AndreaBozzo/ceres-open-data-index huggingface dataset:
Host vs. Pathogen Evolutionary Arms Race: Effects of Exposure History on Individual Response to a Genetically Diverse Pathogen

This data set contains individual adult bighorn sheep entry and exit/censor times for 3 disease states and 2 mortality states: susceptible, infected and recovered and disease-caused death and non-disease related death. These times are used in a time-to-event analysis that employs a mixture model approach to characterize transition rates between states.

Tags: bighorn-sheep, disease-state, environmental-dna, farming, hazards, immune-response, mycoplasma-ovipneumoniae, strain, transmission, usgs-611fde08d34e40dd9c01df2d
Organization: Department of the Interior
Fish movement and colonization in the Wyoming Range 2018-2019

Fish colonization ability may be one factor affecting population resilience after disturbance. We conducted displacement experiments in headwater streams in Wyoming, U.S.A. to evaluate mottled sculpin (Cottus bairdii) and mountain sucker (Catostomus platyrhynchus) colonization ability. Specifically, we (1) determined if fish could colonize sites rapidly after displacement, (2) evaluated site-level factors affecting colonization, and (3) compared species-level differences in movement and colonization capabilities. For the colonization experiment, we removed fish from 31 experimental 100 m reaches to create an experimental displacement and examined short-term colonization dynamics in relation to initial fish abundance and habitat characteristics in 2018 and 2019. We selected four additional sites during 2018 to conduct a movement study and compare species mobility in the absence of experimental displacement. We calculated movement distances for all fish relocations, which included short-distance movements within short (200-meter) PIT tag resurveys and recaptures from long-distance surveys at the four movement sites, as well as six incidental recaptures during fish monitoring efforts across the entire study system.

Tags: biota, colonization, fish, movement, streams, usgs-61200bf9d34e40dd9c01ffaf, wyoming
Organization: Department of the Interior
Land Cover Assignments of 300 locations in the Pacific Northwest in 2000

Area estimates of land cover and land cover change are often based on reference class labels determined by analysts interpreting satellite imagery and aerial photography. Different interpreters may assign different reference class labels to the same sample unit.  This dataset includes land cover attributes for the year 2000 assigned by 7 image analysts, working independently of each other, to a set of 300 sample locations from a region of the Pacific Northwest of the United States.  This data was used in an evaluation of the impact of interpreter variability on variance estimation.

Tags: environment, image-analysis, interpretation, land-use-and-land-cover, usgs-6123965bd34e40dd9c0338f5
Organization: Department of the Interior
Mercury and water level fluctuations in lakes of northern Minnesota - Summary of Sampling Sites Land Cover and Slope Characteristics

Water level fluctuations substantially alter the fauna, flora and microbial community of near-shore aquatic ecosystems. Water level management therefore has the potential to strongly influence a wide variety of ecosystem processes. Many northern temperate lake food webs experience substantial methylmercury contamination, which is partially mediated by the action of sulfate reducing bacteria occurring in sediments that are periodically inundated. For lakes with methylmercury problems, water level management could be designed to reduce methylmercury contamination. These data summarize land cover and slope characteristics within specified, buffered areas around study sites that were sampled in several northern Minnesota lakes, as part of the project described above. The land cover attributes include percent cover (within each buffered area) and number of hectares of each land cover class. The slope attributes include the overall net change in slope within each buffered area, as well as the standard deviation.

Tags: crane-lake, environment, kabetogama-lake, land-use-and-land-cover, little-vermilion-lake, minnesota, namakan-lake, rainy-lake, sand-point-lake, slope, usgs-6123c602d34e40dd9c0350f5, voyageurs-national-park
Organization: Department of the Interior
Hydrogeologic Framework of the Big Lost River Basin, South-Central Idaho: Hydrogeologic Framework Model

Groundwater in the Big Lost River Basin is vital to irrigated agriculture in the basin and water users are concerned about declining groundwater levels. The U.S. Geological Survey, in cooperation with the Idaho Department of Water Resources, developed a hydrogeologic framework to provide a conceptual understanding of groundwater resources in the Big Lost River Basin. A three-dimensional hydrogeologic framework model of the Big Lost River Basin was generated to represent the subsurface distribution and thickness of four hydrogeologic units. This dataset represents the hydrogeologic framework model in an ASCII text file containing coordinate, altitude and hydrogeologic unit data. This hydrogeologic framework model file and the accompanying well database comprise the complete hydrogeologic framework data release.

Tags: arco, big-lost-river, big-lost-river-valley, butte-county, custer-county, geology, groundwater, hydrogeology, id, idaho, inlandwaters, mackay, mathematical-modeling, snake-river-plain, usa, usgs-6123d4dad34e40dd9c036e2f, water-resource-management
Organization: Department of the Interior
Hydrogeologic Framework of the Big Lost River Basin, South-Central Idaho: Well Data

Groundwater in the Big Lost River Basin is vital to irrigated agriculture in the basin and water users are concerned about declining groundwater levels. The U.S. Geological Survey, in cooperation with the Idaho Department of Water Resources, developed a hydrogeologic framework to provide a conceptual understanding of groundwater resources in the Big Lost River Basin. A three-dimensional hydrogeologic framework model of the Big Lost River Basin was generated to represent the subsurface distribution and thickness of four hydrogeologic units. The primary source of data for the hydrogeologic framework model was lithologic data from a well database (621 wells) compiled for this purpose. The well database was built from well-driller reports (584 wells) in Idaho Department of Water Resources files, groundwater level monitoring wells (20) in U.S. Geological Survey and Idaho Department of Water Resources files, and synthetic wells (17) defined in this study. This dataset represents the well database, distributed as three comma-delineated CSV files containing the following well information:  well location, lithology, and well construction. This well database and the accompanying hydrogeologic framework model file comprise the complete hydrogeologic framework data release.

Tags: arco, big-lost-river, big-lost-river-valley, butte-county, custer-county, geology, groundwater, groundwater-flow, hydrogeology, hydrology, id, idaho, inlandwaters, mackay, snake-river-plain, usa, usgs-6123d50fd34e40dd9c036e4a, water-resource-management
Organization: Department of the Interior
Water-Quality and Depth to Water for Groundwater Wells Primarily Completed in the Ogallala Aquifer within the North Plains Groundwater Conservation District, Texas Panhandle, 2012–13 and 2019–20

The Ogallala aquifer is contained in the Tertiary-age Ogallala Formation in the Texas Panhandle and is the primary water-bearing hydrogeologic unit of the High Plains aquifer system. The Ogallala aquifer is the primary source of water used for agricultural and municipal purposes in the Texas Panhandle. The Dockum aquifer is contained in the formations that compose the Triassic-age Dockum Group and serves as an additional source of water in the Texas Panhandle. Depth to groundwater measurements and water-quality samples were collected from 32 monitoring wells in the North Plains Groundwater Conservation District management area within the northern part of the Texas Panhandle as part of two synoptic sampling efforts, one during 2012–13 and the other during 2019–20. Groundwater-quality samples were collected for analysis of dissolved solids, major ions, nutrients, and trace elements. Selected organic compounds were analyzed in samples collected from a subset of 6 wells. Sample results for selected constituents were compared to drinking-water standards and between the two synoptic sampling times in an interpretative report. A previously published report by Baldys and others (2014) discusses the results from the 2012–13 sampling event.

Tags: 20122013, 20192020, dalhart-county, dallam-county, dissolved-solids, dockum-aquifer, dockum-group, dumas-county, follett-county, groundwater, groundwater-levels, hansford-county, hartley-county, high-plains-aquifer, hutchinson-county, lipscomb-county, major-ions, moore-county, north-plains-conservation-district, nutrients, ochiltree-county, ogallala-aquifer, ogallala-formation, organic-compounds, pesticides, sherman-county, stratford-county, texas-panhandle, trace-elements, usgs-6123feded34e40dd9c037285, water-chemistry, water-properties, water-quality, water-resources
Organization: Department of the Interior
Nakula, Maui environmental controls on plant growth and seedling recruitment in a cloud-affected restoration site, 2016-2019

Fog has been demonstrated to support plant growth, survival and ecosystem maintenance spanning rainfall and elevation gradients across the world. Persistent fog and strong winds on high mountain slopes in Hawaiʻi create a unique ecological environment.
We collected stem diameter measurements of three native plant species at Nakula Natural Area Reserve, Maui, during 2016-2019 and numerous environmental variables to examine how rain, fog and soil moisture influence plant water deficit and growth. We also collected seedling growth and survival data within plots where grass was removed, and control plots (no grass removal), to assess if and how grass removal influenced seedling growth and soil moisture.

Tags: cloud-water-interception, dendrometer, fog, maui, maui-county, nakula-natural-area-reserve, non-native-grass, seedling-recruitment, seedling-survival, soil-moisture, usgs-612455b7d34e40dd9c03ca5f
Organization: Department of the Interior
Pb-Pb and U-Pb data of Proterozoic to Phanerozoic cassiterite deposits in Russia

Cassiterite (SnO2), a main ore mineral in tin deposits, was collected by multiple Russian geologists or obtained from museum collections in both the USA and Russia and dated at the U.S. Geological Survey. The dated samples represent four different mining districts spanning the entire country from the village of Pitkäranta in the west (31° E Longitude) to the Merekskoe Deposit in the Russian Far East (134°E Longitude). The samples were recovered from a variety of host deposit types that range from the Proterozoic to Phanerozoic. Cassiterite (in the form of mounted loose grains) was prepared and analyzed for direct age dating on a laser ablation inductively coupled plasma mass spectrometer (LA-ICP-MS) system at the USGS in Denver, Colorado from February 2017 to October 2019.  This data supports the following associated publication:  Neymark, L.A., Larin, A.M., and Moscati, R.J., 2021, Pb-Pb and U-Pb dating of cassiterite by in situ LA-ICPMS: Examples spanning ~1.85 Ga to ~100 Ma deposits in Russia and implications for dating Proterozoic to Phanerozoic tin deposits, Minerals.

Tags: cassiterite, geochronology, geology-geophysics-and-geochemistry-science-center, geoscientificinformation, gggsc, la-icp-ms, laser-ablation-inductively-coupled-plasma-mass-spectrometer, lead, mineral-deposits, mineral-resources-program, mrp, pitkaranta, russia, siberia, thorium, u-pb, u-s-geological-survey, uranium, uranium-lead-analysis, usgs, usgs-612533d8d34e40dd9c03f29c
Organization: Department of the Interior
Reference genome for Phragmites australis (Poaceae, subfamily Arundinoideae) and comparison of North American invasive genotype (ssp. australis) and native (ssp. americanus)

These data represent the first reference genome for the invasive Phragmites australis ssp. australis (1.14 giga base pairs (Gbp)), as well as output from comparative genomic and transcriptomic analyses for invasive and native genotypes coexisting in the Great Lakes region of North America. Genome sequencing data used tillers and associated rhizome tissues collected from a single P. australis patch at the Ottawa National Wildlife Refuge near Toledo, Ohio, USA. Transcriptome analyses were produced from samples collected from three invasive and three native genotype P. australis patches from four sites around the Great Lakes in Michigan and Ohio, USA.

Tags: biota, dna-sequencing, environment, fungal-inoculation, gene-expression, great-lakes, invasive-species, michigan, north-america, phragmites-australis, reference-genome, upper-ohio, usgs-61253eefd34e40dd9c03f2f5, whole-genome-duplication
Organization: Department of the Interior
Aircraft-Borne Thermal Imagery and Derived Terrain Analysis Layers, Pisgah Lava Field, California

This dataset is one of many used in the development of the manuscript 'Advancing Cave Detection using Terrain Analysis Techniques and Thermal Imagery' by Wynne et al. 2021.
Manuscript Abstract:  Since the initial experiments nearly 50 years ago, techniques for detecting caves using airborne and spacecraft acquired thermal imagery have improved markedly. These advances are largely due to a combination of higher instrument sensitivity, modern computing systems, and processor-intensive analytical techniques. Through applying these advancements, our goals were to: (1) determine the utility of methods designed for terrain analysis and applied to thermal imagery; (2) analyze the usefulness of predawn and midday imagery for detecting caves; and, (3) determine which imagery type (predawn, midday, or the difference between the two) was most useful. Using forward stepwise logistic (FSL) and Least Absolute Shrinkage and Selection Operator (LASSO) regression analysis for model selection, and a thermal imagery dataset acquired from the Mojave Desert, California, we examined the efficacy of three well-known terrain descriptors (i.e., slope, topographic position index [TPI], and curvature) on thermal imagery for cave detection. We also included the actual, untransformed thermal DN values (hereafter “unenhanced thermal”) as a fourth dataset. We then compared the thermal signatures of known cave entrances to all non-cave surface locations. We determined these terrain-based analytical methods, which described the “shape” of the thermal landscape, hold significant promise for cave detection. All imagery types produced similar results. Down-selected covariates per imagery type, based upon the FSL models, were: predawn - Slope, TPI, Curvature at 0 m from cave entrance, as well as Slope at 1 m from cave entrance; midday - Slope, TPI, and unenhanced thermal at 0 m from cave entrance; and, difference - TPI and Slope at 0 m from cave entrance, as well as unenhanced thermal and TPI at 3.5 m from cave entrance. We provide recommendations for future research directions in terrestrial and planetary cave detection using thermal imagery.

Tags: curvature, lasso, mojave-desert, nau, northern-arizona-university, pisgah-lava-field, planetary-caves, qwip-thermal-instrument, regression-analysis, slope, terrestrial-caves, topographic-position-index, tpi, usgs-612567b2d34e40dd9c03f3e9
Organization: Department of the Interior
Population genetic data for two species of tiger beetles, Habroscelimorpha dorsalis dorsalis and H. d. media.

This dataset includes microsatellite genotypes for 44 collections of Habroscelimorpha dorsalis dorsalis and 14 collections of H. d. media distributed from Massachusetts to Florida, United States.

Tags: biota, florida, genetic-diversity, massachusetts, tiger-beetle, usgs-6127833fd34e40dd9c0508bc
Organization: Department of the Interior
Enhanced Terrain Imagery of the Neversink River Watershed from Lidar-Derived Elevation Models at 1-Meter Resolution

This imagery dataset consists of 1-meter resolution, lidar-derived imagery of the Neversink Basin area in New York and covers part of the Delaware River Basin. The footprint of this dataset covers USGS Hydrologic Unit Code (HUC) areas HUC 12-020401040301, HUC 12-020401040302, and part of HUC 12-020401040303.
The source data used to construct this imagery consists of 1-meter and 2-meter resolution Lidar-derived digital elevation models (DEMs). The lidar source data were compiled from different acquisitions published between 2009 and 2015 from New York state.  The data were processed using geographic information systems (GIS) software. The data is projected in North America Datum (NAD) UTM Zone 18 North. This representation illustrates the terrain as a hillshade with contrast adjusted to highlight local relief according to a topographic position index (TPI) calculation.

Tags: delaware-river-basin, elevation, imagerybasemapsearthcover, lidar, neversink-basin, new-york, topography, usgs-612791aad34e40dd9c0508cc, watershed
Organization: Department of the Interior
Enhanced Terrain Imagery of the White Clay Creek Watershed from Lidar-Derived Elevation Models at 1-Meter Resolution

This imagery dataset consists of 1-meter resolution, lidar-derived imagery of the White Creek Clay watershed in Pennsylvania and Delaware, which includes part of the Delaware River Basin. The footprint of this dataset covers USGS Hydrologic Unit Code (HUC) areas HUC 12-020402050301, HUC 12-02040205030102, HUC 12-02040205030103, HUC 12-02040205030106, and part of HUC 12-02040205030108.
The source data used to construct this imagery consist of 1-meter Lidar-derived digital elevation models (DEM). The Lidar source data were compiled from different USGS acquisitions published between 2013 and 2015.  The data were processed using geographic information systems (GIS) software. The data are projected in North America Datum (NAD) UTM Zone 18 North. This representation illustrates the terrain as a hillshade with contrast adjusted to highlight local relief according to a topographic position index (TPI) calculation.

Tags: delaware, delaware-river-basin, elevation, imagerybasemapsearthcover, lidar, pennsylvania, topography, usgs-612794add34e40dd9c0508dd, watershed, white-clay-creek
Organization: Department of the Interior
Exogenous and endogenous factors influence invasive reptile movement at multiple scales, 2018 - 2019

These data reflect movement values for brown treesnakes from Guam that were translocated (moved by humans) to new locations or were resident (left in place) on Guam. The data are related to the specimen's treatment group, individual values, locations and other details affiliated with radio telemetry based acquisition and positional changes by the individual snakes across tracking events. The data were collected to help inform early detection and rapid response efforts for brown treesnakes in the Mariana Islands.

Tags: brown-treesnake, early-detection-and-rapid-response, environment, guam, mariana-islands, movement, usgs-6127aa40d34e40dd9c05090d
Organization: Department of the Interior
Earthquake geology inputs for the U.S. National Seismic Hazard Model (NSHM) 2023 (western US)(ver. 2.0, February 2022)

This Data Release contains preliminary versions of two related databases: 1) A fault sections database (“NSHM23_FSD_v2”), which depicts the geometry of faults capable of hosting independent earthquakes, and 2) An earthquake geology site information database (“NSHM23_EQGeoDB_v2”), which contains fault slip-rate constraints at points. These databases were prepared in anticipation of updates to the National Seismic Hazard Model (NSHM) 2023. Fault-specific geologic parameters for the NSHM have not been updated since the 2014 NSHM release. The datasets include the states of Washington, Oregon, California, Idaho, Nevada, Arizona, Montana, Wyoming, Colorado, New Mexico and Texas. Datasets containing fault information for Alaska and the Central and Eastern United States will be the subject of future efforts. These databases are provided as geospatial data (e.g., .SHP and .GeoJSON file formats) and tables (.CSV or .TXT format). Please note: these databases are updated as of February 2022 (version 2), which supersede the databases release in January 2021 (version 1).

Tags: arizona, california, colorado, earthquake, fault, idaho, montana, nevada, new-mexico, oregon, slip-rate, usgs-6127b5d4d34e40dd9c050975, utah, washington, western-united-states, wyoming
Organization: Department of the Interior
Carcass weights, 28S rRNA alignment file and parasite sample vouchers collected from  California tiger salamanders (Ambystoma californiense) CTS and Santa Cruz long-toed salamander (Ambystoma macrodactylum croceum) SCLT from Prospect or Ellicott Pond, on Ellicott Slough National Wildlife Refuge, California U.S.A. recorded September 11, 2019

Animal identification number, weight in grams for carcasses of California tiger salamanders (Ambystoma californiense) CTS and Santa Cruz long-toed salamander (Ambystoma macrodactylum croceum) SCLT from Prospect or Ellicott Pond, on Ellicott Slough National Wildlife Refuge, California U.S.A. submitted to U.S. Geological Survey, National Wildlife Health Center (NWHC) for determination of cause of death. NWHC Case 29381.
MSF Sequence file used to construct a phylogenetic tree. Sequences were generated from samples at NWHC (Px) and using BLAST (https://blast.ncbi.nlm.nih.gov/Blast.cgi) they were compared for base pair similarities with publicly available sequences from GenBank. Sequences selected for the Multi Sequence Fast File (MSF) was based on the number of base pair similarities AND stage of parasite from which the sequence was generated.  An excel file listing all parasites and hosts vouchered with the University of New Mexico, Museum of Southwestern Biology, Division of Parasitology.

Tags: biota, california-tiger-salamanders, ellicott-slough-national-wildlife-refuge, parasites, ribeiroia-ondatrae, santa-cruz-long-toed-salamander, u-s-geological-survey-national-wildlife-health-center-madison-wisconsin, usgs-6127e203d34e40dd9c050adf
Organization: Department of the Interior
Earthquake geology inputs for the National Seismic Hazard Model (NSHM) 2023, version 1.0

This Data Release contains preliminary versions of two related databases: 1) A fault sections database (“NSHM2023_FaultSections_v1”), which depicts the geometry of faults capable of hosting independent earthquakes, and 2) An earthquake geology site information database (“NSHM2023_EQGeoDB_v1”), which contains fault slip-rate constraints at points.  These databases were prepared in anticipation of updates to the National Seismic Hazard Model (NSHM) 2023. Fault-specific geologic parameters for the NSHM have not been updated since the 2014 NSHM release. The datasets include the states of Washington, Oregon, California, Idaho, Nevada, Arizona, Montana, Wyoming, Colorado, New Mexico and Texas.  Datasets containing fault information for Alaska and the Central and Eastern United States will be the subject of future efforts. These databases are provided as geospatial data (e.g., .SHP, .KML, .GeoJSON file formats) and tables (.CSV format).

Tags: arizona, california, colorado, hazards, idaho, montana, new-mexico, oregon, usgs-612800fad34e40dd9c0537e5, utah, washington, wyoming
Organization: Department of the Interior