AndreaBozzo/ceres-open-data-index huggingface dataset:
Transcriptomic Responses to Hexabromocyclododecane in Japanese Quail

This study examined effects of the brominated flame retardant hexabromocyclododecane (HBCD) on the avian endocrine system. Japanese quail (Coturnix japonica) were exposed to multiple doses of HBCD over multiple generations through feed and by maternal deposition into the egg. Liver transcriptomes were examined to identify genes and pathways directly affected by HBCD to better understand the mechanisms of action in birds. RNA was extracted from liver of adults and embryos and analyzed (1x50 bp) on an Illumina HiSeq 2000. NCBI Biosample accessions and the raw counts that were input into the differential expression analysis are provided in this dataset. The raw sequence data are available at the NCBI Sequence Read Archive under Bioproject number PRJNA313931.

Tags: biota, flame-retardants, transcriptomics, usgs-6658c353d34ef3137d35fa86
Organization: Department of the Interior
Airborne magnetic and radiometric survey, Medicine Bow Mountains, Wyoming, 2023

This data release provides digital flight line data for a high-resolution airborne magnetic and radiometric survey over the Medicine Bow Mountains in southern Wyoming. The airborne survey was jointly funded by the Earth Mapping Resources Initiative and the Wyoming State Geological Survey (WSGS). The survey was designed to meet complementary needs related to geologic mapping and characterization of mineral resource potential. A total of 16,400 line km of magnetic and radiometric data were acquired over an irregular-shaped area of 2710 km2. Data were collected from a helicopter flown at a nominal terrain clearance of 80 meters (m) above topography along N-S flight lines spaced at 200 m intervals. The line spacing was tightened to 100 m over the Lake Owen complex, a layered mafic intrusion within the survey area. Tie lines were flown in an E-W direction every 2000 m, and 1000 m over the Lake Owen complex. Data were collected by EON Geosciences Inc. and Woolpert Inc. under contract to the USGS using a helicopter with a magnetometer mounted in a stinger and a fully calibrated gamma-ray spectrometer. The survey operated out of the Laramie, Wyoming, airport from August of 2023 to September of 2023. Files that are available in this publication include flight line data for the magnetic survey, flight line data for the radiometric survey and a report describing the survey parameters, field operations, quality control and data reduction procedures. A zip file is provided that contains the contractor's deliverable products that includes Geosoft databases and grids for the magnetic and radiometric survey and the report describing the survey and data reduction.

Tags: aasg, aeromagnetic-survey, aeroradiometric-survey, airborne-geophysical-survey, association-of-state-geologists, bear-mountain, beaver-creek-hills, biota, blackhall-mountain, centennial-valley, earth-mapping-resources-initiative, earthmri, economic-geology, geology-geophysics-and-geochemistry-science-center, geophysics, geospatial-datasets, gggsc, lake-mountain, lake-owen, lookout-mountain, magnetic-field-earth, medicine-bow-mountains, medicine-bow-national-forest, medicine-bow-river, mineral-resources, mineral-resources-program, mrp, national-cooperative-geologic-mapping-program, north-platte-river, potassium, rock-mountain, sedimentology, sheep-mountain, snowy-range, spruce-mountain, structural-geology, thorium, u-s-geological-survey, united-states, united-states-of-america, uranium, usa, usgs, usgs-6658b79fd34ef3137d35f9fc, wood-mountain, wyoming
Organization: Department of the Interior
Study Reach 5 Terrestrial Light Detection and Ranging Topographic Data in Caulks Creek, Wildwood, Missouri, 2022–2023

Topographic data were collected along study reach 5 in Caulks Creek in Wildwood, Missouri, on multiple dates, using terrestrial light detection and ranging (t-lidar), Global Navigation Satellite System (GNSS), and conventional surveying techniques (Rydlund and Densmore, 2012).
These data are high-resolution topography in laser scan format, collected using a tripod mounted t-lidar at multiple scan setups.  Data collection software integrated and stored the range and angular measurements from the t-lidar equipment.  Computer software was used to process the raw data, align the various scans in reference to one another, classify the data, and extract the topography data in a useable format. 
The topographic data are provided in two subsections (A and B) for each of the four survey dates (February 2022, July 2022, March 2023, and July 2023). The surface point clouds represent the channel, bank, and near overbank surface of the study area and were saved with RGB (red-green-blue) color in LAS format.

Tags: ascii, caulks-creek, elevation, geology, inland-waters, inlandwaters, location, missouri, state-plane, terrestrial-lidar, u-s-geological-survey, usgs, usgs-665897e7d34ef3137d35f8b4, wildwood
Organization: Department of the Interior
Study Reach 4 Terrestrial Light Detection and Ranging Topographic Data in Caulks Creek, Wildwood, Missouri, 2022–2023

Topographic data were collected along study reach 4 in Caulks Creek in Wildwood, Missouri, on multiple dates, using terrestrial light detection and ranging (t-lidar), Global Navigation Satellite System (GNSS), and conventional surveying techniques (Rydlund and Densmore, 2012).
These data are high-resolution topography in laser scan format, collected using a tripod mounted t-lidar at multiple scan setups.  Data collection software integrated and stored the range and angular measurements from the t-lidar equipment.  Computer software was used to process the raw data, align the various scans in reference to one another, classify the data, and extract the topography data in a useable format. 
The topographic data are provided in for the entire reach for each of the four survey dates (March 2022, July 2022, March 2023, and July 2023). The data represent the channel, bank, and near overbank surface and were saved with RGB (red-green-blue) color in LAS format.

Tags: ascii, caulks-creek, elevation, geology, inland-waters, inlandwaters, location, missouri, state-plane, terrestrial-lidar, u-s-geological-survey, usgs, usgs-66588cb3d34ef3137d35f82d, wildwood
Organization: Department of the Interior
Results of elemental analyses of desert tortoise (Gopherus agassizii) burrow spoil and undisturbed surficial soils in California, 2023.

Bighorn sheep (Ovis canadensis) were frequently photographed by wildlife cameras when they visited desert tortoise (Gopherus agassizii) burrows in the eastern San Bernardino Mountains near Palm Springs, California, USA (Mesa Windfarm). A previous study suggested that sheep may have been utilizing the excavated spoil material from burrows as a mineral lick. We aimed to test this possibility by collecting soil samples from the tortoise burrow spoil piles and undisturbed surface soil less than a meter away at two different desert tortoise study sites with bighorn sheep, the second site (Deep Canyon) in the Santa Rosa Mountains near Palm Desert, California. Both study sites are located in the Sonoran Desert ecosystem of Riverside County, CA.  Concentrations of major cations (sodium, magnesium, aluminum, potassium, calcium, iron, and strontium) and other elements (beryllium, vanadium, chromium, manganese, cobalt, nickel, copper, zinc, arsenic, selenium, molybdenum, silver, cadmium, tin, antimony, barium, thallium, lead, bismuth, thorium, uranium) were quantified in the soil samples using inductively coupled plasma-mass spectrometry following microwave-assisted digestion to solubilize the fraction of elements that could become biologically or environmentally available to bighorn sheep following geophagy.

Tags: bighorn-sheep, biota, burrow-spoil-soil, california, chemical-analysis, chemical-elements, desert-tortoise, elements, environment, geophagy, metal-elements, mineral-lick, mineral-resources, riverside-county-ca, soil, soil-chemistry, sonoran-desert-ecosystem, surficial-soil, usgs-66588c82d34ef3137d35f824
Organization: Department of the Interior
Study Reach 3 Terrestrial Light Detection and Ranging and Total Station Survey Topographic Data in Caulks Creek, Wildwood, Missouri, 2022–2023

Topographic data were collected along study reach 3 in Caulks Creek in Wildwood, Missouri, on multiple dates, using terrestrial light detection and ranging (t-lidar), Global Navigation Satellite System (GNSS), and conventional surveying techniques (Rydlund and Densmore, 2012).
The data from the first two surveys are high-resolution topography in laser scan format, collected using a tripod mounted t-lidar at multiple scan setups.  Data collection software integrated and stored the range and angular measurements from the t-lidar equipment.  Computer software was used to process the raw data, align the various scans in reference to one another, classify the data, and extract the topography data in a useable format. The data from the second two surveys are stored in a comma-separated value (csv) format, collected using a tripod mounted Trimble M3 Total Station. The data represent the channel, bank, and near overbank surface and were saved with RGB (red-green-blue) color in LAS format. 
The topographic data are provided for the entire study reach for the first two survey dates (February 2022 and July 2022) with RGB color in LAS format and for the last two survey dates (February 2023 and July 2023) in a single csv file.

Tags: ascii, caulks-creek, elevation, geology, inland-waters, inlandwaters, location, missouri, state-plane, terrestrial-lidar, u-s-geological-survey, usgs, usgs-66588762d34ef3137d35f7ad, wildwood
Organization: Department of the Interior
Study Reach 2 Terrestrial Light Detection and Ranging Topographic Data in Caulks Creek, Wildwood, Missouri, 2022–2023

Topographic data were collected along study reach 2 in Caulks Creek in Wildwood, Missouri, on multiple dates, using terrestrial light detection and ranging (t-lidar), Global Navigation Satellite System (GNSS), and conventional surveying techniques (Rydlund and Densmore, 2012).
These data are high-resolution topography in laser scan format, collected using a tripod mounted t-lidar at multiple scan setups.  Data collection software integrated and stored the range and angular measurements from the t-lidar equipment.  Computer software was used to process the raw data, align the various scans in reference to one another, classify the data, and extract the topography data in a useable format. 
The topographic data are provided in four subsections (A-D) for each of the four survey dates (February 2022, August 2022, February 2023, and July 2023). The data represent the channel, bank, and near overbank surface and were saved with RGB (red-green-blue) color in LAS format.

Tags: ascii, caulks-creek, elevation, geology, inland-waters, inlandwaters, location, missouri, state-plane, terrestrial-lidar, u-s-geological-survey, usgs, usgs-6657953fd34ef3137d35f1e3, wildwood
Organization: Department of the Interior
Geochemical data from selected pre-Middle Jurassic basement rocks beneath the Atlantic and Gulf Coastal Plains in Florida and Alabama

This data release contains whole-rock geochemical analyses from drill cores and cuttings of pre-Middle Jurassic basement rocks that are buried beneath Coastal Plain sedimentary deposits in Florida and Alabama. The analyses were acquired to support geologic mapping and characterization of little-known coastal-plain basement rock units for topical studies as in geochronology, and applications ranging from mineral, energy, and water resources to earthquake hazards. These samples provide rare insights into deeply buried rocks that have no surface exposures and no known exposed correlates. 
The 70 whole-rock samples from drill cores and cuttings were selected and described by Ryan Deasy (USGS) and analyzed for major and trace elements at Activation Laboratories Ltd. (Actlabs) in Ancaster, Ontario, Canada. Analytical methods included lithium borate fusion or multiacid digestion followed by inductively coupled plasma optical emission spectroscopy (ICP-OES) for major elements and inductively coupled plasma mass spectrometry (ICP-MS) for most trace elements. Additional analytical methods included instrumental neutron activation analysis (INAA) for other trace elements, and loss on ignition (LOI) by gravimetric methods. Sample information (location, depth, brief description, etc.) and geochemical data in comma separated values (.csv) format are accompanied by quality control (QC) data (.csv), a data dictionary (.csv), and metadata (.xml). Mineral abundances, determined by application of the Rietveld method to whole-rock powder X-ray diffraction data, of many of the same samples are available in a companion data release (Deasy and others, 2024a). Photographs and photomicrographs of all samples are presented in another companion data release (Deasy and others, 2024b). These data were collected to support the characterization, discrimination, and correlation of map units in the Geologic map of pre-Middle Jurassic basement rocks beneath the Coastal Plain in Florida (Deasy and others, 2024c). Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government.

Tags: alabama, bedrock-geologic-units, borehole-logging, core-analysis, drilling-and-coring, florida, geochemistry, geoscientificinformation, usgs-6657907ed34ef3137d35f1c7
Organization: Department of the Interior
Study Reach 1 Terrestrial Light Detection and Ranging Topographic Data in Caulks Creek, Wildwood, Missouri, 2022–2023

Topographic data were collected along study reach 1 in Caulks Creek in Wildwood, Missouri, on multiple dates, using terrestrial light detection and ranging (t-lidar), Global Navigation Satellite System (GNSS), and conventional surveying techniques (Rydlund and Densmore, 2012).
These data are high-resolution topography in laser scan format, collected using a tripod mounted t-lidar at multiple scan setups.  Data collection software integrated and stored the range and angular measurements from the t-lidar equipment.  Computer software was used to process the raw data, align the various scans in reference to one another, classify the data, and extract the topography data in a useable format. 
The topographic data are provided in seven subsections (A-G) for each of the four survey dates (February 2022, July 2022, March 2023, and July 2023). The data represent the channel, bank, and near overbank surface and were saved with RGB (red-green-blue) color in LAS format.

Tags: ascii, caulks-creek, elevation, geology, inland-waters, inlandwaters, location, missouri, state-plane, terrestrial-lidar, u-s-geological-survey, usgs, usgs-66577e8fd34ef3137d35f0ba, wildwood
Organization: Department of the Interior
Data release for a novel tool to selectively deliver a control agent to filter-feeding silver and bighead carp

Invasive carp pose substantial economic and ecological damage when populations are widespread in freshwater systems within the United States of America (USA). Resource managers in the USA have a limited number of chemical control tools to selectively remove nuisance fish. The present study examined whether Antimycin-A (antimycin) wax encapsulated microparticles could cause selective lethality to invasive carps in a series of laboratory trials, controlled outdoor pond trials, and an experimental pond trial. Datasets include water quality, fish biometrics, fish survival, yttrium consumption, and antimycin microparticle dissipation data.

Tags: biota, invasive-carp, invasive-species, usgs-665757ddd34ef3137d35ee26
Organization: Department of the Interior
Cave climate data in Wood Valley pit crater, Hawai'i

Wood Valley Pit Crater is a nearly circular pit approximately 50m across and 50m deep with vertical walls. This pit is of particular interest because it hosts access to a cave entrance at its base, providing an opportunity to monitor cave climate throughout a type of cave structure that is ordinarily inaccessible. In-situ cave climate observations included cold trapping, cave breathing, possible effects from geothermal heating, and cave fog possibly induced by atmospheric thermal tides. Sensors were emplaced throughout the cave to continuously monitor variations of temperature, atmospheric pressure, and relative humidity.

Tags: atmospheric-and-climatic-processes, atmospheric-properties, cave-microclimate, caves, climatologymeteorologyatmosphere, field-inventory-and-monitoring, geoscientificinformation, usgs-66566271d34ef3137d35eb17
Organization: Department of the Interior
Metabarcoding of environmental DNA samples collected below Jackson Lake Dam (Wyoming) and Palisades Reservoir (Idaho) in 2021-2022 (ver. 2.0, November 2024)

These metadata contain links to the original sequences on GenBank. These data show the final OTU and metadata tables for each environmental sample collected. Additionally, we included OTU tables resulting from bioinformatic decontamination steps (using microDecon) in R.

Tags: biota, dna-sequencing, ecosystem-monitoring, field-methods, idaho, usgs-66564686d34ef3137d35eab3, wyoming
Organization: Department of the Interior
Highway-Runoff Database (HRDB) Version 1.2.0

The Highway-Runoff Database (HRDB) was developed by the U.S. Geological Survey (USGS), in cooperation with the Federal Highway Administration (FHWA) Office of Project Delivery and Environmental Review to provide planning-level information for decision makers, planners, and highway engineers to assess and mitigate possible adverse effects of highway runoff on the Nation's receiving waters (Granato and Cazenas, 2009; Granato, 2013; 2019; Granato and others, 2018; Granato and Friesz, 2021). The HRDB was assembled by using a Microsoft Access database application to facilitate use of the data and to calculate runoff-quality statistics with methods that properly handle censored-concentration data. 
The HRDB was first published as version 1.0 in cooperation with the FHWA in 2009 (Granato and Cazenas, 2009). The second version (1.0.0a) was published in cooperation with the Massachusetts Department of Transportation Highway Division to include data from Ohio and Massachusetts (Smith and Granato, 2010). The third version (1.0.0b) was published in cooperation with FHWA to include a substantial amount of additional data (Granato and others, 2018; Granato and Jones, 2019). The fourth version (1.1.0) was updated with additional data and modified to provide data-quality information within the Graphical User Interface (GUI), calculate statistics for multiple sites in batch mode, and output additional statistics. The fifth version (1.1.0a) was published in cooperation with the California Department of Transportation to add highway-runoff data collected in California. The sixth version published in this release (1.2.0) has been updated to include additional data, correct data-transfer errors in previous versions, add new parameter information, and modify the statistical output. This version includes data from 270 highway sites across the country (26 states); data from 8,108 storm events; and 119,224 concentration values with data for 418 different water-quality constituents or parameters.

Tags: database, highway-runoff, runoff, stochastic-empirical-loading-and-dilution-model, stormwater, usgs-66564652d34ef3137d35eaaa
Organization: Department of the Interior
Preserving Tree-Ring Datasets for Climate and Hazard Research and Understanding Societal Impacts: Carrara Career Samples

Dendrochronological collections during the career of USGS emeritus, Paul Carrara: Douglas-fir (Pseudotsuga menziesii), Black cottonwood (Populus trichocarpa), Spruce (Picea), Shore pine (Pinus contorta contorta), Willow (Salix), Bristlecone pine (Pinus aristate), Engelmann spruce (Picea engelmannii), Aspen (Populus tremuloides), and Limber pine (Pinus flexilis) collections from western North America. The Carrara NGGDPP archive collection is comprised of fifty-two cross-sections obtains for studies of glacial, avalanche, and vegetative histories from Alaska, Montana, and Colorado. Samples were processed following standard dendrochronological methods, including sample surface preparation and annual ring assignment. These tree cross-sections now require preservation. We used high resolution digital photography to capture images of each sample using a system custom designed for digitizing tree rings. Digital images obtained for this archive can then be stored and used by researchers, communities and teachers and students at all education levels.

Tags: alaska, archive, avalanche, climatologymeteorologyatmosphere, colorado, dendrochronology, disturbance-history, environmental, glacier, montana, paleo, usgs-66c4a279d34e03388288d24d
Organization: Department of the Interior
Mississippi River fishes collected by a suite of entanglement and entrapment gears; 2020-2023

Black Carp (Mylopharyngodon piceus) were imported to the United States for use as a biological control in aquaculture and have since escaped with reproducing populations in the wild. Habitat use and capture of this species has not been well documented in the wild, thus questions about catchability by gears and habitats are present. This dataset represents sampling effort to capture Black Carp with common large-river gears. Data represent Black Carp catch  and the co-occurring catch of Mississippi River fish sampled by the described gears from the lowest reach of the Missouri River and Mississippi rivers near their confluence. Gears consisted of trammel nets, gill nets, and predominately hoop nets fished among mainstem habitats of an open river segment from 2020-2023.

Tags: aquatic-ecosystems, biota, bycatch, field-methods, fish, fish-nets, hoopnets, meramec-river, mississippi-river, missouri-river, usgs-66561490d34ef3137d35e9b7
Organization: Department of the Interior
Environmental DNA qPCR detection results and covariates from Idaho, Missouri, Montana, and New York rivers sampled in 2023

This dataset contains quantitative results from, and covariate attributes of, environmental DNA water samples collected across multiple rivers in 2023. Samples were analyzed for eDNA of round goby in the Hudson River (NY), westslope cutthroat trout (Oncorhynchus clarkii lewisi) in Cherry Creek (MT), lake trout (Salvelinus namaycush) and Spectaclecase mussels (Cumberlandia monodonta) in Big Piney River (MO), and rainbow trout (O. mykiss) and Western Pearlshell (Margaritifera falcata) in Loggers Creek (ID).

Tags: biota, environmental-dna, fish, genetics, idaho, missouri, montana, new-york, usgs-66560e0fd34ef3137d35e9a6
Organization: Department of the Interior