AndreaBozzo/ceres-open-data-index huggingface dataset:
Metagenomic detection and reconstruction of Lake Sinai Virus from honey bee sequence data

A survey of public honey bee sequence data was performed to detect infections by Lake Sinai Virus (LSV). The Sequence Read Archive of the National Center for Biotechnology Information (NCBI) was queried to identify accessions of RNA sequence data derived from honey bee. These were filtered as described below and then up to 50 million reads or read pairs were downloaded and searched against a reference database of conserved LSV sequence. Accessions with matches above a specified threshold were downloaded in their entirety and assembled into longer contiguous sequences (contigs). The result contigs were searched against each open reading frame (ORF) of the reference LSV genome present in the NCBI database (accession NC_032433.1) and matching regions from each contig. These ORF sequences were aligned with additional sequences identified in NCBI databases through the BLAST web service. These alignments provide the basis for computing phylogenetic trees, rates of nucleotide substitution, codon usage bias, and other evolutionary parameters.

Tags: climatologymeteorologyatmosphere, farming, rna, usgs-5c634809e4b0fe48cb35592b, viruses
Organization: Department of the Interior
High-resolution acoustic backscatter data collected southwest of Montague Island, Alaska during field activity 2014-622-FA

High-resolution acoustic backscatter data were collected by the U.S. Geological Survey (USGS) and the Alaska Department of Fish and Game in May of 2014 southwest of Montague Island, Alaska. Data were collected aboard the Alaska Department of Fish and Game vessel, R/V Solstice, during USGS field activity 2014-622-FA, using a pole mounted 100-kHz Reson 7111 multibeam echosounder.

Tags: acoustic-methods, bainbridge-passage, cmhrp, coastal-and-marine-hazards-and-resources-program, dangerous-passage, distributions, geophysics, geoscientificinformation, geospatial-datasets, gulf-of-alaska, icy-bay, imagerybasemapsearthcover, jackpot-bay, knight-island-passage, mapping, marine-geophysics, montague-island, montague-strait, multibeam-sonar, nassau-bay, north-pacific-ocean, pacific-coastal-and-marine-science-center, pacific-ocean, pcmsc, port-bainbridge, prince-william-sound, sea-floor-acoustic-reflectivity, sea-floor-characteristics, seabed, state-of-alaska, substrate, u-s-geological-survey, usgs, usgs-5c5ccc5be4b0fe48cb312599, whale-bay
Organization: Department of the Interior
Elevation of marsh units in Cape Cod National Seashore salt marsh complex, Massachusetts


    Elevation distribution in the Cape Cod National Seashore (CACO) salt marsh complex and approximal wetlands is given in terms of mean elevation of conceptual marsh units defined by Defne and Ganju (2019). The elevation data is based on the 1-meter resolution Coastal National Elevation Database (CoNED), where data gaps exist. Through scientific efforts initiated with the Hurricane Sandy Science Plan, the U.S. Geological Survey has been expanding national assessment of coastal change hazards and forecast products to coastal wetlands. The intent is to provide federal, state, and local managers with tools to estimate their vulnerability and ecosystem service potential. For this purpose, the response and resilience of coastal wetlands to physical factors need to be assessed in terms of the ensuing change to their vulnerability and ecosystem services. CACO is one of the selected domains to expand this study.
    
    References:
    Defne, Z., and Ganju, N.K., 2019, Conceptual marsh units for Cape Cod National Seashore salt marsh complex, Massachusetts: U.S. Geological Survey data release, https://doi.org/10.5066/P955K1Y2
   

Tags: atlantic-ocean, barnstable-county, cape-cod-bay, cape-cod-national-seashore, coastal-ecosystems, coastal-processes, elevation, environment, estuary, geospatial-datasets, herring-cove, inlandwaters, little-pleasant-bay, long-term-ecological-research, lter, marsh-health, massachusetts, oceans, outer-cape, salt-marsh, united-states, usgs-5c62f56ae4b0fe48cb34c8ca, vegetation, wellfleet-harbor, wetland-ecosystems, wetland-functions
Organization: Department of the Interior
Unvegetated to vegetated marsh ratio in Cape Cod National Seashore salt marsh complex, Massachusetts


    Unvegetated to vegetated marsh ratio (UVVR) in the Cape Cod National Seashore (CACO) salt marsh complex and approximal wetlands is computed based on conceptual marsh units defined by Defne and Ganju (2019). UVVR was calculated based on U.S. Department of Agriculture National Agriculture Imagery Program (NAIP) 1-meter resolution imagery. Through scientific efforts initiated with the Hurricane Sandy Science Plan, the U.S. Geological Survey has been expanding national assessment of coastal change hazards and forecast products to coastal wetlands. The intent is to provide federal, state, and local managers with tools to estimate their vulnerability and ecosystem service potential. For this purpose, the response and resilience of coastal wetlands to physical factors need to be assessed in terms of the ensuing change to their vulnerability and ecosystem services. CACO is one of the selected domains to expand this study.
    
    References:
    Defne, Z., and Ganju, N.K., 2019, Conceptual marsh units for Cape Cod National Seashore salt marsh complex, Massachusetts: U.S. Geological Survey data release, https://doi.org/10.5066/P955K1Y2
   

Tags: atlantic-ocean, barnstable-county, cape-cod-bay, cape-cod-national-seashore, coastal-ecosystems, coastal-processes, environment, estuary, geospatial-datasets, herring-cove, inlandwaters, little-pleasant-bay, long-term-ecological-research, lter, marsh-health, massachusetts, oceans, outer-cape, salt-marsh, united-states, usgs-5c62f414e4b0fe48cb34c8b9, uvvr, vegetation, wellfleet-harbor, wetland-ecosystems, wetland-functions
Organization: Department of the Interior
Floodplain data from the Queets River in Olympic National Park, 1939-2013

Floodplain characteristics were quantified for the Queets River in Olympic National Park, Washington, USA, using orthophoto imagery taken between 1939-2013. Each zipped folder contains a shapefile and its associated metadata record.

Tags: environment, geomorphology, geoscientificinformation, hydrogeology, inlandwaters, natural-resources-condition-assessment, olympic-national-park, river-channel, usgs-5c65f50ce4b0fe48cb390934, washington
Organization: Department of the Interior
Mean tidal range in marsh units of Cape Cod National Seashore salt marsh complex, Massachusetts


    Biomass production is positively correlated with mean tidal range in salt marshes along the Atlantic coast of the United States of America. Recent studies support the idea that enhanced stability of the marshes can be attributed to increased vegetative growth due to increased tidal range. This dataset displays the spatial variation of mean tidal range (i.e. Mean Range of Tides, MN) in the Cape Cod National Seashore (CACO) salt marsh complex and approximal wetlands based on conceptual marsh units defined by Defne and Ganju (2019). MN was based on the calculated difference in height between mean high water (MHW) and mean low water (MLW) using the VDatum (v3.5) database ( http://vdatum.noaa.gov/ ). 
    
    Through scientific efforts initiated with the Hurricane Sandy Science Plan, the U.S. Geological Survey has been expanding national assessment of coastal change hazards and forecast products to coastal wetlands. The intent is to provide federal, state, and local managers with tools to estimate their vulnerability and ecosystem service potential. For this purpose, the response and resilience of coastal wetlands to physical factors need to be assessed in terms of the ensuing change to their vulnerability and ecosystem services. CACO is one of the selected domains to expand this study.
    
    References:
    Defne, Z., and Ganju, N.K., 2019, Conceptual marsh units for Cape Cod National Seashore salt marsh complex, Massachusetts: U.S. Geological Survey data release, https://doi.org/10.5066/P955K1Y2
   

Tags: atlantic-ocean, barnstable-county, cape-cod-bay, cape-cod-national-seashore, coastal-ecosystems, coastal-processes, environment, estuary, geospatial-datasets, herring-cove, inlandwaters, little-pleasant-bay, long-term-ecological-research, lter, marsh-health, massachusetts, oceans, outer-cape, salt-marsh, tidal-range, tides-oceanic, united-states, usgs-5c62e48ce4b0fe48cb34c80c, vegetation, wellfleet-harbor, wetland-ecosystems, wetland-functions
Organization: Department of the Interior
Modeling soil pore water salinity response to drought in tidal freshwater forested wetlands

Model generated soil pore water salinity (psu) values under scenarios of drought and normal conditions at Tidal Freshwater Forested Wetlands (TFFW) sites along the Waccamaw River and Savannah River in the Southeastern United States.

Tags: coastal-environment, droughts, evapotranspiration, forested-wetlands, georgia, iso-19115-topic-category, saline-intrusion, savannah-river, soil-salinity, south-carolina, usa, usgs-5c62e264e4b0fe48cb34c7fa, waccamaw-river
Organization: Department of the Interior
Larval Fish Abundance, Identification, and Auxiliary Data from the Great Lakes and Their Connecting Channels

This dataset contains data collected on various vessel operations on the Great Lakes and their connecting channels, primarily the St. Clair River, Lake St. Clair, Detroit River, and western Lake Erie, although other locations have been sampled and included in this dataset. This dataset contains the field variables, environmental conditions, larval catches (numbers), larval fish identifications, and associated auxiliary information with the sampling locations.

Tags: acipenser-fulvescens, biota, burbot, coregonus-clupeaformis, detroit-river, fish-larvae, lake-erie, lake-huron, lake-saint-clair, lake-sturgeon, lake-whitefish, lampreys, perca-flavescens, petromyzon-marinus, phenology, saint-clair-river, sander-vitreus, usgs-5c61df79e4b0fe48cb32fe87, walleye, yellow-perch
Organization: Department of the Interior
Pre-restoration vegetation data, Little Saint Francis River chat pile site, Missouri, USA, 2017 and 2018

This data set includes geospatial data and tables providing location, environmental, and vegetation data collected in 2017 and 2018 at the Little Saint Francis River chat pile restoration site, Fredericktown, Madison County, Missouri. Restoration actions are being implemeneted as part of the settlement for the Madison County Mines Superfund site to compensate the public for losses of natural resources and the services they provide as part of the Natural Resource Damage Assessment and Restoration Southeast Missouri Lead Mining District case. Data were collected prior to and during the early stages of restoration actions to restore bottomland habitat, reduce invasive species abundance, and improve upland woodland habitat by introducing prescribed burning to reduce stem density and favor fire-tolerant species. Restoration monitoring was designed to quantify changes in plant community attributes relevant to these goals. Pre-restoration vegetation sampling quantified plant community composition, enabled refinement of restoration objectives and identification of management strategies appropriate for USDA Ecological Site Descriptions, and yielded maps to visualize baseline invasive species abundances and inform eradication planning.

Tags: biota, contamination, environment, fredericktown, hydrology, little-saint-francis-river, madison-county, madison-county-mines-superfund-site, missouri, restoration, soils, southeast-missouri-lead-mining-district, usgs-5c61bf8ee4b0fe48cb32fd35, vegetation
Organization: Department of the Interior
Deployments of autonomous, GPS ocean ocean-surface drifters, Makua, Kauai, USA, August 2016

Satellite-tracked, DGPS-equipped Lagrangian surface-current drifter deployments were conducted over 6 days between 30 July and 4 August 2016 at various locations and stages of the tide over the coral reef off Makua, HI. The drifters internally logged their location every 1 minute, and they transmitted their positions to satellites every 5 minutes. A drogue was attached to the drifters at 1 m below sea level in order to track the currents at that depth.

Tags: cmhrp, coastal-and-marine-hazards-and-resources-program, geoscientificinformation, island-of-kauai, kauai, kauai-county, makua-reef, ocean-circulation, ocean-currents, ocean-processes, oceans, pacific-coastal-and-marine-science-center, pcmsc, physical-oceanography, state-of-hawaii, tunnels-beach, u-s-geological-survey, usgs, usgs-5c6f25f7e4b0fe48cb41fb31, water-column-features
Organization: Department of the Interior
Data for Assessing the Status of Macroinvertebrate Communities and Sediment Toxicity in the Buffalo River Area of Concern, New York

Data from 10-day sediment toxicity tests of bed sediments from the Buffalo River Area of Concern (AOC) and reference reaches on the Buffalo River upstream of the AOC, Erie County, New York, respectively. Specifically, the data was used to compare the survival and growth of two macroinvertebrate species in sediments from study sites and laboratory controls. Results are from 10-day sediment exposures of two test species, Chironomus dilutus and Hyalella azteca. Sediment samples were collected from 8 sites within the AOC and from 6 reference sites upstream of the AOC. Bed-sediments were collected from depositional areas using a petite Ponar (0.03 square meter) dredge. At each site, approximately five grabs were composited into a bucket, mixed, and a 4-liter (L) subsample was stored in a polyethylene container. Sediment toxicity testing were then conducted by a contract laboratory to quantify toxicity with the dipteran, Chironomus dilutus, and the amphipod, Hyalella azteca, during 10-day survival and growth bioassays following USEPA test methods 100.2 and 100.1, respectively. (U.S. Environmental Protection Agency, 2000, Methods for measuring the toxicity and bioaccumulation of sediment associated contaminants with freshwater invertebrates. Second edition: U.S. Environmental Protection Agency, Office of Research and Development EPA 600/R-99/064.) This spreadsheet contains 16 columns. The first 8 columns describe the sample collection information, the remaining 8 columns provide the survival and growth results of two test species used in sediment toxicity tests. The data include the stream name, site ID, National Water Information System (NWIS) ID, latitude and longitude, replicate number, and site type. The following eight columns present results from 10-day sediment exposures of two test species, Chironomus dilutus and Hyalella azteca. The following endpoints were measured for each species following the 10-day exposure: number of surviving organisms, percentage of organisms surviving (hereafter survival), average ash-free dry weight of the surviving organisms (hereafter growth), and ash-free dry weight of the surviving organisms divided by the initial number of organisms (hereafter biomass).

Tags: benthic-ecosystems, buffalo-river, contamination-and-pollution, erie-county, new-york, usgs-5c5f19d3e4b0fe48cb32eef4
Organization: Department of the Interior
Archive of Chirp Subbottom Profile, Imagery, and Geospatial Data Collected in 2021 Near Pensacola Beach, Florida

From June 2 through 9, 2021, researchers from the U.S. Geological Survey (USGS) conducted an inshore and offshore geophysical survey to map the shoreface and determine Holocene stratigraphy near Pensacola Beach, Florida (FL). The Coastal Resource Evaluation for Management Applications (CREMA) project objective includes the investigation of nearshore geologic controls on surface morphology. This publication serves as an archive of high-resolution chirp subbottom trace data, survey trackline map, navigation files, geographic information system (GIS) data, and formal Federal Geographic Data Committee (FGDC) Content Standard for Digital Geospatial Metadata (CSDGM). Processed subbottom profile images are also provided. The archived trace data are in standard Society of Exploration Geophysicists (SEG) SEG-Y revision 0 format (Barry and others, 1975). In addition to this data release, the SEG-Y files can be downloaded from the USGS Coastal and Marine Geoscience Data System (CMGDS) at, https://cmgds.marine.usgs.gov. Coastal multibeam bathymetry data were also collected for this project offshore of the Santa Rosa Island coast (during USGS Field Activity Number 2019-326-FA) and are provided in another data release (Farmer and others, 2020).

Tags: 2021-322-fa, barrier-island-mapping, chirp, coastal-processes, distributions, escambia, field-activity-logs, florida, geology, geoscientificinformation, geospatial-datasets, gulf-islands-national-seashore, gulf-of-mexico, image-collections, marine-geology, navigational-data, oceans, okaloosa, pensacola, physical-habitats-and-geomorphology, santa-rosa, seg-y, seismic-reflection, seismic-reflection-profiling, society-of-exploration-geophysicists, sub-bottom-profiling, usgs-5c5dfaf2-d4ab-40a9-80ea-f9f962c9af81
Organization: Department of the Interior
Ohia Dieback Study - Dieback Model Results Table

Several previously published reports and geographic information system (GIS) data layers were used to code  information on site attributes for each assessment plot using the spatial join tool in ArcMap. This information was used for an analysis of dieback and non-dieback habitat characteristics. The results of this analysis are presented in this table which depicts the probability of heavy to severe canopy dieback occurring at some time at a particular 30 x 30 m pixel location within the study area.

Tags: analytical-modeling, biota, canopy-dieback, metrosideros-polymorpha, ohia, rain-forests, regeneration, usgs-5c5dfa8ce4b0fe48cb32e7da, vegetation
Organization: Department of the Interior
Tops file for the Niobrara interval of the Upper Cretaceous Cody Shale and associated strata in the Wind River Basin, Wyoming

The Wind River Basin is a large Laramide (Late Cretaceous through Eocene) structural and sedimentary basin that encompasses about 7,400 square miles in central Wyoming (fig. 1). The basin is bounded by the Washakie Range and Owl Creek and southern Bighorn Mountains on the north, the Casper arch on the east, the Granite Mountains on the south, and Wind River Range on the west (figs. 1).
Many important conventional and unconventional oil and gas resources have been discovered and produced from reservoirs ranging from Mississippian through Tertiary in age (Keefer, 1969; Fox and Dolton, 1989, 1996; De Bruin, 1993; Johnson and others, 1996, 2007).  It has been suggested by numerous authors including: Keefer, 1969; Meissner and others, 1984; Fox and Dolton, 1989, 1996; Johnson and Rice, 1993; Nuccio and others, 1996; and Schelling and Wavrek, 1999, 2001: that various Upper Cretaceous marine shales are the principal hydrocarbon source rocks for many of these accumulations.  With new drilling and well completion technologies, equivalent marine source rock intervals, in particular the Niobrara Formation, are now important continuous (unconventional) shale gas and shale oil objectives in other Rocky Mountain basins ((Matthews, 2011; Sonnenberg, 2011; Williams and Lyle, 2011; Durham, 2012a,b, 2013; Taylor and Sonnenberg, 2014; and Hawkins, 2016).  In the Wind River Basin the Niobrara is represented by shales, calcareous shales, marls, siltstones, and sandstones in the lower shaly member of the Upper Cretaceous Cody Shale (Finn, 2017) (fig. 2). 
Please see supplemental information for associated references.  Selected figures have also been included to help describe this data release.  These figures are provided in pdf and jpg format.  These include:
Fig. 1_Rocky Mountain basins.pdf/jpg.  Map of Rocky Mountain region showing locations of Laramide sedimentary and structural basins and intervening uplifts.  
Fig. 2_Regional Cretaceous X section.pdf/jpg.  Regional east-west stratigraphic cross section of Cretaceous rocks in the Wind River Basin.  
Each modified from Finn (2017).

Tags: cody-formation, continuous-assessment, energy-resources, geology, geoscientificinformation, national-and-global-assessment-oil-and-gas, natural-gas, natural-gas-resources, niobrara-formation, oil, oil-resources, oil-shale-resources, oilgas, resource-assessment, unconventional-assessment, united-states, usgs-5c5da62be4b0fe48cb32e3ea, wind-river-basin, windriverbasin, wyoming
Organization: Department of the Interior
Map of canopy dieback on Hawaii Island in 1977

This shapefile describes the canopy status and distribution of of ohia (Metrosideros polymorpha) forests on the eastern side of the island relative to a landscape-scale canopy dieback that impacted this area in the 1970s.

Tags: biota, canopy-dieback, metrosideros-polymorpha, ohia, usgs-5c5dfa05e4b0fe48cb32e7ce
Organization: Department of the Interior
Model archive—Regional regression models for estimating flood-frequency characteristics of rural, unregulated Ohio streams

Dataset is a model archive containing all relevant files to create regression models that are discussed in the report: Koltun, G.F., 2019, Flood-frequency estimates for Ohio streamgages based on data through water year 2015 and techniques for estimating flood-frequency characteristics of rural, unregulated Ohio streams: U.S. Geological Survey Scientific Investigations Report 2019-5018. WREG R source code, regression results and associated output files are also included in the archive.

Tags: expected-moments-algorithm, flood-frequency, indiana, kentucky, michigan, ohio, pennsylvania, regional-regression, usgs-5c5df6b7e4b0fe48cb32e7bd, west-virginia
Organization: Department of the Interior