AndreaBozzo/ceres-open-data-index huggingface dataset:
Experimental In-vitro Propagation Data for Alasmidonta heterodon and Alasmidonta undulata from June 2019- January 2020

Many freshwater mussel species are critically imperiled, and propagation is essential for species‘ recovery. Fungal contamination can negatively affect in vitro propagation of freshwater mussels; thus, we investigated methods of mitigating fungal contamination. Specifically, we tested the effect of medium replacement frequency, antifungal (Amphotericin B) concentrations, and antifungal addition method on risk of fungal contamination and transformation success of two species, Alasmidtonta heterodon and congener, Alasmidonta undulata. We found that
contamination risk was higher in treatment groups that were replenished with Amphotericin B every one or two days (vs. every three days), but contamination risk was not affected by Amphotericin B concentrations. Although contamination severity reduced transformation success, we found no significant difference in transformation success based on medium replacement frequency. Amphotericin B concentration was negatively correlated with transformation success, suggesting toxicity at higher concentrations. Additionally, we identified the fungal pathogen (Candida parapsilosis), the first knowledge of this fungus during mussel culture. Our findings suggest that low contamination results in high probability for transformation success, however, there is a tradeoff of apparent toxicity in higher concentrations of Amphotericin B. This study offers new ideas for improving mussel propagation techniques that may better control fungal contamination and increase transformation success.

Tags: amphotericin-b, biota, cell-culture, culture-contamination, dwarf-wedgemussel, environment, in-vitro-propagation, massachusetts, new-england, traingle-floater, unionid, usgs-6238c95ad34e915b67cc471f, usgs-ema-low-fwd-species-identification-disease-investigation-and-pathogen-discovery, usgs-ema-low-sb-smc-freshwater-mussels
Organization: Department of the Interior
Acoustic Doppler Current Profiler (ADCP) field measurements of flow depth and velocity from the Tanana River, Alaska, collected on August 18, 2021

Field measurements of depth-averaged flow velocity and water depth were acquired from the Tanana River near Nenana, Alaska, August 18, 2021, to support research on estimating surface flow velocities and water depths from remotely sensed data. The depth and velocity measurements included in this data release were obtained using a TRDI RiverRay acoustic Doppler current profiler (ADCP) deployed from a boat with an outboard motor. These data were collected along 8 cross-sections on the Tanana River; two passes across the channel were made at each cross-section. This data release provides depth-averaged flow velocities and total flow depths derived from the raw ADCP data using the TRDI WinRiver II processing software. The WinRiver II output was imported into the USGS Velocity Mapping Toolbox (VMT), which was used to project measurements made along each pass back and forth across the channel onto a common mean cross-section and smooth the data. VMT and custom MATLAB functions were then used to generate text files with projected spatial coordinates, depth-averaged velocity vector components in the east and north directions, and flow depths. The spatial location of each measurement was obtained using a differential GPS included as part of the RiverRay instrument package. The map projection and datum for these data are UTM Zone 6 N and NAD 83, respectively. This data release includes a comma-delimited (*.csv) text file consists of six columns: Cross_Section_ID, UTM_East_m, UTM_North_m, Velocity_East_Component_m_per_s, Velocity_North_Component_m_per_s, and Depth_m. The first column is an integer identifying the cross section, the next two columns are the easting and northing spatial coordinates, respectively, the fourth column is the east component of the the depth-averaged velocity magnitude in meters per second, the fifth column is the north component of the the depth-averaged velocity magnitude in meters per second, and the sixth column is the water depth in meters. This field-based data set was used to assess the accuracy of remotely sensed estimates of surface flow velocities and water depths derived from fixed wing aircraft-based optical image sequences.

Tags: acoustic-doppler-current-profiler-adcp, ak, alaska, depth, flow-velocity, nenana, remote-sensing, river, tanana-river, usa, usgs-62389ff6d34e915b67cc45bc
Organization: Department of the Interior
Geospatial data to assess karst aquifer systems between Albany and Buffalo, New York (ver. 4.0, January 2024)

Using publicly available data for Madison and Oneida counties, New York, a series of geospatial overlays were created at 1:24,000 scale to examine the bedrock geology, groundwater table, soils, and surficial geology. Bedrock and surficial geology were refined using extant bedrock maps, well and borehole data from water- and gas-wells, soil data, and lidar data. Groundwater data were collected from New York State Department of Environmental Conservation and U.S. Geological Survey water-well databases to estimate the groundwater table. Soil data were used to examine soil thickness over bedrock and infiltration. 
An inventory of closed depressions was created using reconditioned lidar-derived bare-earth digital elevation models (DEMs) and a modeled stream network. Closed depressions were identified from the processed DEMs using threshold criteria of 10 and 30 centimeters (3.9 and 11.8 inches) for depth and 100 square meters (1076 square feet) for area. A combination of hydrologic, mining, and cultural features was used to eliminate false positives and filter out features that overlie existing waterbodies, streams, and mines and to remove artificial dams along roadways and railways. 
This data release includes shapefiles containing the well data information including location, well depth, depth to bedrock, and groundwater depth; bedrock geology; surficial geology; interpolated bedrock surface contours; interpolated groundwater surface contours; soil saturated hydraulic conductivity; soil classes; and modeled closed depressions of 10 cm and 30 cm depth thresholds. This release also contains rasters of the interpolated bedrock surface, interpolated groundwater surface and land use.

Tags: closed-depression, groundwater, karst, madison-county, new-york, oneida-county, united-states, usgs-6234e0dcd34ec9f19eebd4f8
Organization: Department of the Interior
Predicted relative habitat selection for migrating whooping cranes in the United States Great Plains, non-drought

The whooping crane (Grus americana) is a listed, endangered species in North America, protected under federal legislation in the United States and Canada.  The only self-sustaining and wild population of Whooping Cranes nests at and near Wood Buffalo National Park near the provincial border of Northwest Territories and Alberta, Canada.  Birds from this population migrate through the Great Plains of North America and spend a nonbreeding period along the Gulf Coast of Texas at Aransas National Wildlife Refuge and surrounding lands.  These data represent predictions from a resource selection function using GPS locations between 2010 and 2016 during migration. This surface is a composite of drought and non-drought conditions calculated using the average drought occurrence at each pixel during our study period. Pixel values can be used to represent the relative probability of whooping crane use during migration, based on landscape conditions in 2020. These values should not be interpreted as absolute values of probability of use. See additional information about resource selection functions and interpretation of output as needed.

Tags: biota, birds, endangered-species, environment, kansas, migration-organisms, migratory-birds, montana, nebraska, north-dakota, oklahoma, plant-and-animal-tracking, south-dakota, texas, usgs-62349543d34ec9f19eeb7ee3
Organization: Department of the Interior
Predicted relative habitat selection for migrating whooping cranes in the United States Great Plains, drought

The whooping crane is a listed endangered species in North America, protected under federal legislation in the United States and Canada.  The only self-sustaining and wild population of Whooping Cranes nests at and near Wood Buffalo National Park near the provincial border of Northwest Territories and Alberta, Canada.  Birds from this population migrate through the Great Plains of North America and winter along the Gulf Coast of Texas at Aransas National Wildlife Refuge and surrounding lands.  These data represent predictions from a resource selection function using GPS locations between 2010 and 2016 during migration. This surface represents predictions under drought conditions across the study area. Pixel values can be used to represent the relative probability of whooping crane use during migration, based on landscape conditions in 2020. These values should not be interpreted as absolute values of probability of use. See additional information about resource selection functions and interpretation of output as needed.

Tags: biota, birds, endangered-species, environment, kansas, migration-organisms, migratory-birds, montana, nebraska, north-dakota, oklahoma, plant-and-animal-tracking, south-dakota, texas, usgs-62349520d34ec9f19eeb7e80
Organization: Department of the Interior
Whooping crane migration habitat selection disturbance data, 2010–2016

These data were developed to support an effort to understand how whooping cranes select stopover habitat in the presence of human infrastructure. Location and associated data came from whooping cranes (Grus americana) from the Aransas-Wood Buffalo Population, 2010–2016. We marked a sample of 57 whooping cranes with leg-mounted transmitters that acquired locations via the global positioning system (GPS) network and transmitted those data through the Argos satellite system. Cranes were captured either at their natal areas in and adjacent to Wood Buffalo National Park in Canada or at their southern terminus along the Texas Gulf Coast, USA. Data herein include 9,347 ground locations used by whooping cranes during migration coupled with 19 potentially available locations for each used location (see processing steps for more information). Predictor variables hypothesized to explain variation in space use were included for all locations (used and available).

Tags: biota, birds, endangered-species, environment, kansas, migration-organisms, migratory-birds, montana, nebraska, north-dakota, oklahoma, plant-and-animal-tagging, south-dakota, texas, usgs-62349481d34ec9f19eeb7c2d, wind-energy
Organization: Department of the Interior
Keamuku Maneuver Area vegetation, soil, and foliar data 2013-2016

This data release includes data and metadata on “(1) outplant survival, (2) post-disturbance percent cover, (3) post-disturbance shrub counts, (4) point-intercept vegetation data, (5) random plot coordinates, (6) soil chemistry and ratios, and (7) soil moisture. All sites were within Keamuku Maneuver Area on Hawaii Island. This study looked at how microtopography and biotic interactions influence post-disturbance recovery and native planting success in native shrub-dominated and non-native, invasive grass-dominated dryland habitats.

Tags: avian-diet, botany, ecology, exotic-grass, forest-restoration, hawaii, hawaii-island, keamuku-maneuver-area, land-use-change, plant-competition, plant-ecology, seed-limitation, seedling-recruitment, tropical-forest-dynamics, usgs-6233e15cd34ec9f19eeb4abc
Organization: Department of the Interior
Data supporting a new three-dimensional Lagrangian particle tracking model for predicting transport of carp eggs in turbulent rivers

Grass carp, bighead carp, and silver carp spawn in flowing water. Their eggs,and then larvae, develop while drifting. Hydraulic conditions control spawning locations, egg survival, and the downstream distance traveled before the hatched larvae can swim for low velocity nursery habitats. Existing egg drift models simulate the fluvial transport of carp eggs but have limitations in capturing the effect of localized turbulence on egg transport due to inadequate dimensions of hydrodynamics and/or empirical parameterization of river dispersion. We present a three-dimensional Lagrangian particle tracking model that uses fully resolved river hydrodynamics and a continuous random walk
algorithm driven by local turbulent kinetic energy and its dissipation rate. We incorporate a new set of equations to compute evolving egg characteristics with fully resolved 3-D hydrodynamics. To demonstrate the performance of the model, we conducted a case study in an eight-kilometer reach of Missouri River at the discharge of approximately 25% daily flow exceedance.
Three-dimensional river hydrodynamics was modeled, calibrated, and evaluated with measurement data. Egg drift was modeled and compared using fully three-dimensional, depth-averaged two-dimensional, and zone-averaged one-dimensional hydrodynamics. The comparison shows a generally good agreement among models of downstream egg transport due to advection but a different dispersion pattern of eggs in the river, as a result of turbulent diffusion and shear induced dispersion.

Tags: ecological-processes, elevation, environment, freshwater-ecosystems, geoscientificinformation, hydrology, inlandwaters, missouri, missouri-river, missouri-river-basin, model, usgs-6233a4a4d34ec9f19eeb4a43
Organization: Department of the Interior
Santa Ana River Native Fish Population and Habitat Data, Santa Ana River, California, 2021

This dataset includes 2021 reach fish data and reach habitat data collected to support development of the upper Santa Ana River Habitat Conservation Plan for the Santa Ana Sucker (Catostomus santaanae) and the Arroyo Chub (Gila orcutti) in the Santa Ana River, California.

Tags: arroyo-chub-gila-orcutti, habitat-use, population-estimate, santa-ana-sucker-catostomus-santaanae, usgs-6233a0bbd34ec9f19eeb4a20
Organization: Department of the Interior
LANDFIRE 2016 Remap National Vegetation Classification (NVC) Micronesia

LANDFIRE's (LF) 2016 Remap (Remap) National Vegetation Classification (NVC) represents the current distribution of vegetation groups within the U.S. National Vegetation Classification System ([version 2.0] http://usnvc.org/). Groups within the NVC IAerarchy are defined as combinations of relatively narrow sets of diagnostic plant species, including dominants and co-dominants, broadly similar composition, and diagnostic growth forms. NVC groups are mapped using decision tree models informed by field reference data, Landsat imagery, elevation data, and biophysical gradient inputs. NVC models are developed separately for each lifeform, including sparse vegetation,  and for each Environmental Protection Agency (EPA) Level III Ecoregion (https://www.epa.gov/eco-research/ecoregions). Riparian, alpine, sparse and other site-specific EVTs are constrained by predetermined masks. Urban and developed areas are derived from the National Land Cover Database (NLCD), whereas agricultural lands originate from the Cropland Data Layer (CDL) and Common Land Unit (CLU) database. Developed ruderal classes are identified by combining wildland-urban-interface (WUI) data with population density information from the US Census Bureau. Annual Disturbance products are included to describe areas that have experienced landscape change within the previous 10-year period. NVC is reconciled through QA/QC measures to ensure lifeform is synchronized with both Existing Vegetation Cover (EVC) and Height (EVH) products.

Tags: biota, federated-states-of-micronesia, fires, geographic-information-systems, geospatial-datasets, hazard-preparedness, ia, image-collections, imagerybasemapsearthcover, insular-areas, landfire-2016-remap, lf-2016-remap, micronesia, nvc, oconus, raster-digital-data, remote-sensing, u-s-forest-service-usfs, u-s-geological-survey-usgs, u-s-national-vegetation-classification-nvc, united-states, us, usgs-62321a2d-e937-4696-8f4e-c93a56839d5c
Organization: Department of the Interior
Fluvial Erosion Hazard Rapid Geomorphic Assessment Data from the Marengo Watershed, Ashland County, Wisconsin

An extreme flood in 2016 caused widespread culvert blockages and road failures across northern Wisconsin, including extensive damage along steep tributaries and ravines in the Marengo River watershed. Along with the flooding, there were fluvial erosion hazards (FEH) associated with a large amount of erosion in headwater areas. Of special concern were FEHs associated with gullying, loss of wetland storage, and valley-side mass wasting. In 2020, a pilot study was begun to map and classify ephemeral and perennial streams and wetlands in terms of their susceptibility to fluvial erosion hazards. This study combines rapid geomorphic field assessments of river corridor erosion and coupled sediment and debris delivery with mapping geomorphic vulnerability zones in a Geographic Information System (GIS). The FEH assessment results will ultimately be used to identify and prioritize natural flood management projects related to stream and wetland restoration.

Tags: ashland, bad-montreal, erosion, geomorphology, geoscientificinformation, great-lakes, north-america, sediment-transport, sedimentation, southwestern-lake-superior, united-states, usgs-6230edbad34ec9f19eeaf615, wisconsin
Organization: Department of the Interior
New Milan Reservoir (Elmwood Lake) near Milan, Missouri, 2020

Water supply lakes are the primary source of water for many communities in northern and western Missouri.  Therefore, accurate and up-to-date estimates of lake capacity are important for managing and predicting adequate water supply. Many of the water supply lakes in Missouri were previously surveyed by the U.S. Geological Survey in the early 2000s (Richards, 2013) and in 2013 (Huizinga, 2014); however, years of potential sedimentation may have resulted in reduced water storage capacity. Periodic bathymetric surveys are useful to update the area/capacity table and to determine changes in the bathymetric surface.
New Milan Reservoir (locally known as Elmwood Lake) is a water supply lake used by the city of Milan in north-central Missouri. The surface area of New Milan Reservoir is about 282 acres at the flood pool level of the emergency spillway (877.2 feet above the North American Vertical Datum of 1988).  No previous bathymetric survey has been completed at this lake.  In July 2020, the U.S. Geological Survey, in cooperation with the Missouri Department of Natural Resources and in collaboration with the City of Milan, completed a bathymetric survey of New Milan Reservoir using a multibeam echosounder.  The water-surface elevation during the survey was about 871.9 feet. The echosounder data can be combined with light detection and ranging (lidar) data to prepare a bathymetric map and a surface area and capacity table for the lake.
The gridded bathymetric point data (ElmwoodLake2020_bathy_pts.zip) were computed on a 1.64-foot (0.50-meter) grid using the Combined Uncertainty and Bathymetry Estimator (CUBE) method, which is used as the source of points to create the bathymetric surface.
Bathymetric quality-assurance data (ElmwoodLake2020_QA_raw.zip) were collected to evaluate the vertical accuracy of the gridded bathymetric point data.
Each of these two zip files contains a shapefile with an attribute table. Attribute/column labels of each table are described in the "Entity and attribute" section of the metadata file.
References Cited:
Huizinga, R.J., 2014, Bathymetric surveys and area/capacity tables of water-supply reservoirs for the city of Cameron, Missouri, July 2013: U.S. Geological Survey Open-File Report 2014–1005, 15 p., https://doi.org/10.3133/ofr20141005.
Richards, J.M., 2013, Bathymetric surveys of selected lakes in Missouri—2000–2008: U.S. Geological Survey Open-File Report 2013–1101, 9 p. with appendix, https://pubs.usgs.gov/of/2013/1101.

Tags: bathymetry, bathymetry-and-elevation, elmwood-lake, milan, missouri, multibeam, multibeam-sonar, new-milan-reservoir, sullivan-county, u-s-geological-survey, usgs, usgs-6230d067d34ec9f19eeaf53d
Organization: Department of the Interior
Number 41 Lake (Milan Golf Course Lake) near Milan, Missouri, 2020

Water supply lakes are the primary source of water for many communities in northern and western Missouri.  Therefore, accurate and up-to-date estimates of lake capacity are important for managing and predicting adequate water supply. Many of the water supply lakes in Missouri were previously surveyed by the U.S. Geological Survey in the early 2000s (Richards, 2013) and in 2013 (Huizinga, 2014); however, years of potential sedimentation may have resulted in reduced water storage capacity. Periodic bathymetric surveys are useful to update the area/capacity table and to determine changes in the bathymetric surface.
Number 41 Lake (locally known as Milan Golf Course Lake) is a water supply lake used by the city of Milan in north-central Missouri. The surface area of Number 41 Lake is about 49 acres at the full pool level of the primary spillway (865.8 feet above the North American Vertical Datum of 1988).  No previous bathymetric survey has been completed at this lake.  In July 2020, the U.S. Geological Survey, in cooperation with the Missouri Department of Natural Resources and in collaboration with the City of Milan, completed a bathymetric survey of Number 41 Lake using a multibeam echosounder.  The water-surface elevation during the survey was about 865.7 feet. The echosounder data can be combined with light detection and ranging (lidar) data to prepare a bathymetric map and a surface area and capacity table for the lake.
The gridded bathymetric point data (MilanGolfCourseLake2020_bathy_pts.zip) were computed on a 0.82-foot (0.25-meter) grid using the Combined Uncertainty and Bathymetry Estimator (CUBE) method, which is used as the source of points to create the bathymetric surface.
Bathymetric quality-assurance data (MilanGolfCourseLake2020_QA_raw.zip) were collected to evaluate the vertical accuracy of the gridded bathymetric point data.
Each of these two zip files contains a shapefile with an attribute table. Attribute/column labels of each table are described in the "Entity and attribute" section of the metadata file.
References Cited:
Huizinga, R.J., 2014, Bathymetric surveys and area/capacity tables of water-supply reservoirs for the city of Cameron, Missouri, July 2013: U.S. Geological Survey Open-File Report 2014–1005, 15 p., https://doi.org/10.3133/ofr20141005.
Richards, J.M., 2013, Bathymetric surveys of selected lakes in Missouri—2000–2008: U.S. Geological Survey Open-File Report 2013–1101, 9 p. with appendix, https://pubs.usgs.gov/of/2013/1101.

Tags: bathymetry, bathymetry-and-elevation, milan, milan-golf-course-lake, missouri, multibeam, multibeam-sonar, number-41-lake, sullivan-county, u-s-geological-survey, usgs, usgs-6230d038d34ec9f19eeaf53b
Organization: Department of the Interior