AndreaBozzo/ceres-open-data-index huggingface dataset:
Hilaria jamesii data for the Colorado Plateau of the southwestern United States

These data were compiled to investigate the demographic, phylogeographic, and adaptation history of Hilaria jamesii. The data release consists of three tab delimited text files that may be used to infer population structure or putative adaptive loci (hija_adaptation_dataset.stru), relationships among sampling localities (hija_phylogeny_dataset.phylip), or genetic diversity statistics (hija_diversity_stats.vcf). All files record genetic variation on an individual (.stru and .vcf) or sampling locality (.phylip) level. The .vcf file contains all of the information contained in the other files, but the file structures vary based on the programs used for analysis. These files may be opened and edited in a text editor program, such as Notepad ++ (PC) or BBEdit (Mac). The .vcf file can be loaded into the Stacks population program (Catchen et al. 2013) to calculate genetic diversity statistics. The .phylip file can be uploaded to phyML to generate a tree-based visualization of relationships ( http://www.atgc-montpellier.fr/phyml/). The .stru file can be used in the STRUCTURE program (Falush et al. 2007) to estimate population structure.

Tags: adaptation, arizona, biogeography, biota, colorado, colorado-plateau, demographics, demography, ecosystem-management, ecosystem-restoration, environmental-gradients, evolution, genetic-diversity, great-basin, hilaria-jamesii, intermountain-west, native-plant-materials-development, native-species, nevada, new-mexico, north-america, phylogeny, phylogeography, population-structure, restoration, seed-transfer-guidelines, usgs-5dbc9b08e4b06957974edf52, utah, western-united-states, wyoming
Organization: Department of the Interior
Beach topography and near-shore bathymetry of Lake Superior at Minnesota Point, Duluth, MN, August 2019

This dataset is a digital elevation model (DEM) of the beach topography and near-shore bathymetry of Lake Superior at Minnesota Point, Duluth, Minnesota.  The DEM has a 10-meter (m; 32.8084 feet) cell size and was created from a LAS dataset of terrestrial light detection and ranging (LiDAR) data representing the beach topography and sonar data representing the bathymetry to approximately 1.3 kilometers (0.8 miles) offshore.  Average point spacing of the LAS files in the dataset are as follows:  LiDAR, 0.137 m; multi-beam sonar, 1.029 m; single-beam sonar, 0.999 m.  LiDAR data were collected August 10, 2019 using a boat-mounted Optech ILRIS scanner and methodology similar to that described by Huizinga and Wagner (2019).  Multi-beam sonar data were collected August 7-11, 2019 using an R2Sonic 2024 sonar unit and methodology similar to that described by Richards and Huizinga (2018).  Single-beam sonar data were collected August 27-28, 2019 using a CEESCOPE echosounder and methodology similar to that described by Wilson and Richards (2006).

Tags: bathymetry, bathymetry-and-elevation, dem, digital-elevation-models, duluth, elevation, great-lakes, hydroacoustic, inlandwaters, lake-superior, las, lidar, limnology, sonar, southwestern-lake-superior, superior, usgs-5dbc9a51e4b06957974edf4c, xyz
Organization: Department of the Interior
Data on serology results for green turtles with and without fibropapillomatosis from Hawaii and Florida

Fibropapillomatosis (FP) is a tumor disease associated with a herpesvirus (Chelonid herpesvirus 5-ChHV5) that affects mainly green turtles globally.  Understanding the epidemiology of FP has been hampered by lack of robust serological assays to monitor exposure to ChHV5.  This is due in part to inability to efficiently culture the virus in vitro for neutralization assays.  Here, we expressed two glycoproteins (FUS4 and FUS8) from ChHV5 using baculovirus.  These proteins were immobilized on ELISA plates in their native form, and assayed for reactivity to two types of antibodies, the full length 7S and truncated 5.7S IgY.  In Florida, turtles were uniformly seropositive regardless of tumor status.  In contrast, in Hawaii, we detected strong antibody reactivity mainly from tumored animals with lower antibody response in non-tumored animals, including those from FP Enzootic areas.  In Hawaii, turtles actively shedding ChHV5 were more seropositive than non-shedders.   In trying to account for differences in serological responses to ChHV5 between Hawaii and Florida, we rejected cross reactivity of antibodies to other herpesviruses, differences in viral epitopes, or differences in procedure as likely explanations.  Rather, behavioral differences between green turtles from Hawaii and Florida, respectively, have led to the emergence of biologically different viral strains. While Florida strains apparently spread independent of tumors, transmission of the Hawaiian subtype apparently relies heavily on tumor formation.

Tags: biota, chelonia-mydas, fibropapilloma, florida, green-turtle, hawaii, herpesvirus, igy, serology, usgs-5dbc6116e4b06957974ede68
Organization: Department of the Interior
Shorelines from 1948 to 2016 for the north coast of Alaska, Icy Cape to Cape Prince Wales used in shoreline change analysis

This dataset includes shorelines that span 68 years, from 1948 to 2016, for the north coast of Alaska from Icy Cape to Cape Prince of Wales. Shorelines were compiled from topographic survey sheets (T-sheets; National Oceanic and Atmospheric Administration (NOAA)) and aerial orthophotographs (U.S. Geological Survey (USGS) and Alaska High Altitude Photography (AHAP)). Historical shoreline positions serve as easily understood features that can be used to describe the movement of beaches through time. These data are used to calculate rates of shoreline change for the U.S. Geological Survey's National Assessment of Shoreline Change Project. Rates of long-term and short-term shoreline change were generated in a GIS using the Digital Shoreline Analysis System (DSAS) version 4.4. DSAS uses a measurement baseline method to calculate rate-of-change statistics. Transects are cast from the reference baseline to intersect each shoreline, establishing measurement points used to calculate shoreline change rates.

Tags: arctic, bering-land-bridge-national-preserve, cape-espenberg, cape-krusenstern-national-monument, cape-lisburne, cape-prince-of-wales, cape-thompson, chukchi-sea, cmhrp, coastal-and-marine-hazards-and-resources-program, coastal-processes, deering, digital-shoreline-analysis-system, distributions, dsas, environment, geoscientificinformation, icy-cape, kivalina, kotzebue-sound, north-slope, oceans, pacific-coastal-and-marine-science-center, pcmsc, physical-chemical-features, point-hope, point-lay, red-dog-dock, shishhmaref, shoreline, shoreline-accretion, shoreline-change, shoreline-erosion, u-s-geological-survey, usgs, usgs-5dbb7ac3e4b06957974eda38, wales
Organization: Department of the Interior
DisMOSH, Cost, MOSH_Shoreline: Distance to foraging areas for piping plovers including foraging shoreline, cost mask, and least-cost path distance: Cobb Island, VA, 2014

Understanding how sea-level rise will affect coastal landforms and the species and habitats they support is critical for crafting approaches that balance the needs of humans and native species. Given this increasing need to forecast sea-level rise effects on barrier islands in the near and long terms, we are developing Bayesian networks to evaluate and to forecast the cascading effects of sea-level rise on shoreline change, barrier island state, and piping plover habitat availability. We use publicly available data products, such as lidar, orthophotography, and geomorphic feature sets derived from those, to extract metrics of barrier island characteristics at consistent sampling distances. The metrics are then incorporated into predictive models and the training data used to parameterize those models. This data release contains the extracted metrics of barrier island geomorphology and spatial data layers of habitat characteristics that are input to Bayesian networks for piping plover habitat availability and barrier island geomorphology. These datasets and models are being developed for sites along the northeastern coast of the United States. This work is one component of a larger research and management program that seeks to understand and sustain the ecological value, ecosystem services, and habitat suitability of beaches in the face of storm impacts, climate change, and sea-level rise.

Tags: atlantic-ocean, barrier-island, bayesian-network, biota, charadrius-melodus, cmgp, coastal-and-marine-geology-program, coastal-habitat, cobb-island, delmarva-peninsula, ecology, environment, foraging-ecology, geographic-information-systems, geography, geomorphology, geospatial-analysis, geospatial-datasets, gis, mean-high-water, mhw, north-america, piping-plovers, st-petersburg-coastal-and-marine-science-center, u-s-geological-survey, united-states, usa, usgs, usgs-5daa37a6e4b09fd3b0c9cead, va, virginia, virginia-coast-reserve, woods-hole-coastal-and-marine-science-center
Organization: Department of the Interior
Offshore baseline generated to calculate shoreline change rates for the north coast of Alaska, Icy Cape to Cape Prince of Wales

This dataset includes a reference baseline used by the Digital Shoreline Analysis System (DSAS) to calculate rate-of-change statistics for the exposed coast of Alaska from Icy Cape and Cape Prince Wales for the time period 1948 to 2016. This baseline layer serves as the starting point for all transects cast by the DSAS application and can be used to establish measurement points used to calculate shoreline-change rates.

Tags: arctic, bering-land-bridge-national-preserve, cape-espenberg, cape-krusenstern-national-monument, cape-lisburne, cape-prince-of-wales, cape-thompson, chukchi-sea, cmhrp, coastal-and-marine-hazards-and-resources-program, coastal-processes, deering, digital-shoreline-analysis-system, distributions, dsas, environment, geoscientificinformation, icy-cape, kivalina, kotzebue-sound, north-slope, oceans, pacific-coastal-and-marine-science-center, pcmsc, physical-chemical-features, point-hope, point-lay, red-dog-dock, shishhmaref, shoreline, shoreline-accretion, shoreline-change, shoreline-erosion, u-s-geological-survey, usgs, usgs-5dbb7aa1e4b06957974eda35, wales
Organization: Department of the Interior
Oahu Island Hawaiian stilt GPS satellite tracking data, 2017-2018

Lotek Pinpoint Global Positioning System (GPS) Argos Satellite tracking tags were placed on 4 Hawaiian Stilts on Oahu island in 2017. The birds were tracked from 19 July 2017 to 12 February 2018, with locations taken daily every 1.5 hours from 0400to 2000 Hawaii Standard Time. For each location, a description of the general habitat as 1) Wetland, 2) undeveloped field, 3) sport field, and 4) developed area was determined through a visual evaluation of the location using WorldView 2 satellite imagery.

Tags: biota, gps-satellite-tracking, himantopus-mexicanus-knudseni, usgs-5dbb7922e4b06957974eda2f
Organization: Department of the Interior
2012 Geomagnetic Repeat Station Data

Repeat Stations are temporary magnetic installations, where the Earth’s magnetic field, or geomagnetic field, is measured for several days, with the goal of producing mean values of the vector components of the field, when the geomagnetic field is in a quiescent state.  The data consist of approximately 72 hours of the vector magnetic field variations at each site plus calibration data measured periodically during the collection of the time series data.  The time series data were digitally recorded using a 3-axis Narod fluxgate magnetometer and GEM GSM-19 overhauser magnetometer.  The data were stored in files that could be used in a spreadsheet.  The calibration or Absolute data were recorded manually using a Declination-Inclination magnetometer.  The data were entered into a spreadsheet to compute the Absolute and baseline values.

Tags: magnetic-field-earth, usgs-5dbb5ef7e4b06957974eda12
Organization: Department of the Interior
DisOcean: Distance to the ocean: Monomoy Island, MA, 2014

Understanding how sea-level rise will affect coastal landforms and the species and habitats they support is critical for crafting approaches that balance the needs of humans and native species. Given this increasing need to forecast sea-level rise effects on barrier islands in the near and long terms, we are developing Bayesian networks to evaluate and to forecast the cascading effects of sea-level rise on shoreline change, barrier island state, and piping plover habitat availability. We use publicly available data products, such as lidar, orthophotography, and geomorphic feature sets derived from those, to extract metrics of barrier island characteristics at consistent sampling distances. The metrics are then incorporated into predictive models and the training data used to parameterize those models. This data release contains the extracted metrics of barrier island geomorphology and spatial data layers of habitat characteristics that are input to Bayesian networks for piping plover habitat availability and barrier island geomorphology. These datasets and models are being developed for sites along the northeastern coast of the United States. This work is one component of a larger research and management program that seeks to understand and sustain the ecological value, ecosystem services, and habitat suitability of beaches in the face of storm impacts, climate change, and sea-level rise.

Tags: atlantic-ocean, barrier-island, cape-cod, cmhrp, coastal-and-marine-hazards-and-resources-program, coastal-habitat, environment, geographic-information-systems, geomorphology, geospatial-analysis, geospatial-datasets, gis, ma, massachusetts, mean-high-water, mhw, monomoy-island, monomoy-national-wildlife-refuge, north-america, oceans, st-petersburg-coastal-and-marine-science-center, u-s-geological-survey, united-states, usa, usgs, usgs-5daa372de4b09fd3b0c9ce2c, woods-hole-coastal-and-marine-science-center
Organization: Department of the Interior
Data for generating statistical maps of soil cobalt concentrations in the conterminous United States

The product data are six statistics that were estimated for the chemical concentration of cobalt in the soil C horizon of the conterminous United States (Smith and others, 2013). The estimates are made at 9998 locations that are uniformly distributed across the conterminous United States. The six statistics are the mean for the isometric log-ratio transform of the concentrations, the equivalent mean for the concentrations, the standard deviation for the isometric log-ratio transform of the concentrations, the probability of exceeding a concentration of 24.4 milligrams per kilogram, the 0.95 quantile for the isometric log-ratio transform of the concentrations, and the equivalent 0.95 quantile for the concentrations. Each statistic may be used to generate a statistical map that shows an attribute of the distribution of cobalt concentration.

Tags: cobalt, geochemistry, geology-geophysics-and-geochemistry-science-center, gggsc, kriging, mineral-resource-program, mrp, soil-chemistry, u-s-geological-survey, usgs, usgs-5dbb5d1de4b06957974eda06
Organization: Department of the Interior
Suspended-sediment concentration data from water samples collected in 2016-17 in Grand Bay, Alabama and Mississippi

Suspended-sediment transport is a critical element governing the geomorphology of tidal marshes and estuaries. Marsh elevation, relative to sea level, is maintained by both organic material and the deposition of inorganic sediment. Additionally, horizontal marsh extent is altered by lateral erosion and accretion. In wetlands within and near Grand Bay National Estuarine Research Reserve, parts of the salt marsh are eroding relatively rapidly. To understand the connection between sediment fluxes and these processes, the U.S. Geological Survey made oceanographic and water-quality measurements from August 2, 2016, to January 28, 2017, to quantify suspended-sediment concentration and sediment transport in tidal channels and open embayments in and near Grand Bay National Estuarine Research Reserve.

Tags: bayou-heron, bayou-middle, grand-bay, grand-bay-national-estuarine-research-reserve, grand-bay-national-wildlife-refuge, inlandwaters, kreole, middle-bayou, mississippi, oceans, sediment-transport, suspended-material-water, usgs-5dbb3772e4b06957974ec455
Organization: Department of the Interior
Aerial photographs from the Yampa and Little Snake Rivers in northwest Colorado used to characterize channel changes occurring between 1954 and 1961

Aerial photographs of the Yampa and Little Snake Rivers acquired in 1954 and 1961 were used to examine channel changes occurring along these two rivers during this time period.  In addition, these data were used to develop and test a generalizable new approach to characterizing the uncertainty associated with analyses of channel change based on time series of remotely sensed data, which we term the Spatially Distributed Probabilistic (SDP) method.  This technique accounts for errors introduced during: 1) image co-registration and geo-referencing; 2) interpreting the location of the channel boundary; and 3) digitizing the channel boundary.  The method provides a probability distribution of channel locations and can be used to calculate error bounds associated with polygons of erosion and deposition and thus net sediment flux.  The Yampa and Little Snake Rivers were used as a case study to illustrate an application of the new SDP method and this data release provided all of the data needed to perform an SDP analysis for this example.  The data sets available here include: 1) air photo mosaics from 1954, 1961, and 2017, with the most recent coverage used as a base for geo-referencing the older photos; 2) test points used to quantify spatially varying co-registration error; and 3) active channel polygons digitized from the 1954 and 1961 air photos and used to create polygons of erosion and deposition.  Software for implementing the SDP method and an example script that illustrates how to perform this type of analysis using data from the Yampa and Little Snake Rivers as a case study is available from the Center for Colorado River Studies at Utah State University.

Tags: aerial-photographs, channel-change, colorado-co, deerlodge, geo-referencing, little-snake-river, remote-sensing, river, uncertainty, usgs-5dbb2aa9e4b06957974ec011, yampa-river
Organization: Department of the Interior
Dissolved Pesticides in Weekly Water Samples from the NAWQA California Stream Quality Assessment (2017)

Dissolved pesticides were measured in weekly water samples from 85 wadeable streams in Central Coastal California over a variable six-week period during March–May, 2017, as part of the California Stream Quality Assessment (CSQA) study conducted by the U.S. Geological Survey's (USGS) Regional Stream-Quality Assessment (RSQA) Project. The 85 streams consisted of 40 urban sites (5–100% urban land in the lower basin), 9 agricultural sites, 24 mixed land-use sites, and 12 undeveloped sites. Water samples were filtered (0.7 micrometers) and analyzed for 253 pesticide compounds by direct-injection liquid chromatography with tandem mass-spectrometry (LC-MS/MS). Two similar LC-MS/MS methods were used: a broad-spectrum (223 compounds) method in use since 2012 and a newly developed method for 30 new-generation fungicides and diamide and neonicotinoid insecticides. This Data Release provides sampling-site locations, analyte information, concentration data for pesticide compounds in environmental weekly water samples, quality-control data for the new method (to supplement previously published quality control data for the standard method), aquatic-life benchmark and Pesticide Toxicity Index toxicity concentration values that were used to assess potential toxicity, estimates of agricultural and nonagricultural pesticide-use data, and streamflow data for gaged sites, in support of the journal article, “New-generation pesticides are prevalent in California’s Central Coast streams,” by Sandstrom, M.W., Nowell, L.H., Mahler, B.J., and Van Metre, P.C.

Tags: 2017, april, california, central-california-foothills-ecoregion, central-coastal-california, coastal-mountains-ecoregion, diamide, fungicide, herbicide, insecticide, march, may, mixtures, national-water-quality-assessment, nawqa, neonicotinoid, pesticide, pesticide-degradate, spring, stream, surface-water, united-states, usgs-5dbb187ae4b06957974ebfb0, water-quality
Organization: Department of the Interior
Locations of mines and mining activity in the contiguous United States 2013

This dataset includes locations and associated information about mines and mining activity in the contiguous United States.  The database was developed by combining publicly available national datasets of mineral mines, uranium mines, and minor and major coal mine activities.  This database was developed in 2013, but temporal range of mine data varied dependent on source. Uranium mine information came from the TENORM Uranium Location Database produced by the US Environmental Protection Agency (U.S. EPA) in 2003.  Major and minor coal mine information was from the USTRAT (Stratigraphic data related to coal) database 2012, and the mineral mine data came from the USGS Mineral Resource Program.

Tags: coal, mine-sites, mineral-deposits, mineral-resources, uranium, usgs-5dbb12fbe4b06957974ebf9f
Organization: Department of the Interior
Ground Penetrating Radar data from West Fork of Dall Creek, AK 2019

Five ground penetrating radar (GPR) profiles were collected on 4/4/2019 at the West Fork of Dall Creek in interior Alaska. The West Fork of Dall Creek contains a burn scar (2004 Dall City fire) surrounded by unburned black spruce forest. Collected profiles except for the central midpoint survey (CMP) cross the burn scar with the beginning and end of each transect ending in the unburned black spruce forest. Data were collected with a Sensors and Software pulseEKKO pro unit and 100 mHz antennas. Four of the lines were conducted as common offset surveys with manual data collection that employed a consistent antenna separation of 1m and data traces being collected every 25cm along the transect. A central midpoint survey (CMP) was collected along Line3 (a common offset line) where antennas started at a 1m separation and antennas were moved out 10cm at a time for each subsequent trace increasing the antenna separation.

Tags: geophysics, permafrost, usgs-5dbb0dc5e4b06957974ebf83
Organization: Department of the Interior
Soil Temperature Data from West Fork of Dall Creek,  AK 2019

The West Fork of Dall Creek contains a burn scar surrounded by unburned black spruce forest. Soil temperature sensors were installed in the unburned black spruce forest adjacent to the burn scar on 5/10/2017 and removed on 6/26/2018. Data were collected from depths of 10, 30, 50, and 70 cm.

Tags: permafrost, soil-temperature, usgs-5dbb0d52e4b06957974ebf7e
Organization: Department of the Interior
Nuclear Magnetic Resonance Data from West Fork of Dall Creek,  AK 2019

The West for of Dall Creek contains a burn scar (Dall City Fire 2004) surrounded by unburned black spruce forest. Nuclear magnetic resonance (NMR) data were acquired with a Dart down-borehole tool (Vista Clara, Inc., Mukilteo, Washington) form both within the burn scar from the unburned black spruce forest. Boreholes were augered to various depths throughout the study, and PVC was permanently installed in boreholes WFD1, WFD2, WFD3, and WFD4 in June of 2018. The Dart measures a thin (i.e. ~1–2 mm) cylindrical shell of soil ~ 15 cm from the center of the tool and extending vertically ~23 cm from the tool center. Dart data were logged upwards from the bottom of the borehole in 12.5- cm intervals. Resulting T2 decay time-series were analyzed using proprietary software (Vista Clara, Inc.). Data products include volumetric water content for periods of maximum freeze and thaw from 2018-2019.

Tags: geophysics, hydrology, nuclear-magnetic-resonance, permafrost, talik, usgs-5dbb0972e4b06957974ebf65
Organization: Department of the Interior