AndreaBozzo/ceres-open-data-index huggingface dataset:
Science to Inform Management of Floodplain Conservation Lands on the Middle Mississippi River

Within large-river ecosystems, floodplains serve a variety of important ecological functions. A recent survey of 80 managers of floodplain conservation lands along the Upper and Middle Mississippi and Lower Missouri Rivers in the central United States found that the most critical information needed to improve floodplain management centered on metrics for characterizing depth, extent, frequency, duration, and timing of inundation. These metrics can be delivered to managers efficiently through cloud-based interactive maps. To calculate these metrics, we interpolated an existing one-dimensional HEC-RAS hydraulic model for the Middle Mississippi River, which simulated water surface elevations at cross sections spaced  (&lt;1 kilometer) to sufficiently characterize water surface profiles along an approximately 800 kilometer stretch upstream from the confluence with the Mississippi River over an 80-year record at a daily time step. To translate these water surface elevations to inundation depths, we subtracted a merged terrain model consisting of floodplain LIDAR and bathymetric surveys of the river channel.  We completed these calculations for an 800 kilometer stretch of the Missouri River, spanning from Rulo, Nebraska to the river's confluence with the Mississippi River. Analyzed areas include the entirety of the Mississippi River floodplain, with the exception of the St. Louis metropolitan area in which analysis was constrained to currently unleveed areas only. This approach resulted in a 29,000+ day time series of inundation depths across the floodplain using grid cells with 30 meter spatial resolution. This dataset presents 14 metrics for each of two scenarios, one using a baseline timeseries of stages from the HEC-RAS simulation and one using a timeseries of stages adjusted to account for removal of existing levees from the floodplain. These metrics are calculated on a per pixel basis and encompass a variety of temporal criteria generally relevant to flora and fauna of interest to floodplain managers, including, for example, the average number of days inundated per year within a growing season. We also include the base elevation layer that we generated to calculate depth of inundation from interpolated water-surface elevations.

Tags: environment, floodplains, floods, inlandwaters, river-systems, streamflow-and-mathematical-modeling, upper-mississippi, upper-mississippi-cape-girardeau, upper-mississippi-meramec, usgs-5fdbb41ad34e30b9123d25e4, wetland-ecosystems
Organization: Department of the Interior
No Levee (Altered) Inundation Metrics for the Middle Mississippi River

Within large-river ecosystems, floodplains serve a variety of important ecological functions. A recent survey of 80 managers of floodplain conservation lands along the Upper and Middle Mississippi and Lower Missouri Rivers in the central United States found that the most critical information needed to improve floodplain management centered on metrics for characterizing depth, extent, frequency, duration, and timing of inundation. These metrics can be delivered to managers efficiently through cloud-based interactive maps. To calculate these metrics, we interpolated an existing one-dimensional HEC-RAS hydraulic model for the Middle Mississippi River, which simulated water surface elevations at cross sections spaced  (&lt;1 kilometer) to sufficiently characterize water surface profiles along an approximately 800 kilometer stretch upstream from the confluence with the Mississippi River over an 80-year record at a daily time step. To translate these water surface elevations to inundation depths, we subtracted a merged terrain model consisting of floodplain LIDAR and bathymetric surveys of the river channel.  We completed these calculations for an 800 kilometer stretch of the Missouri River, spanning from Rulo, Nebraska to the river's confluence with the Mississippi River. Analyzed areas include the entirety of the Mississippi River floodplain, with the exception of the St. Louis metropolitan area in which analysis was constrained to currently unleveed areas only. This approach resulted in a 29,000+ day time series of inundation depths across the floodplain using grid cells with 30 meter spatial resolution. This dataset presents 14 metrics for each of two scenarios, one using a baseline timeseries of stages from the HEC-RAS simulation and one using a timeseries of stages adjusted to account for removal of existing levees from the floodplain. These metrics are calculated on a per pixel basis and encompass a variety of temporal criteria generally relevant to flora and fauna of interest to floodplain managers, including, for example, the average number of days inundated per year within a growing season. We also include the base elevation layer that we generated to calculate depth of inundation from interpolated water-surface elevations.

Tags: environment, floodplains, floods, inlandwaters, river-systems, streamflow-and-mathematical-modeling, upper-mississippi, upper-mississippi-cape-girardeau, upper-mississippi-meramec, usgs-5fdbb4f4d34e30b9123d261e, wetland-ecosystems
Organization: Department of the Interior
With Levee (baseline) Inundation Metrics for the Middle Mississippi River

Within large-river ecosystems, floodplains serve a variety of important ecological functions. A recent survey of 80 managers of floodplain conservation lands along the Upper and Middle Mississippi and Lower Missouri Rivers in the central United States found that the most critical information needed to improve floodplain management centered on metrics for characterizing depth, extent, frequency, duration, and timing of inundation. These metrics can be delivered to managers efficiently through cloud-based interactive maps. To calculate these metrics, we interpolated an existing one-dimensional HEC-RAS hydraulic model for the Middle Mississippi River, which simulated water surface elevations at cross sections spaced  (&lt;1 kilometer) to sufficiently characterize water surface profiles along an approximately 800 kilometer stretch upstream from the confluence with the Mississippi River over an 80-year record at a daily time step. To translate these water surface elevations to inundation depths, we subtracted a merged terrain model consisting of floodplain LIDAR and bathymetric surveys of the river channel.  We completed these calculations for an 800 kilometer stretch of the Missouri River, spanning from Rulo, Nebraska to the river's confluence with the Mississippi River. Analyzed areas include the entirety of the Mississippi River floodplain, with the exception of the St. Louis metropolitan area in which analysis was constrained to currently unleveed areas only. This approach resulted in a 29,000+ day time series of inundation depths across the floodplain using grid cells with 30 meter spatial resolution. This dataset presents 14 metrics for each of two scenarios, one using a baseline timeseries of stages from the HEC-RAS simulation and one using a timeseries of stages adjusted to account for removal of existing levees from the floodplain. These metrics are calculated on a per pixel basis and encompass a variety of temporal criteria generally relevant to flora and fauna of interest to floodplain managers, including, for example, the average number of days inundated per year within a growing season. We also include the base elevation layer that we generated to calculate depth of inundation from interpolated water-surface elevations.

Tags: environment, floodplains, floods, inlandwaters, river-systems, streamflow-and-mathematical-modeling, upper-mississippi, upper-mississippi-cape-girardeau, upper-mississippi-meramec, usgs-5fdbb57ad34e30b9123d2640, wetland-ecosystems
Organization: Department of the Interior
Liquid Chromatography Triple Quadrupole Mass Spectrometry (LC/MS/MS) analysis of cyanotoxins and algal toxins in estuary samples collected from California, USA, in 2016-17

Cyanobacteria known to produce cyanotoxins have been reported worldwide. As monitoring efforts have improved, they have been detected in not only freshwater, but also in estuary and marine waters. To assess the occurrence of cyanotoxins and algal toxins in California estuaries, the NOAA MERHAB funded project collected samples monthly from 11 Californian estuary locations, with 5 locations sampled in 2016 as event response. This data release includes liquid chromatography triple quadrupole mass spectrometry (LC/MS/MS) results for 21 cyanotoxins and algal toxins in estuary samples collected from California in 2016-2017.

Tags: chemical-analysis, cyanotoxins, domoic-acid, environmental-health, liquid-chromatography, mass-spectrometry, microcystins, usgs-5fdbddf8d34e30b9123d290f
Organization: Department of the Interior
Using Targeted Training Data to Develop Site Potential for the Upper Colorado River Basin from 2000 - 2018

Defining site potential for an area establishes its possible long-term vegetation growth productivity in a relatively undisturbed state, providing a realistic reference point for ecosystem performance. Modeling and mapping site potential helps to measure and identify naturally occurring variations on the landscape as opposed to variations caused by land management activities or disturbances (Rigge et al. 2020). We integrated remotely sensed data (250-m enhanced Moderate Resolution Imaging Spectroradiometer (eMODIS) Normalized Difference Vegetation Index (NDVI) (https://earthexplorer.usgs.gov/)) with land cover, biogeophysical (i.e., soils, topography) and climate data into regression-tree software (Cubist®). We integrated these data to create a snapshot of spatially explicit predictions of shrub and grass site potential in the Upper Colorado River Basin (UCRB) in the western U.S. The predictions are limited to pixels classified by the 2016 National Land Cover Database (NLCD) as shrub or grassland/herbaceous (https://www.mrlc.gov). The site potential datasets will be incorporated as independent variables into mapping models that delineate statistically significant deviations between actual NDVI values and modeled NDVI values in the UCRB.
Rigge, MB., Homer, C., Shi, H., Wylie, BK. 2020. Departures of rangeland fractional component cover and land cover from landsat-based ecological potential in Wyoming, USA. Rangeland Ecology &amp; Management. DOI: 10.1016/j.rama.2020.03.009.

Tags: arid, arizona, colorado, geoscientificinformation, grass, land-cover-monitoring-assessment-amp-projection, lcmap, machine-learning, modeling, monitoring-trends-in-burn-severity, mtbs, national-land-cover-database, new-mexico, nlcd, polaris-soils, prism-normals-1981-2010, rangeland, regression-tree, semiarid, shrub, spatial-analysis, united-states, upper-colorado-river-basin, usgs-5fdcbd2bd34e30b9123d2f60, utah, west, western-united-states, wyoming
Organization: Department of the Interior
Mean flea counts from prairie dogs and their burrows in Utah (2000), New Mexico (2010-2012), and Montana (2016, 2019)

Mean flea counts from prairie dogs and their burrows in Utah (2000), New Mexico (2010-2012), and Montana (2016, 2019). Prairie dogs were live-trapped, anesthetized with isoflurane, and combed thoroughly for 30 or 45 seconds to remove and count fleas. Prairie dogs were allowed to recover from anesthesia and released at their trapping locations. Randomly selected prairie dog burrows were swabbed for fleas using a plumber’s snake to insert a white flannel-cloth as deep as possible into each tunnel; the cable was shook ~30 seconds, and the cloth was removed from the burrow and quickly sealed in a re-sealable zipper storage bag. Fleas were later removed from swabs and counted. Mean flea counts were calculated for each sampling site, and sampling interval, as the total number of fleas collected (from prairie dogs or burrows) divided by the total number of sampling occasions (combings or swabbings). 
Funding and logistical support were provided by the U.S. Geological Survey; Turner Endangered Species Fund; Turner Enterprises Incorporated; Colorado State University; Centers for Disease Control and Prevention; U.S. Fish and Wildlife Service; Charles M. Russell National Wildlife Refuge; Shortgrass Steppe Long-Term Ecological Research Project; National Science Foundation; and the U.S. Department of Defense Strategic Environment Research and Development Program.

Tags: biota, capturing-animals, cynomys, disease-vectors, flea, grassland-ecosystems, montana, new-mexico, prairie-dog, usgs-5fdd51b1d34e30b9123d3706, utah
Organization: Department of the Interior
Confirmed cases of snake fungal disease in historical museum specimens

Snake fungal disease (SFD) represents a conservation threat to wild snake populations. The disease was reported in North America early in the 21st century, but the history of SFD has not been investigated. We examined museum specimens and confirmed cases of SFD based on clinical signs, histopathologic lesions, and detection of the causative agent Ophidiomyces ophidiicola.  The first confirmed cases of SFD in these specimens was &gt;50 years prior to the disease’s reported emergence.

Tags: biota, fungal-disease, morehead-state-university-museum-morehead-kentucky, museum-collection, reptile-disease, snake, u-s-geological-survey-national-wildlife-health-center-madison-wisconsin, university-of-wisconsin-zoological-museum-madison-wisconsin, usgs-5fe0d62ed34e30b9123eeda9
Organization: Department of the Interior
Groundwater Quality Data from the Mohawk and Western New York River Basins, New York, 2016

From July through December 2016, 56 environmental samples were collected from the Mohawk and Western New York River Basins. Samples were collected from nine production wells and 13 domestic wells in the Mohawk River Basin, and 17 production wells and 17 domestic wells in the Western New York River Basins. Samples were collected and processed using standard USGS methods and analyzed for 320 constituents including physicochemical properties, dissolved gases, major ions, nutrients, trace elements, pesticides, volatile organic compounds, radionuclides, and indicator bacteria. Analytical methods are described and referenced in Gaige and others (2023). 
Five of the Mohawk River Basin wells (HE 622, HE 624, OE1468, SA1501, and MT 406) were also sampled in 2002, 2006, and (or) 2011. Seven of the Western New York River Basins wells (AG 265, CU2131, E1903, E1904, GS 216, WO 351, and OL  19) were also sampled in 2006 and (or) 2011. Results from these wells and years are tabulated for comparison.

Tags: albany-county, allegany-county, cattaraugus-county, chautauqua-county, erie-county, fulton-county, genesee-county, greene-county, groundwater, groundwater-quality, hamilton-county, herkimer-county, hydrogeology, mohawk-river-basin, monroe-county, montgomery-county, oneida-county, orleans-county, saratoga-county, schenectady-county, schoharie-county, usgs-5fe0de70d34e30b9123eedbd, water-chemistry, water-resources, western-new-york-river-basins, wyoming-county
Organization: Department of the Interior
Pseudogymnoascus destructans detections by US county (2008-2012)

This data represents the number of positive and negative Pd (Pseudogymnoascus destructans) detections by county over the sampling period 2008-2012. Pd is the fungus that is the causative agent of white-nose syndrome.

Tags: bats, biota, fungal-disease, pathogen-spread, usgs-5fe10cb4d34e30b9123f00d8, wildlife-disease
Organization: Department of the Interior
Area where the Arikaree aquifer is absent, Pine Ridge Indian Reservation and Bennett County, South Dakota

This data set describes the area within the Pine Ridge Indian Reservation where the Arikaree aquifer 
(Arikaree Formation) is absent. This absent area includes areas where the Arikaree Formation has 
been eroded and where outcrops of geologic units older than the Arikaree Formation are present at 
the land surface.

Tags: arikaree-aquifer, bennett-county, geology, inlandwaters, jackson-county, pine-ridge-indian-reservation, shannon-county, south-dakota, usgs-5f85674c-c738-4c0d-986a-2549e513f2a9
Organization: Department of the Interior
Data for Machine Learning Predictions of Nitrate in Groundwater Used for Drinking Supply in the Conterminous United States

A three-dimensional extreme gradient boosting (XGB) machine learning model was developed to predict the distribution of nitrate in groundwater across the conterminous United States (CONUS). Nitrate was predicted at a 1-square-kilometer (km) resolution for two drinking water zones, each of variable depth, one for domestic supply and one for public supply. The model used measured nitrate concentrations from 12,082 wells, and included predictor variables representing well characteristics, hydrologic conditions, soil type, geology, land use, climate, and nitrogen inputs. Predictor variables derived from empirical or numerical process-based models were also included to integrate information on controlling processes and conditions. This data release documents the model and provides the model results. The model and results are discussed in the associated journal article, Ransom and others (2021).
Included in this data release are, 1) a model archive of the R project: source code, input files (including model training and hold-out data, rasters of all final predictor variables, and rasters representing domestic and public supply depth zones), and output files (two rasters of predicted nitrate concentration at the depth zones typical of domestic and public supply wells), 2) a read_me file describing the model archive and an explanation of its use, and 3) tables describing model variables, model fit statistics, and model results [these tables are also included in the Supporting Information published with the journal article Ransom and others (2021)].

Tags: cycle-3, domestic-well-water-use, environment, geoscientificinformation, groundwater, machine-learning, nawqa, nitrate, public-supply-water-use, usgs-5fe122a7d34e30b9123f02d9, water-quality, water-well
Organization: Department of the Interior
APEX Electrical Resistivity Tomography (ERT) Data and Models from 2018

Geophysical measurements and related field data were collected by the U.S. Geological Survey (USGS) at the Alaska Peatland Experiment (APEX) site in Interior Alaska from 2018 to 2020 to characterize subsurface thermal and hydrologic conditions along a permafrost thaw gradient. The APEX site is managed by the Bonanza Creek LTER (Long Term Ecological Research). Nine instrument monitoring sites (APEX1-APEX9) were established in April 2018. To quantify permafrost and thaw zone characteristics along the instrumented gradient, electrical resistivity tomography (ERT) data were collected in August 2018 along four 82 meter (m)-long transects between select sites: APEX1-3, APEX5-3, APEX5-7, and APEX6-8. Data were collected for both dipole-dipole (DD) and inverse Schlumberger (IS) survey geometries. Inverted models of electrical resistivity were produced from the separate DD and IS datasets, as well as the combination of both datasets inverted jointly (labeled DDIS). The resulting models of electrical resistivity revealed the spatial variability in soil lithology and thermal state (frozen vs. thawed) to depths up to 10-15 m below the surface. Manual permafrost-probe measurements of thaw depths were collected at set intervals along each ERT transect and used for comparison to the resistivity models.

Tags: active-layer-thickness, alaska, bonanza-creek, disturbance, electrical-resistivity-imaging, electrical-resistivity-tomography, environment, fairbanks-north-star, field-monitoring-stations, geology-geophysics-and-geochemistry-science-center, geoscientificinformation, gggsc, hydrologic-processes, land-change-science-program, permafrost, u-s-geological-survey, usgs, usgs-5fe12d7bd34e30b9123f0383
Organization: Department of the Interior
APEX Borehole Nuclear Magnetic Resonance (NMR) Data and Models from 2018-2020

Geophysical measurements and related field data were collected by the U.S. Geological Survey (USGS) at the Alaska Peatland Experiment (APEX) site in Interior Alaska from 2018 to 2020 to characterize subsurface thermal and hydrologic conditions along a permafrost thaw gradient. The APEX site is managed by the Bonanza Creek LTER (Long Term Ecological Research). Nine instrument sites were established in April 2018, seven of which were given a borehole approximately 2.3 meters (m) deep for repeat nuclear magnetic resonance (NMR) logging to quantify unfrozen water content and soil properties in the near surface. NMR data were collected from each borehole a total of ten times between April 2018 and October 2020, at a nominal vertical interval of 12.5 centimeters (cm) from 0-2 m depth. The raw spin-echo decay data, T2 decay data, and inverted models of unfrozen water content and pore-size distributions are provided in comma-separated files (*csv). The original binary (*lvm) files are also provided within the compressed zip folder.

Tags: active-layer-thickness, alaska, bonanza-creek, borehole-nuclear-magnetic-resonance, disturbance, environment, fairbanks-north-star, field-monitoring-stations, geology-geophysics-and-geochemistry-science-center, geoscientificinformation, gggsc, hydrologic-processes, land-change-science-program, permafrost, u-s-geological-survey, usgs, usgs-5fe12da0d34e30b9123f0388
Organization: Department of the Interior
APEX Soil Temperature and Moisture Data from 2018-2020

Geophysical measurements and related field data were collected by the U.S. Geological Survey (USGS) at the Alaska Peatland Experiment (APEX) site in Interior Alaska from 2018 to 2020 to characterize subsurface thermal and hydrologic conditions along a permafrost thaw gradient. The APEX site is managed by the Bonanza Creek LTER (Long Term Ecological Research). In July 2018, soil temperature and moisture sensors were installed at six out of the nine instrument locations (APEX1, APEX2, APEX3, APEX4, APEX7, APEX9). Thermistors (PS103J2, US Sensor, Orange, CA, USA) were placed at depths of 5, 30, 60, 120, and 180 centimeters (cm) with three replicates. Three sites (APEX1, APEX4, APEX9) contained an additional single 240 cm thermistor. Each soil temperature record was processed to remove erroneous values and spikes. Two time-domain reflectometry (TDR) probes (CS-616, Campbell Scientific, Logan UT, USA) were installed at the same six instrument sites to record soil moisture. The first TDR was inserted at a 45-degree angle down from the ground surface (0-20 cm), and the second from 20-40 cm. We applied an organic soils correction to the raw TDR data following the procedure in Bourgeau‐Chavez et al. (2010). Soil temperature and moisture data were recorded continuously from July 2018 through October 2020 on Campbell Scientific data loggers, with some data gaps due to power loss.

Tags: alaska, bonanza-creek, disturbance, environment, fairbanks-north-star, field-monitoring-stations, geology-geophysics-and-geochemistry-science-center, geoscientificinformation, gggsc, hydrologic-processes, land-change-science-program, permafrost, soil-moisture, soil-temperature, u-s-geological-survey, usgs, usgs-5fe12dc3d34e30b9123f038b
Organization: Department of the Interior