AndreaBozzo/ceres-open-data-index huggingface dataset:
Data for gene transcription patterns in response to low level petroleum contaminants in Mytilus trossulus from field sites and harbors in southcentral Alaska

Marine mussels are a ubiquitous and crucial component of the nearshore environment, and new genomic technologies exist to quantify molecular responses of individual mussels to stimuli, including exposure to polycyclic aromatic hydrocarbons (PAHs). We used gene-based assays of exposure and physiological function to assess lingering oil damage from the 1989 Exxon Valdez oil spill using the Pacific blue mussel, Mytilus trossulus. We developed a diagnostic gene transcription panel to investigate exposure to PAHs and other contaminants and their effects on mussel physiology and health. Mussels were collected annually from 2012 through 2015 at five field sites (mussel beds) in western Prince William Sound: Herring Bay, Hogan Bay, Iktua Bay, Johnson Bay, and Whale Bay. These five sites were randomly selected and are sampled annually as part of the ongoing Gulf Watch Alaska long-term monitoring program (Dean et al. 2014, Bodkin et al. this volume). Reference samples of mussels were collected from three harbors that support high levels of commercial and recreational boating activity: Cordova Harbor in 2014, and Seward Harbor and Whittier Harbor in 2015. The five random sites represented approximately 3000 km2 in western Prince William Sound, and all were within the area of potential 1989 spill effects. Mussels were collected on the morning rising tide and dissected as soon as possible following collection, generally within one hour.  
These data support the following publication: Lizabeth Bowen, A. Keith Miles, Brenda Ballachey, Shannon Waters, James Bodkin, Mandy Lindeberg, Daniel Esler, Gene transcription patterns in response to low level petroleum contaminants in  from field sites and harbors in southcentral Alaska, Deep Sea Research Part II: Topical Studies in Oceanography, 2017, ISSN 0967-0645, https://doi.org/10.1016/j.dsr2.2017.08.007. 
References: 
Dean, T. A., Bodkin, J.L., Coletti, H.A., 2014. Protocol Narrative for Nearshore Marine Ecosystem Monitoring in the Gulf of Alaska, version 1.1. Natural Resource Report NPS/SWAN/NRR -2014/756. Fort Collins, Colorado.  
Bodkin, J.L., Coletti, H.A., Ballachey, B.E., Monson, D.H., Esler, D., Dean, T.A., this volume. Variation in abundance of Pacific blue mussel in the northern Gulf of Alaska, 2006-2015. Deep Sea Res. II.

Tags: exxon-valdez-oil-spill, gene-expression, gulf-watch-alaska, mussels, mytilus-trossulus, pah, prince-william-sound, usgs-5909184fe4b0fc4e44900045
Organization: Department of the Interior
Phytoplankton Species Composition, Abundance and Cell Size in San Francisco Bay: Microscopic Analyses of USGS Samples Collected 1992-2014

This Data Release makes available measurements of phytoplankton species composition, abundance and cell size made on samples collected in San Francisco Bay (CA) from April 1992 through March 2014. Phytoplankton samples were collected at 31 stations along a 145-km transect where the variability of salinity, temperature, turbidity and nutrient concentrations reflected a broad range of environmental factors that regulate phytoplankton growth and abundance (station map on ScienceBase homepage). Whole water samples were preserved with acid Lugol’s solution, and 2 to 50 ml aliquots were settled in chambers for 6 to 24 hours (Utermöhl 1958). Phytoplankton cells were then counted and identified using a phase-contrast inverted microscope at 125x magnification, all cells greater than 30 μm diameter were enumerated. Cells smaller than 30 μm were counted at 1250x magnification; following the APHA (1989) strip count method, at least 100 cells of the most numerous taxon were counted. Cell volumes were estimated from measured linear dimensions and geometric formulas that varied with cell shapes. Phytoplankton samples representing 923 distinct date, station and depths were included. The 16,442 entries in this dataset include 609 different taxa within 11 functional groups. Diatoms dominated the total biovolume contributed by each functional group (77%) followed by dinoflagellates (14%) and cryptophytes (4.5%). The top 5 species contributing to the summed biovolume in all samples were: Thalassiosira punctigera, Chaetoceros socialis, Ditylum brightwellii, Thalassiosira rotula and Noctiluca scintillans. By frequency of occurrence, the top 5 species were: Teleaulax amphioxeia, Nannochloropsis spp., Plagioselmis prolonga var. nordica, Skeletonema costatum and Thalassiosira eccentrica. 
APHA. (1989). Standard methods for the examination of water and wastewater, 17th edn. American Public Health Association, Washington, DC 
Utermöhl H. (1958). Zur Vervollkommnung der quantitativen Phytoplankton-Methodik. Mitt Int Verh Theor Angew Limnol 9:1-38

Tags: california, diatom, dinoflagellate, estuary, microalgae, microscopy, phytoplankton, san-francisco-bay, taxonomy, usgs-5908f489e4b0fc4e448ffff1
Organization: Department of the Interior
Radiocarbon ages, age-model code, and other supplemental data for Nelson et al. (2021), A maximum rupture model for the central and southern Cascadia subduction zone—assessing ages for coastal evidence of megathrust earthquakes and tsunamis

This data release contains supplemental data for the following paper:
Nelson, A.R., DuRoss, C.B., Mahan, S.A., Gray, H.J., Engelhart, S.E., Witter, R.C., Hawkes, A.D., Horton, B.P., Kelsey, H.M., and Padgett, J.S., 2021, A maximum rupture model for the central and southern Cascadia subduction zone—assessing ages for coastal evidence of megathrust earthquakes and tsunamis: Quaternary Science Reviews 261, https://doi.org/10.1016/j.quascirev.2021.106922.
The data include a compilation of new and previously published radiocarbon ages from the original cores from Bradley Lake of Kelsey et al. (2005; odt format), and tables of new and previously published radiocarbon data for 7 of the 13 tidal wetland sites along the coasts of Oregon and northern California, whose ages we compare with the ages from Bradley Lake (odt format). The data files (odt format) also include code for the OxCal (version 4.4; https://c14.arch.ox.ac.uk/oxcal.html) Bayesian software models used with selected radiocarbon ages to calculate age probability density functions for the lake’s earthquake or tsunami-caused disturbance events, and for the stratigraphic contacts produced by earthquakes and tsunamis at 12 of the 13 tidal wetland sites (odt format). An additional text file (odt format) explains the addition of variance to the errors on laboratory reported radiocarbon ages in the tables analyzed prior to 1998, and those analyzed by the National Ocean Sciences AMS Facility (NOSAMS) at the Woods Hole Oceanographic Institution, Woods Hole, Massachusetts. Data describing the results of our recent unsuccessful attempt to use optical dating methods (OSL and IRSL) on quartz grains from tsunami deposits in Bradley Lake to date the deposits can be found in Mahan et al. (2021; U.S. Geological Survey data release, https://doi.org/10.5066/P9YWIDOW).

Tags: cascadia-megathrust, cascadia-subduction-zone, coastal-hazards, earthquake-contact, earthquake-hazard-program, earthquake-hazards, earthquake-history, geologic-hazards-science-center, ghsc, lake-tsunami-history, large-earthquake-ruptures, paleoearthquake-correlation, radiocarbon-dating, seismic-hazard, tsunami-contact, tsunami-hazard-planning, usgs-5908a1b3e4b0fc4e448ffe23
Organization: Department of the Interior
Coastwide Reference Monitoring System (CRMS) 2005, 2008, 2012, and 2015 Site 0609 Land-Water Matrix

Wetland restoration efforts conducted by the Coastal Wetlands Planning, Protection, and Restoration Act (CWPPRA) in Louisiana rely on monitoring efforts to determine the efficacy of these efforts. The Coastwide Reference Monitoring System (CRMS) was developed to assist in a multiple-reference approach that uses aspects of hydrogeomorphic functional assessments and probabilistic sampling for monitoring. The CRMS program includes a suite of approximately 390 sites that encompass the range of hydrological and ecological conditions for each stratum.  As part of CRMS, land and water classifications are created from Wetland restoration efforts conducted by the Coastal Wetlands Planning, Protection, and Restoration Act (CWPPRA) in Louisiana rely on monitoring efforts to determine the efficacy of these efforts. The Coastwide Reference Monitoring System (CRMS) was developed to assist in a multiple-reference approach that uses aspects of hydrogeomorphic functional assessments and probabilistic sampling for monitoring. The CRMS program includes a suite of approximately 390 sites that encompass the range of hydrological and ecological conditions for each stratum.  As part of CRMS, land and water classifications are created from Digital Orthophoto Quarter Quadrangles (DOQQs) approximately every three years at all CRMS sites.  This dataset consists of a matrix of four land-water products (2005, 2008, 2012, and 2015).  The resulting matrix has 16 possible classes defined by the combination of land and water categories on those four dates.

Tags: cartography, coastal, crms, doqq, geographic-information-system, imagerybasemapsearthcover, land-water, louisiana, mapping, marsh, protection, restoration, state-of-louisiana, usgs-5938763be4b0764e6c5d6c29, wetland
Organization: Department of the Interior
Agricultural Pesticide Use Estimates for Selected Watersheds of the Surface Water Trends Project, 1992-2014, National Water Quality Program

The U.S. Geological Survey (USGS) National Water Quality Program (NWQP) provides an understanding of water-quality conditions; whether conditions are getting better or worse over time; and how natural features and human activities affect those conditions. The Surface Water Trends (SWT) project of NWQP evaluates the directions, periods, and statistical significance of trends in water quality in streams and rivers. This data release was generated for SWT and provides annual agricultural pesticide use (1992-2014) for selected watersheds where long-term water quality is measured and where subsequent trend analysis will be conducted. County-level pesticide use estimates for 33 compounds were allocated to agricultural land for 70 SWT watersheds.

Tags: agriculture, pesticides, river-systems, usgs-59088f3ee4b0fc4e448ffe08, water-quality
Organization: Department of the Interior
Coastwide Reference Monitoring System (CRMS) 2005, 2008, 2012, and 2015 Site 2189 Land-Water Matrix

Wetland restoration efforts conducted by the Coastal Wetlands Planning, Protection, and Restoration Act (CWPPRA) in Louisiana rely on monitoring efforts to determine the efficacy of these efforts. The Coastwide Reference Monitoring System (CRMS) was developed to assist in a multiple-reference approach that uses aspects of hydrogeomorphic functional assessments and probabilistic sampling for monitoring. The CRMS program includes a suite of approximately 390 sites that encompass the range of hydrological and ecological conditions for each stratum.  As part of CRMS, land and water classifications are created from Wetland restoration efforts conducted by the Coastal Wetlands Planning, Protection, and Restoration Act (CWPPRA) in Louisiana rely on monitoring efforts to determine the efficacy of these efforts. The Coastwide Reference Monitoring System (CRMS) was developed to assist in a multiple-reference approach that uses aspects of hydrogeomorphic functional assessments and probabilistic sampling for monitoring. The CRMS program includes a suite of approximately 390 sites that encompass the range of hydrological and ecological conditions for each stratum.  As part of CRMS, land and water classifications are created from Digital Orthophoto Quarter Quadrangles (DOQQs) approximately every three years at all CRMS sites.  This dataset consists of a matrix of four land-water products (2005, 2008, 2012, and 2015).  The resulting matrix has 16 possible classes defined by the combination of land and water categories on those four dates.

Tags: cartography, coastal, crms, doqq, geographic-information-system, imagerybasemapsearthcover, land-water, louisiana, mapping, marsh, protection, restoration, state-of-louisiana, usgs-59387892e4b0764e6c5d6cf7, wetland
Organization: Department of the Interior
Coastwide Reference Monitoring System (CRMS) 2005, 2008, 2012, and 2015 land-water matrices

Wetland restoration efforts conducted by the Coastal Wetlands Planning, Protection and Restoration Act (CWPPRA) in Louisiana rely on monitoring efforts to determine the efficacy of these efforts. The Coastwide Reference Monitoring System (CRMS) was developed to assist in a multiple-reference approach that uses aspects of hydrogeomorphic functional assessments and probabilistic sampling for monitoring. The CRMS program includes a suite of approximately 390 sites that encompass the range of hydrological and ecological conditions for each stratum. As part of CRMS, land and water classifications are created from Wetland restoration efforts conducted by the Coastal Wetlands Planning, Protection, and Restoration Act (CWPPRA) in Louisiana rely on monitoring efforts to determine the efficacy of these efforts. The Coastwide Reference Monitoring System (CRMS) was developed to assist in a multiple-reference approach that uses aspects of hydrogeomorphic functional assessments and probabilistic sampling for monitoring. The CRMS program includes a suite of approximately 390 sites that encompass the range of hydrological and ecological conditions for each stratum. As part of CRMS, land and water classifications are created from Digital Orthophoto Quarter Quadrangles (DOQQs) approximately every three years at all CRMS sites. This dataset consists of a matrix of four land-water products (2005, 2008, 2012, and 2015). The resulting matrix has 16 possible classes defined by the combination of land and water categories on those four dates.

Tags: cartography, coastal, crms, doqq, geographic-information-system, imagerybasemapsearthcover, land-water, louisiana, mapping, marsh, protection, restoration, state-of-louisiana, usgs-59088c56e4b0fc4e448ffe03, wetland
Organization: Department of the Interior
Accelerometer scour monitor data on the Cedar River, Washington, 2013 - 2014

Accelerometer scour monitors were deployed on the Cedar River, Washington from 2013 to 2014 as part of a study on the timing of streambed scour at 73 locations in salmon-spawning habitat. This data release contains data of the three-dimensional orientation recorded at 20- to 30-minute intervals for the 46 accelerometer monitors that were recovered in 2014. Each accelerometer scour monitor was comprised of three individual accelerometers that were deployed in a vertical profile within the streambed.

Tags: fluvial-geomorphology, scour, usgs-5907bceae4b0fc4e448eb143
Organization: Department of the Interior
Coastwide Reference Monitoring System (CRMS) 2005, 2008, 2012, and 2015 Site 0614 Land-Water Matrix

Wetland restoration efforts conducted by the Coastal Wetlands Planning, Protection, and Restoration Act (CWPPRA) in Louisiana rely on monitoring efforts to determine the efficacy of these efforts. The Coastwide Reference Monitoring System (CRMS) was developed to assist in a multiple-reference approach that uses aspects of hydrogeomorphic functional assessments and probabilistic sampling for monitoring. The CRMS program includes a suite of approximately 390 sites that encompass the range of hydrological and ecological conditions for each stratum.  As part of CRMS, land and water classifications are created from Wetland restoration efforts conducted by the Coastal Wetlands Planning, Protection, and Restoration Act (CWPPRA) in Louisiana rely on monitoring efforts to determine the efficacy of these efforts. The Coastwide Reference Monitoring System (CRMS) was developed to assist in a multiple-reference approach that uses aspects of hydrogeomorphic functional assessments and probabilistic sampling for monitoring. The CRMS program includes a suite of approximately 390 sites that encompass the range of hydrological and ecological conditions for each stratum.  As part of CRMS, land and water classifications are created from Digital Orthophoto Quarter Quadrangles (DOQQs) approximately every three years at all CRMS sites.  This dataset consists of a matrix of four land-water products (2005, 2008, 2012, and 2015).  The resulting matrix has 16 possible classes defined by the combination of land and water categories on those four dates.

Tags: cartography, coastal, crms, doqq, geographic-information-system, imagerybasemapsearthcover, land-water, louisiana, mapping, marsh, protection, restoration, state-of-louisiana, usgs-5938764ee4b0764e6c5d6c32, wetland
Organization: Department of the Interior
Surface-sediment grain-size data from the mouth of the Columbia River, Oregon and Washington, 2013

This portion of the USGS data release presents sediment grain-size data from samples collected from the mouth of the Columbia River, Oregon and Washington, in 2013. Surface sediment was sampled using a small ponar, or 'grab', sampler on May 9, 2013 from the F/V Cape Windy at 3 locations. A handheld global navigation satellite system (GNSS) receiver was used to determine the locations of sediment samples. The grain size distributions of samples were determined using standard techniques developed by the USGS Pacific Coastal and Marine Science Center sediment lab. The grain-size data are provided in a comma-delimited spreadsheet (.csv).

Tags: clatsop-county, columbia-river, global-positioning-system-gps-observations, gps-global-positioning-system, grain-size-analysis, ocean-processes, oceans, pacific-county, sediment, sediment-transport, sedimentation, state-of-oregon, state-of-washington, substrate, usgs-590795e0e4b0fc4e448eb01d
Organization: Department of the Interior
Hydrodynamic modeling of the mouth of the Columbia River, Oregon and Washington, 2013

A process-based numerical model of the mouth of the Columbia River (MCR) and estuary, Oregon and Washington, was applied to simulate hydrodynamic conditions for the time period of the Office of Naval Research-funded River and Inlets Dynamics (RIVET II) field experiment conducted between May 9 and June 15, 2013.  The model application was constructed using Delft3D, an open-source software package used to solve the unsteady shallow water equations to simulate water motion due to tides, waves, wind, and buoyancy effects. This portion of the USGS data release describes the model application for this experiment and presents input files necessary to run the Delft3D model, as well as selected output from the model simulation.

Tags: clatsop-county, cmgp, coastal-and-marine-geology-program, columbia-river, delft3d, geoscientificinformation, hydrodynamics, marine-water-quality, modeling, oceans, pacific-coastal-and-marine-science-center, pacific-county, pcmsc, physical-oceanography, rivet-ii, state-of-oregon, state-of-washington, tides, u-s-geological-survey, usgs, usgs-59079594e4b0fc4e448eb013, water-column-features, waves, wind
Organization: Department of the Interior
Lagrangian drifter data from the mouth of the Columbia River, Oregon and Washington, 2013

Lagrangian surface currents were measured using drifters equipped with global navigation satellite system (GNSS) receivers. A total of 8 drifter deployments were performed between May 25 and June 8, 2013. For each deployment, drifters were released within the MCR and their positions were recorded until the drifters were recovered. The average duration of the drifter deployments varied between 1.6 h and 17.2 h and the number of drifters released in a deployment ranged between 11 and 84. The initial positions and timing of the release of the drifters relative to the tidal cycle varied throughout the drifter deployments. Digital files containing the drifter data from each deployment are available in NetCDF format.

Tags: clatsop-county, columbia-river, currents, geoscientificinformation, ocean-circulation, oceans, pacific-county, physical-oceanography, state-of-oregon, state-of-washington, usgs-5907955fe4b0fc4e448eb011, water-column-features
Organization: Department of the Interior
The influence of local- and landscape-level factors on wetland breeding birds in the Prairie Pothole Region of North and South Dakota dataset

The data set consists of data collected in 1995, 1996, and 1997 in wetlands in the Prairie Pothole Region of North Dakota and South Dakota.  The data were summarized and used in the analysis for a U.S. Geological Survey Open File Report entitled: The influence of local- and landscape-level factors on wetland breeding birds in the Prairie Pothole Region of North and South Dakota. The data consist of two data sets.  A species data set includes the common names, scientific names (species and genus), and four-letter alpha codes for 133 bird species observed during the three-year study.  The bird abundance data set includes the abundance of wetland birds by wetland class (temporary, seasonal, semipermanent, permanent, alkali), wetland type (natural or restored), and landowner group (private or federal). In conjunction with surveys of wetland birds, the following wetland variables also were recorded: wetland size, date (julian date), location (easting and northing), local-level habitat variables (percent coverage of open water, emergent vegetation, wet meadow, and shoreline/mudflat) and landscape-level habitat variables (number of wetlands and percent cover of grass and wetlands within 800 m of a wetland).

Tags: aquatic-birds, arrowwood-wetland-management-district, audubon-wetland-management-district, biota, birds, chase-lake-wetland-management-district, des-lacs-wetland-management-district, devils-lake-wetland-management-district, environmental-restoration, huron-wetland-management-district, j-clark-salyer-wetland-management-district, kulm-wetland-management-district, lake-andes-wetland-management-district, land-ownership, landscape, landscape-factors, local-factors, long-lake-wetland-management-district, lostwood-wetland-management-district, madison-wetland-management-district, north-dakota, prairie-pothole-region, sand-lake-wetland-management-district, south-dakota, tewaukon-wetland-management-district, usgs-59075940e4b0fc4e448ea87a, valley-city-wetland-management-district, waubay-wetland-management-district, wetland-birds, wetland-classification, wetland-ecosystems, wetland-restoration, wetlands
Organization: Department of the Interior