, usgs-5d823dc6e4b0c4f70d058e1b, water-quality
Organization: Department of the Interior
Estimated daily loads of nutrients, sediment, and chloride at USGS edge-of-field stations, tributaries to Lum Drain, Genesee County, Michigan, water years 2012-17

As part of the Great Lakes Restoration Initiative, the U.S. Department of Agriculture, Natural Resources Conservation Service; U.S. Environmental Protection Agency; and the U.S. Geological Survey (USGS) have partnered to evaluate agricultural conservation practices focused on nutrient management. Monitoring methods allow for rapid assessment of water-quality changes in response to conservation efforts by focusing on subsurface-tile drainage and direct surface runoff from fields. 
Estimated daily loads presented within this dataset are from one surface-runoff monitoring station (USGS station identification number 0414826544; approximated drainage area of 60.6 hectare) and one tile-runoff monitoring station (USGS station identification number 0414826545; approximated drainage area of 28.6 hectare). The monitored field is a row-crop parcel planted in a biennial corn-soybean crop rotation. Best-management practices were applied during part of the monitoring period: cover crops were planted in the fall of each year from 2014 to 2016; nutrient management methods were employed and a filter strip was installed on the field each spring from 2015 to 2017.

Tags: agriculture, alger-creek, field-monitoring-stations, genesee-county, hydrology, lum-drain, michigan, nutrient-content-water, suspended-material-water, swartz-creek, usgs-5a5e665de4b06e28e9be4a1b, water-chemistry, water-quality, water-resource-management
Organization: Department of the Interior
Aquatic insect community data and taxa list for larvae collected from mesocosms exposed to bifenthrin

Direct and indirect ecological effects of the widely used insecticide bifenthrin on stream ecosystems are largely unknown. To investigate such effects, a manipulative experiment was conducted in stream mesocosms that were colonized by aquatic insect communities and exposed to bifenthrin-contaminated sediment; implications for natural streams were interpreted through comparison of mesocosm results to a survey of 100 Midwestern streams, USA. In the mesocosm experiment, direct effects of bifenthrin exposure included reduced larval macroinvertebrate abundance, richness, and biomass at concentrations (EC50s ranged 197.6 – 233.5 ng bifenthrin/ g organic carbon) previously thought safe for aquatic life. Indirect effects included a trophic cascade in which periphyton abundance increased after macroinvertebrate scrapers decreased. Adult emergence dynamics and corresponding terrestrial subsidies were altered at all bifenthrin concentrations tested. Extrapolating these results to the Midwestern stream assessment suggests pervasive ecological effects, with altered emergence dynamics likely in 40% of streams and a trophic cascade in 7% of streams. This study provides new evidence that a common pyrethroid might alter aquatic and terrestrial ecosystem function at the regional scale.  
This data file includes counts and identifications of aquatic insect larvae collected from mesocosms at the end of the experiment. Included is an identifier for each mesocosm, size class of each individual insects, data on quality control, and finally estimates of biomass for each taxa.

Tags: adult-emergence, aquatic-insect-communities, aquatic-terrestrial-linkages, bifenthrin, contaminants, illinois, indiana, iowa, kansas, kentucky, mesocosm, michigan, midwest, minnesota, missouri, nebraska, ohio, pesticides, sediment-quality, south-dakota, suspended-sediment, trophic-cascade, usgs-5797d1f6e4b0589fa1c61b26, water-quality, wisconsin
Organization: Department of the Interior
California Pronghorn Clear Lake Migration Routes

The Clear Lake herd contains migrants, but this herd does not migrate between traditional summer and winter seasonal ranges. Instead, much of the herd displays a nomadic tendency, slowly migrating north, east, or south for the summer using various high use areas as they move. Therefore, annual ranges were modeled using year-round data to demarcate high use areas in lieu of modeling specific winter ranges. The areas adjacent to Clear Lake Reservoir were heavily used during winter by many of the collared animals. A few collared individuals persisted west of State Route 139 year-round, seemingly separated from the rest of the herd due to this highway barrier. However, some pronghorn cross this road near Cornell and join this subgroup. Summer ranges are spread out, with many individuals moving southeast through protected forests or over the state border into Oregon. A few outliers in the herd moved long distances south, crossing State Route 139 to Oak Ridge, or east into Likely Tables pronghorn herd areas. Drought, increasing fire frequency, invasive annual grasses, and juniper encroachment negatively affect pronghorn habitat. Recent population surveys indicate a declining population (Trausch and others, 2020). Juniper removal on public and private lands has potential to improve habitat quality and potentially reduce predation (Ewanyk, 2020).
These mapping layers show the location of the migration routes for pronghorn (Antilocapra americana) in the Clear Lake population in California. They were developed from 72 migration sequences collected from a sample size of 23 animals comprising GPS locations collected every 1-6 hours.

Tags: animal-behavior, biota, california, cornell, migration-organisms, migratory-species, united-states, usgs-6584b4a2d34eff134d42d9cc
Organization: Department of the Interior
Soil-Water-Balance MODEL OUTPUT for simulations of net infiltration, runoff, and irrigation water use in the Mississippi Embayment Regional Aquifer System, 2000 to 2020

This item provides water budget simulations for the Mississippi Embayment Regional Aquifer System (MERAS) during the period 2000 to 2020. Gridded daily data (1 kilometer resolution) include net infiltration (water that might become groundwater recharge), rejected net infiltration, runoff, irrigation, actual evapotranspiration and gross precipitation  The model output files are in netcdf4 format and all water budget components are in inches.   The net infiltration, rejected net infiltration, runoff, irrigation, and actual evapotranspiration data sets are from simulations done with the USGS SWB model (version 2; Westenbroek and others, 2018). The precipitation and temperature data used as input for the SWB model application are derived from PRISM Climate products (PRISM Climate Group, 2020).   
Further details about this application of the SWB model can be found in the related primary publication.

Tags: environment, geoscientificinformation, groundwater, groundwater-recharge, groundwater-recharge-model, hydrology, inlandwaters, irrigation, irrigation-water-use, mississippi, mississippi-river-delta, net-infiltration, soil-water-balance-model, swb, usgs-60500b6bd34eb12031232aaa, usgssoilwaterbalancemodel, water-availability, water-budget
Organization: Department of the Interior
Archive of Digitized Analog Boomer Seismic Reflection Data Collected from the Mississippi-Alabama-Florida shelf During Cruises Onboard the R/V Kit Jones, June 1990 and July 1991

In June of 1990 and July of 1991, the U.S. Geological Survey (USGS) conducted geophysical surveys to investigate the shallow geologic framework of the Mississippi-Alabama-Florida shelf in the northern Gulf of Mexico, from Mississippi Sound to the Florida Panhandle. Work was done onboard the Mississippi Mineral Resources Institute R/V Kit Jones as part of a project to study coastal erosion and offshore sand resources. This report is part of a series to digitally archive the legacy analog data collected from the Mississippi-Alabama SHelf (MASH). The MASH data rescue project is a cooperative effort by the USGS and the Minerals Management Service (MMS). This report serves as an archive of high-resolution scanned Tagged Image File Format (TIFF) and Graphics Interchange Format (GIF) images of the original boomer paper records, navigation files, trackline maps, Geographic Information System (GIS) files, cruise logs, and formal Federal Geographic Data Committee (FGDC) metadata.

Tags: 90013, 90ki1, 90ki2, 91020, 91ki2, 91ki2-1, 91ki2-2, alabama, boomer, distributions, florida, gulf-of-mexico, j-12-90-gm, j-2-91-gm, kit-jones-90-1, kit-jones-90-2, kit-jones-91-2, ktjn90-1, ktjn90-2, ktjn91-2, marine-geophysics, marine-seismic-reflection, mash-data-rescue, mississippi, mississippi-alabama-florida-shelf, mississippi-sound, r-v-kit-jones, scanned-analog-seismic-data, seismic-reflection, seismic-reflection-methods, sub-bottom-profiling, substrate, usgs-5f3c1bf4-dc01-42dd-af4f-2b1e1aeb52af
Organization: Department of the Interior
Lithogeochemical Character of Near-Surface Bedrock in the Connecticut, Housatonic and Thames River Basins

This data layer shows the generalized lithologic and geochemical
(lithogeochemical) character of near-surface bedrock in the
Connecticut, Housatonic, and Thames River Basins and several
other small basins that drain into Long Island Sound from Connecticut.
The area includes most of Connecticut, western Massachusetts, eastern
Vermont, western New Hampshire, and small parts of Rhode Island, New
York, and Quebec, Canada.
		
Bedrock geologic rock formations are classified into 29 lithogeochemical
rock units, based on the relative reactivity of their constituent
minerals to dissolution and other weathering reactions and the presence
of carbonate or sulfide minerals. The 29 lithogeochemical units can be
summarized into 6 major categories: 
(1) carbonate-rich rocks,
(2) carbonate-poor, clastic sedimentary rocks restricted to distinct
depositional basins, 
(3) metamorphosed, clastic sedimentary rocks
(primarily noncalcareous), 
(4) mafic igneous rocks and their metamorphic
equivalents, 
(5) ultramafic rocks, and 
(6) felsic igneous and plutonic rocks and their metamorphic equivalents.  
Lithogeochemical rock units also are grouped into nine lithologic and 
physiographic provinces (lithophysiographic domains), which can be 
summarized into three major
regions: 
(1) western highlands and lowlands, 
(2) central lowlands, and
(3) eastern highlands.

Tags: 1-125, bedrock, connecticut-river, environment, geoscientificinformation, inlandwaters, lithogeochemical, nawqa, usgs-b0104dce-c0e5-4722-8d24-852fea8b0ff2
Organization: Department of the Interior
US Fish and Wildlife Service Fire Atlas- Burn Severity Mosaic for CONUS in 2004

The U. S. Fish and Wildlife Service (FWS) requests burn severity assessments through an agreement with the U.S. Geological Survey (USGS) to be completed by analysts with the Monitoring Trends in Burn Severity (MTBS) Program. These data products are burned area boundary shapefiles derived from post-fire sensor data (including Landsat TM, Landsat ETM+, Landsat OLI). The pre-fire and post-fire subsets included were used to create Normalized Burn Ratio (NBR) and then a differenced Normalized Burn Ratio (dNBR) image. The objective of this assessment was to generate burned area boundaries for each fire. Data bundles also include post-fire subset, pre-fire subset, NBR, and dNBR images. This map layer is a thematic raster image of burn severity classes for all inventoried fires occurring in CONUS during calendar year 2004. Fires omitted from this mapped inventory are those where suitable satellite imagery was not available, or fires which were not discernable from available imagery.

Tags: burn-severity, burned-area, continental-u-s, conus, differenced-normalized-burn-ratio, fire-location, fire-occurrence, fws, imagerybasemapsearthcover, landsat, location, normalized-burn-ratio, prescribed-fire, sentinel, united-states, us, usgs-65b19270d34e36a39044c6e5, wildfire, wildland-fire
Organization: Department of the Interior
Migration Stopovers of Elk in the West Goose Lake Herd in California

The winter range of the West Goose Lake Rocky Mountain elk (Cervus canadensis nelsoni) sub-herd is located north of Alturas and west of Highway 395 within the Devil’s Garden Ranger District of the Modoc National Forest. This area is characterized by juniper (Juniperus occidentalis) woodlands, and sagebrush flats with some stands of lodgepole (Pinus contorta) and ponderosa pine (Pinus ponderosa) throughout flat, rocky terrain. From this area, a portion of the herd migrates approximately 50 miles north into Oregon’s Fremont National Forest, habitat that primarily consists of lodgepole and ponderosa pine forests. Minimal barriers exist along this migration route since the corridor primarily occurs on land managed by the US Forest Service. Additionally, although the core migration route does cross Highway 140, little to no impacts are known to exist from this crossing.
These data provide the location of {migration stopovers for elk in the West Goose Lake population in California and Oregon. They were developed from 25 migration sequences collected from a sample size of 12 animals comprising GPS locations collected every 4-8 hours.

Tags: animal-behavior, california, farming, geoscientificinformation, migration, migration-organisms, migratory-species, modoc, oregon, united-states, usgs-620e4a95d34e6c7e83baa352
Organization: Department of the Interior
GW Basin divides

Groundwater basin divides within the Floridan Aquifer System include the Dougherty Plain Apalachicola, Southeast Georgia, Northeast Florida, South Carolina, Panhandle, Thomsville-Tallahasse Suwannee, West Central Florida, East Central Florida and South Florida.

Tags: alabama, florida, floridan-aquifer, georgia, geoscientificinformation, ground-water, potentiometric-surface, south-carolina, upper-floridan-aquifer, usgs-5a219c4de4b03852baf470d8, wells
Organization: Department of the Interior
Louisiana Outer Coast Restoration Project – 2022 habitat map, Whiskey Island

This data release includes 2022 data for the Louisiana Outer Coast Restoration Project for Whiskey Island. Specifically, this data release includes a detailed habitat map, general habitat map, and georeferenced imagery. These habitat maps are developed using the methods and classification scheme from Louisiana Coastal Protection and Restoration Authority’s (CPRA) Barrier Island Comprehensive Monitoring (BICM) program. For more details on BICM habitat classes, see the Entity and Attribute Information section of the metadata. Please consult the accompanying readME.txt file for information and recommendations on the contents of this dataset (that is, dataset and recommended symbology). For more information about BICM habitat mapping, see Enwright and others (2020).
Enwright, N.M., SooHoo, W.M., Dugas, J.L., Conzelmann, C.P., Laurenzano, C., Lee, D.M., Mouton, K., and Stelly, S.J., 2020, Louisiana Barrier Island Comprehensive Monitoring Program—Mapping habitats in beach, dune, and intertidal environments along the Louisiana Gulf of Mexico shoreline, 2008 and 2015–16: U.S. Geological Survey Open-File Report 2020–1030, 57 p.,
https://doi.org/10.3133/ofr20201030.

Tags: environment, geoscientificinformation, gulf-of-mexico, imagerybasemapsearthcover, louisiana, terrebonne, usgs-65a7f808d34e02097d049ab1
Organization: Department of the Interior
Digital Orthorectified Aerial Image of Cottonwood Lake Study Area Wetland T2 from 26 July 1996

Orthorectified image from aerial photograph of wetland T2 in the Cottonwood Lake Study Area, Stutsman County, North Dakota. This image is part of a collection of photographs of the study area acquired during July and early August from 1975 to 2015.

Tags: aerial-photography, chase-lake-wetland-management-districtgtstutsman-county-waterfowl-production-areagteddy, chase-lake-wetland-management-districtgtstutsman-county-waterfowl-production-areagtshuler, cottonwood-lake-study-area, earth-sciencegtbiospheregtecosystemsgtaquatic-ecosystemsgtwetlands, earth-sciencegtbiospheregtecosystemsgtterrestrial-ecosystemsgtwetlands, environment, image-collections, imagerybasemapsearthcover, inlandwaters, north-dakota, northern-great-plains, platformgtaerial-photographs, prairie-pothole-region, stutsman-county, surface-water-non-marine, united-states-of-america, usgs-5881392ee4b00a0623570016, wetland-ecosystems
Organization: Department of the Interior
Continuous Temperature and Specific Conductance from the Yukon River and Arctic Rivers in Alaska

This data release includes continuous measurements of stream temperature and specific conductance from 24 sites on the Yukon River and other arctic rivers in Alaska. Measurements were collected at selected U.S. Geological Survey stream gages and in communities along major rivers.

Tags: alakanuk, alaska, andreafsky-river, arctic-village, atigun-river, canada, chandalar-river, chena-river, colville-river, cryosphere, eagle-village, environment, fairbanks, field-inventory-and-monitoring, fort-yukon, frozen-ground, geoscientificinformation, hulahula-river, hydrology, koyukuk-river, kuparuk-river, minto-lakes, nenana, pilot-station, porcupine-river, rivers-streams, sagavanirktok-river, surface-water-chemistry, tagish-river, tanana-river, tolovano-river, usgs-6765bec8d34e5335adae333b, water-quality-water-chemistry, watson-lake, wheaton-river, wulik-river, yukon-river, yukon-territory
Organization: Department of the Interior
Coastwide Reference Monitoring System (CRMS) 2005, 2008, 2012, and 2016 Site 5035 land-water matrix

Wetland restoration efforts conducted by the Coastal Wetlands Planning, Protection and Restoration Act (CWPPRA) in Louisiana rely on monitoring efforts to determine the efficacy of these efforts. The Coastwide Reference Monitoring System (CRMS) was developed to assist in a multiple-reference approach that uses aspects of hydrogeomorphic functional assessments and probabilistic sampling for monitoring. The CRMS program includes a suite of approximately 390 sites that encompass the range of hydrological and ecological conditions for each stratum. As part of CRMS, land and water classifications are created from Wetland restoration efforts conducted by the Coastal Wetlands Planning, Protection, and Restoration Act (CWPPRA) in Louisiana rely on monitoring efforts to determine the efficacy of these efforts. The Coastwide Reference Monitoring System (CRMS) was developed to assist in a multiple-reference approach that uses aspects of hydrogeomorphic functional assessments and probabilistic sampling for monitoring. The CRMS program includes a suite of approximately 390 sites that encompass the range of hydrological and ecological conditions for each stratum. As part of CRMS, land and water classifications are created from Digital Orthophoto Quarter Quadrangles (DOQQs) approximately every three years at all CRMS sites. This dataset consists of a matrix of four land-water products (2005, 2008, 2012, and 2016).  The resulting matrix has 16 possible classes defined by the combination of land and water categories on those four dates.

Tags: alteration-of-wetland-habitats, cartography, coastal, crms, doqq, emergent-wetland, forested-wetland, geographic-information-system, imagerybasemapsearthcover, land-water, louisiana, mapping, marsh, protection, restoration, scrub-shrub-wetland, state-of-louisiana, usgs-5b631b5ee4b006a11f7178aa, wetland, wetland-ecosystems, wetlands
Organization: Department of the Interior