AndreaBozzo/ceres-open-data-index huggingface dataset:
Infection prevalence and viral load in pacific herring exposed to erythrocytic necrosis virus (ENV) at 3 temperatures

Viral erythrocytic necrosis (VEN) is a disease of marine and anadromous fishes, which is poorly understood, largely because its causative iridovirus, erythrocytic necrosis virus (ENV), is intractable to cell culture. Natural VEN epizootics and observations studies in wild populations suggest that temperature may be an important disease cofactor. Here, a controlled laboratory exposure study provides evidence for a direct relationship between temperature and the progression of viral erythrocytic necrosis (VEN) in Pacific herring. Waterborne exposure of Pacific herring to kidney homogenates containing ENV resulted in the establishment of infections, characterized by high infection prevalence (89%; 40/45) and mean viral loads (5.5 log10- gene copies / ug DNA) in kidney tissues at 44 d post exposure. Viral loads were higher in herring from the ambient (9.0 °C) and warm (13.5 °C) treatments (6.1 - 6.2 log10- gene copies / total DNA) than from the cool (6.9 °C) treatment (4.3 log10- gene copies / total DNA). Similarly, the peak proportion of diseased fish was directly related to temperature (P  0.001), with cytoplasmic inclusion bodies detected in 21% of herring from the cool, 52% from the ambient, and 60% from the warm treatments. The mean disease load in each fish (enumerated as the percent of erythrocytes with cytoplasmic inclusions), increased with temperature from 15% in the cool, 36% in the ambient, and 32% in the warm treatments at 44 days post exposure. Transcriptional analysis indicated that the number of differentially expressed genes among ENV-exposed herring increased with temperature, time post exposure, and viral load. Correlation network analysis of transcriptomic data showed robust activation of interferon and viral immune responses in hepatic tissue of infected individuals independent of other experimental variables.

Tags: biota, climate-change, disease-progression, dna-virus, herring, immune-response, pathogen, temperature, transcriptome, usgs-649f0f56d34ef77fcb041d7c, viral-load
Organization: Department of the Interior
Fractional estimates of invasive annual grass cover in dryland ecosystems of western United States (2016 – 2018).

Invasive annual grasses, such as cheatgrass (Bromus tectorum L.), have proliferated in dryland ecosystems of the western United States, promoting increased fire activity and reduced biodiversity that can be detrimental to socio-environmental systems. Monitoring exotic annual grass cover and dynamics over large areas requires the use of remote sensing that can support early detection and rapid response initiatives. Here, we integrated in situ observations, weekly composites of harmonized Landsat and Sentinel-2 (HLS) data, maps of biophysical variables (e.g. soils and topography) and machine learning techniques to develop fractional estimates of exotic annual grass cover at a 30-m spatial resolution from 2016 to 2018. Comparisons with Bureau of Land Management Assessment, Inventory, and Monitoring (AIM) field data (2016 and 2017) indicate good agreement between observed and mapped values (n = 1700; r = 0.83; mean absolute error [MAE] = 11), as constructed from an ensemble of regression tree models, with slightly lower agreement between mapped values and independent field observations (n = 112; r = 0.65; MAE =14). Geographic coverage of the study area includes portions of Oregon, California, Idaho, and Nevada.

Tags: biota, cheatgrass, imagerybasemapsearthcover, invasive-species, rangeland-ecosystems, remote-sensing, usgs-5e00f1c6e4b0b207aa033d39
Organization: Department of the Interior
Coastwide Reference Monitoring System (CRMS) 2005, 2008, 2012, 2016, 2018, and 2021 Site 0377 land-water matrix

Wetland restoration efforts conducted by the Coastal Wetlands Planning, Protection and Restoration Act (CWPPRA) in Louisiana rely on monitoring to determine the efficacy of these projects. 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 six land-water products (2005, 2008, 2012, 2016, 2018, and 2021).  The resulting matrix has 64 possible classes defined by the combination of land and water categories on those six dates.

Tags: alteration-of-wetland-habitats, cartography, coastal, coastal-louisiana, crms, doqq, emergent-wetland, forested-wetland, geographic-information-system, imagerybasemapsearthcover, land-water, louisiana, mapping, marsh, protection, restoration, scrub-shrub-wetland, state-of-louisiana, usgs-6541501fd34ee4b6e05bce76, wetland, wetland-ecosystems, wetland-restoration
Organization: Department of the Interior
Basin Characteristics and Streamflow Statistics for Selected Gages, Alaska, USA (ver. 2.0, September, 2022)

This data release documents the data used for the associated publication "Evaluating hydrologic region assignment techniques for ungaged watersheds in Alaska, USA" (Barnhart and others, 2022) The data sets within this release are stored in 14 files: (1) Streamflow observations and sites used. (2) Statistically estimated streamflow values computed for each site. (3) Streamflow statistics computed from observed and estimated streamflow values at each site, basin characteristics for each site, and hydrologic regions (clusters) for each site. (4) A dataset describing the optimal number of hydrologic regions into which the considered sites were grouped. (5) P-values from a multiple comparisons analysis testing for statistical differences between clusters for each basin characteristic and streamflow statistic. (6) A matrix of zeros and ones describing the performance of each hydrologic region assignment technique considered in the publication associated with this release. (7) A dataset of variable importance generated by random forest modeling-based hydrologic region assignment techniques evaluated. (8-14) Daily datasets of simulated SnowModel (Liston and Elder, 2006) runoff (snowmelt + rainfall), precipitation, glacial melt, snow water equivalent, snow covered area, liquid precipitation, and air temperature for Alaska, USA at a 1 km grid cell size.

Tags: hydrologic-region, inlandwaters, random-forest, regionalization, snow-and-ice-cover, usgs-61561875d34e0df5fb9ec108
Organization: Department of the Interior
Water Chemistry of Great Lakes Tributaries, 2017-2018

Chemical composition of fish bones can be used to trace fish migrations and other movements (e.g., use of tributaries for spawning). Chemical composition of water is required to be able to trace fish migrations or movements to particular rivers or streams. Because water chemistry can change over time due to changes in land use, tectonic movements that alter groundwater pathways, pollution, industrial activity, and potentially other sources, periodic re-assessment of water chemistry is required. Here we present data on concentrations of common elements for several tributary streams to Lake Michigan, Lake Erie, and Lake Ontario collected in 2017 and 2018. These data will be useful to anyone desiring to track fish usage of these tributaries or changes in water chemistry resulting from land use changes.

Tags: environment, great-lakes, inlandwaters, lake-erie, lake-michigan, lake-ontario, usgs-5d306afde4b01d82ce84a7a1, water-chemistry
Organization: Department of the Interior
Geologic Faults of Afghanistan (fltafg)

This shapefile contains polylines that describe geologic faults in Afghanistan taken from the Geologic and Mineral Resource Map of Afghanistan..

Tags: af, afghan, geologic-faults, geoscientificinformation, islamic-state-of-afghanistan, northern-afghanistan, oilgas, usgs-60a81721d34ea221ce4e5b5c, wep, worldgeologicmaps
Organization: Department of the Interior
Wind rose plots for the volcano: 300082  Tolmachev Dol

This zip folder contains ASCII text files of vectors at the specified volcano at 
12-hour intervals, 
from January 1, 1990 through December 28, 2009.  
The wind vectors are divided into five files, names by their elevation range above 
sea level in the atmosphere: 00-05km.txt; 05-11km.txt; 11-16km.txt; 16-24km.txt; 
and 24-30km.txt. 
The zip folder also contains a subfolder "figures", with Wind rose plots of wind 
direction and speed over 
this time period.  The plots are by season, and by elevation, given a total of 20 
plots (4 seasons, 5 
elevation ranges).  A summary plot is also included which gives the year-round 
wind pattern at the volcano, 
at 0-5 km elevation.  Plots are in both jpg and pdf format.

Tags: meteorology, usgs-58d01474e4b0236b68f52e34, volcanic-ash, volcanic-eruption-forecasting, wind
Organization: Department of the Interior
DS926 Digital surfaces and thicknesses of selected hydrogeologic units of the Floridan aquifer system in Florida and parts of Georgia, Alabama, and South Carolina -- Polygons representing thickness of the upper confining unit of the Floridan aquifer system

Digital surfaces and thicknesses of selected hydrogeologic units of the Floridan aquifer system 
were developed to define an updated hydrogeologic framework as part of the U.S. Geological 
Survey Groundwater Resources Program. This feature class contains polygon regions that 
represent thickness of the upper confining unit of the Floridan aquifer system.

Tags: alabama, environment, extent, florida, floridan-aquifer-system, geology, georgia, geoscientificinformation, hydrogeology, ias, icu, inlandwaters, intermediate-aquifer-system, intermediate-confining-unit, regional-groundwater-availability-study, regions, south-carolina, stratigraphy, thickness, united-states-geological-survey, upper-confining-unit, usgs, usgs-3c2a6d2e-c552-4cbf-8c1b-b4dbd8fd39b4
Organization: Department of the Interior
U.S. Geological Survey calculated recurrence interval of sediment mobility at select points in the South Atlantic Bight for May 2010 to May 2011 (SAB_mobile_freq, Geographic, WGS 84)

The U.S. Geological Survey has been characterizing the regional variation in shear stress on the sea floor and sediment mobility through statistical descriptors.  The purpose of this project is to identify patterns in stress in order to inform habitat delineation or decisions for anthropogenic use of the continental shelf.  The statistical characterization spans the continental shelf from the coast to approximately 120 m water depth, at approximately 5 km resolution.  Time-series of wave and circulation are created using numerical models, and near-bottom output of steady and oscillatory velocities and an estimate of bottom roughness are used to calculate a time-series of bottom shear stress at 1-hour intervals.  Statistical descriptions such as the median and 95th percentile, which are the output included with this database, are then calculated to create a two-dimensional picture of the regional patterns in shear stress.  In addition, time-series of stress are compared to critical stress values at select points calculated from observed surface sediment texture data to determine estimates of sea floor mobility.

Tags: alteration-of-benthic-habitats, atlantic-ocean, bottom-shear-stress, cape-canaveral, carolinian-ecoregion, chesapeake-bay, cmgp, cmhrp, cmsp, coastal-and-marine-geology-program, coastal-and-marine-hazards-and-resources-program, coastal-and-marine-spatial-planning, continental-island-shelf, current, florida-keys, floridian-ecoregion, geoscientificinformation, grant-madsen, habitat-alteration-and-disturbance, marine-nearshore-subtidal, marine-offshore-subtidal, mathematical-modeling, north-america, numerical-modeling, ocean-processes, oceans, outer-banks, pamlico-sound, predictions, recurrence-interval, roms, sea-floor, sea-floor-characteristics, sea-floor-habitat, seabed, seafloor, sediment-mobility, sediment-transport, south-atlantic-bight, substrate, swan, u-s-east-coast, u-s-geological-survey, united-states, usgs, usgs-52fb8c61-0469-4fee-bb9e-325a207bc4d7, wave, whcmsc, woods-hole-coastal-and-marine-science-center
Organization: Department of the Interior
Regional-scale Model Predictions of the Relation Between Biological Integrity and Streamflow Modification

The US Geological Survey (USGS) conducted a study (Carlisle and others 2017) with a national-scale dataset composed of ecological data from the USGS National Water-Quality Assessment Project and the US Environmental Protection Agency, matched to USGS streamgaging sites.  In a follow-up study (Carlisle and others 2019), additional data from three regional assessments conducted by USGS were combined with data from the original study, and these new data are published here.  Using all of the aforementioned datasets, the follow-up study (Carlisle and others, 2019) then developed regional-scale model predictions of the relation between streamflow modification and indicators of biological integrity.  These model predictions, presented as graphics, are published here.

Tags: biota, central-and-southern-plains-united-states, conterminous-united-states, eastern-highlands-united-states, ecological-assessment, northeast-highlands-ecoregion, northeast-united-states, southeast-united-states, southern-rocky-mountains-ecoregion, streamflow, usgs-5c0fcd6fe4b0c53ecb2d1b40, western-mountains-united-states, western-xeric-united-states
Organization: Department of the Interior
Study Reach 6 Terrestrial Light Detection and Ranging Topographic Data in Caulks Creek, Wildwood, Missouri, 2022–2023

Topographic data were collected along study reach 6 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 six subsections (A-F) for each of the four survey dates (March 2022, July 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-66510d43d34e702fe8748c79, wildwood
Organization: Department of the Interior
Lake Houston (Texas) EFDC hydrodynamic model for water-surface elevation and specific conductance simulations, 2009-2017

The U.S. Geological Survey (USGS), in a partnership with ExxonMobil Corporation, developed an updated Lake Houston EFDC model for predicting water-surface elevation, residence time, water temperature, and salinity. The original model was developed and calibrated by using 2009 data and verified by using 2010 data, whereas the enhanced model (baseline model) of this project was calibrated for the years 2009 through 2011 and verified using 2012 through 2017 data. Modifications were made to the original Lake Houston EFDC model (Rendon and Lee, 2015). One of the primary partnership goals was to understand the impact of the Luce Bayou Interbasin Transfer on specific conductance. Three additional model simulations were run to evaluate different proposed Luce Bayou Interbasin Transfer flow scenarios.

Tags: efdc, harris-county, houston-tx, lake-houston, surface-water, usgs-5c76aee5e4b0fe48cb4bdb12, water-quality
Organization: Department of the Interior
Wind rose plots for the volcano: 300710  Iettunup

This zip folder contains ASCII text files of vectors at the specified volcano at 
12-hour intervals, 
from January 1, 1990 through December 28, 2009.  
The wind vectors are divided into five files, names by their elevation range above 
sea level in the atmosphere: 00-05km.txt; 05-11km.txt; 11-16km.txt; 16-24km.txt; 
and 24-30km.txt. 
The zip folder also contains a subfolder "figures", with Wind rose plots of wind 
direction and speed over 
this time period.  The plots are by season, and by elevation, given a total of 20 
plots (4 seasons, 5 
elevation ranges).  A summary plot is also included which gives the year-round 
wind pattern at the volcano, 
at 0-5 km elevation.  Plots are in both jpg and pdf format.

Tags: meteorology, usgs-58d01508e4b0236b68f52ee4, volcanic-ash, volcanic-eruption-forecasting, wind
Organization: Department of the Interior
Coastwide Reference Monitoring System (CRMS) 2005, 2008, 2012, and 2015 Site 0656 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-5938772fe4b0764e6c5d6ca3, wetland
Organization: Department of the Interior
A finite-difference algorithm used to simulate one-dimensional diffusion and adsorption of trichloroethene in a rock matrix

Simulations of one-dimensional (1-D) diffusion and adsorption of trichloroethene (TCE) in a 
rock matrix are conducted using rock properties identified from a mudstone aquifer in the 
Newark Basin, near West Trenton, New Jersey. The simulations are conducted using a 
finite-difference algorithm that was prepared for this investigation to solve the equation 
for 1-D diffusion and linear equilibrium adsorption. The simulations are conducted for a 
hypothesized 1-D section of a rock matrix and the georeferencing is based on the locations 
of the rock core samples that were collected and analyzed as part of this investigation. 
The rock matrix is assumed to be adjacent to a fracture, where the TCE concentration 
in the fracture is responsible for diffusion into and out of the rock matrix. The fraction of 
organic carbon (foc) in the rock matrix can either be spatially uniform or spatially variable. 
Spatial variability in foc is defined from the mean and standard deviation of a log-normally 
distributed parameter. Other rock properties controlling the diffusion and adsorption of TCE 
in the rock matrix are assumed to be spatially uniform. Simulations of diffusion and adsorption 
into the rock matrix are conducted for four cases. These cases are: 
(1) spatially uniform foc equal to the average of foc from all rock samples; 
(2) spatially uniform foc equal to the maximum foc from all rock samples; 
(3) spatially uniform foc equal to the average foc from the Black Fissile (BLK-FIS) mudstone samples; 
(4) spatially variable foc defined from the statistics of the BLK-FIS mudstone samples. This USGS 
data release contains all of the input and output files for the simulations described in the associated 
journal article (https://doi.org/10.1016/j.jconhyd.2018.09.001).

Tags: adsorption, carbon, contaminant-transport, environment, geoscientificinformation, inlandwaters, lockatong-formation, mathematical-simulation, mercer-county, mudstone, new-jersey, newark-basin, sedimentary-rocks, usgs-9da6cb09-c60a-4ea9-a7ee-2fbbab3e258c, usgsgroundwatermodel, west-trenton
Organization: Department of the Interior
Bathymetric trackline navigation collected by the U.S. Geological Survey within the St. Clair River between Michigan and Ontario, Canada, 2008 (ESRI VECTOR SHAPEFILE, 08016_SWATHPLUS_TRK.SHP)

In 2008, the U.S. Geological Survey (USGS), Woods Hole Coastal and Marine Science Center (WHCMSC), in cooperation with the U.S. Army Corps of Engineers conducted a geophysical and sampling survey of the riverbed of the Upper St. Clair River between Port Huron, MI, and Sarnia, Ontario, Canada. The objectives were to define the Quaternary geologic framework of the St. Clair River to evaluate the relationship between morphologic change of the riverbed and underlying stratigraphy. This report presents the geophysical and sample data collected from the St. Clair River, May 29-June 6, 2008 as part of the International Upper Great Lakes Study, a 5-year project funded by the International Joint Commission of the United States and Canada to examine whether physical changes in the St. Clair River are affecting water levels within the upper Great Lakes, to assess regulation plans for outflows from Lake Superior, and to examine the potential effect of climate change on the Great Lakes water levels ( http://www.iugls.org). This document makes available the data that were used in a separate report, U.S. Geological Survey Open-File Report 2009-1137, which detailed the interpretations of the Quaternary geologic framework of the region. This report includes a description of the suite of high-resolution acoustic and sediment-sampling systems that were used to map the morphology, surficial sediment distribution, and underlying geology of the Upper St. Clair River during USGS field activity 2008-016-FA . Video and photographs of the riverbed were also collected and are included in this data release. Future analyses will be focused on substrate erosion and its effects on river-channel morphology and geometry. Ultimately, the International Upper Great Lakes Study will attempt to determine where physical changes in the St. Clair River affect water flow and, subsequently, water levels in the Upper Great Lakes.

Tags: bathymetry, canada, cmgp, coastal-and-marine-geology-program, esri-vector-shapefile, geophysics, geoscientificinformation, geospatial-datasets, great-lakes, inlandwaters, interferometry, lake-huron, michigan, navigational-data, north-america, ontario, sea-swathplus-234-khz, st-clair-river, swath-bathymetry, trackline-navigation, u-s-geological-survey, united-states, upper-great-lakes, upper-st-clair-river, usgs, usgs-573e95d1-ec46-431a-8de2-5c2d647df453, usgs-r-v-rafael, whcmsc, whcmsc-field-activity-serial-number-08016, woods-hole-coastal-and-marine-science-center
Organization: Department of the Interior