AndreaBozzo/ceres-open-data-index huggingface dataset:
Xenpous leavis deiodinase type 3 enzyme activity characterization and chemical screening data

Data set includes optimized assay parameters and kinetic characterization for xenopus laevis deiodinase type 3 enzyme, and inhibition activity of 352 ToxCast chemicals against this enzyme. 

This dataset is associated with the following publication:
Mayasich, S., J. Korte, J. Denny, P. Hartig, J. Olker, P. Degoey, J. O'Flanagan, S. Degitz, and M. Hornung. Xenopus laevis and human type 3 iodothyronine deiodinase enzyme cross-species sensitivity to inhibition by ToxCast chemicals.   TOXICOLOGICAL SCIENCES. Society of Toxicology, RESTON, VA,  73: 105141, (2021).

Tags: deiodinase, enzyme-activity, thyroid, xenopus
Organization: U.S. Environmental Protection Agency
Estuarine Habitat and Juvenile Dungeness Crab Data (2010-2011)

This dataset contains juvenile Dungeness crab (Cancer magister) abundance data and associated habitat data from three estuaries in Oregon (Tillamook, Yaquina, and Alsea bays).  These data were collected by EPA surveys in 2010-2011.  Additionally, this dataset includes areal data on National Wetlands Inventory (NWI) habitat classes within our study areas. 

This dataset is associated with the following publication:
Lewis, N., D. Young, C. Folger, and T. DeWitt. Assessing the Relative Importance of Estuarine Nursery Habitats – a Dungeness Crab (Cancer magister) Case Study.   Estuaries and Coasts. Estuarine Research Federation, Port Republic, MD, USA,  s12237-020-00821-1, (2020).

Tags: ecological-production-function, ecosystem-services, estuary, final-ecosystem-goods-and-services-fegs, fishery, habitat, shellfish
Organization: U.S. Environmental Protection Agency
Application of a multiplex salivary immunoassay to detect sporadic incident norovirus infections

Epidemiology data from beachgoers including demographic details. Results from saliva tests for markers of  infection with waterborne pathogens. This dataset is not publicly accessible because: EPA cannot release personally identifiable information regarding living individuals, according to the Privacy Act and the Freedom of Information Act (FOIA). This dataset contains information about human research subjects. Because there is potential to identify individual participants and disclose personal information, either alone or in combination with other datasets, individual level data are not appropriate to post for public access. Restricted access may be granted to authorized persons by contacting the party listed. It can be accessed through the following means: Contact Tim Wade (wade.tim@epa.gov) for details regarding data access. Format: Data are stored in SAS datasets and MS Excel files. Data are documented with codebooks in MS Word describing variables. 

This dataset is associated with the following publication:
Wade, T., S. Griffin, A. Egorov, E. Sams, E. Hudgens, S. Augustine, S. Deflorio-Barker, T. Plunkett, A. Dufour, J. Styles, and K. Oshima. Application of a multiplex salivary immunoassay to detect sporadic incident norovirus infections.   Scientific Reports. Nature Publishing Group, London,  UK, 9(19576): 1, (2019).

Tags: beach-water-quality, diarrhea, swimming
Organization: U.S. Environmental Protection Agency
Quantitative response-response relationships linking aromatase inhibition to decreased fecundity are conserved across three fishes with asynchronous oocyte development

Data used in the creation of each figure and table cited in Doering et al. (2019; DOI: 10.1021/acs.est.9b02606) are provided. 

This dataset is associated with the following publication:
Doering, J., D. Villeneuve, S. Poole, B. Blackwell, K. Jensen, M. Kahl, A. Kittelson, D. Feifarek, C. Tilton, C. Lalone, and G. Ankley. Quantitative response-response relationships linking aromatase inhibition to decreased fecunditiy are conserved across three fishes with asynchronous oocyte development.   ENVIRONMENTAL SCIENCE & TECHNOLOGY. American Chemical Society, Washington, DC, USA, 53(17): 10470-10478, (2019).

Tags: adverse-outcome-pathway, aquatic-ecosystems, ecotoxicology, endocrine-disruption, fathead-minnow, japanese-medaka, screening-and-prioritization, zebrafish
Organization: U.S. Environmental Protection Agency
ESR1 expression and DNA methylation data for FHM exposed to EE2

This dataset contains data for adult male fathead minnows exposed to EE2 (a synthetic estrogen). It is a targeted study on the response of the esr1 gene (expression and DNA methylation profiles) to estrogen exposure. It contains mean and standard deviation for DNA methylation levels per treatment group, and gene expression data. 

Tags: dna-methylation, epigenetics, esr1, estrogen-receptor, fathead-minnow, gene-expression
Organization: U.S. Environmental Protection Agency
Intersection of Natural Hazard Vulnerability and Superfund Site Location

Spreadsheet lists all active and upcoming Superfund sites and their vulnerability to 12 natural hazards using a vulnerability score between 0 and 100. 

This dataset is associated with the following publication:
Summers, K., A. Lamaper, and K. Buck. National Hazards Vulnerability and the Remediation, Restoration and Revitalization of Contaminated Sites – 1. Superfund.   ENVIRONMENTAL MANAGEMENT. Springer-Verlag, New York, NY, USA,  14, (2021).

Tags: exposure, natural-hazards, superfund, toxic-releases
Organization: U.S. Environmental Protection Agency
Intersection of Natural Hazard Vulnerability and RCRA Site Location

Co-occurrence of natural hazard exposures and RCRA site locations at the county level where natural hazards are in the top quartile of exposures. 

This dataset is associated with the following publication:
Summers, K., A. Lamper, and K. Buck. National Hazards Vulnerability and the Remediation, Restoration and Revitalization of Contaminated Sites – 2. RCRA Sites..   Sustainability. MDPI AG, Basel,  SWITZERLAND, 13(2): 16, (2021).

Tags: exposure, natural-hazards, rcra, toxic-releases
Organization: U.S. Environmental Protection Agency
Data for effects resulting from exposure to dioxin, and observed survival and fecundity by age and size for unexposed populations

These laboratory data for estimates of change in fertility and survival rates observed relative to control (unexposed) conditions for fundulus heteroclitus exposed to varying levels of 2,3,7,8-tetrachlorodibenzo-p-dioxin including 112, 296, and 875 pg/g are relative rates, and thus they are unitless.

The data for observed survival and fecundity by age and size for populations of fundulus heteroclitus that were considered unexposed to chemical stressors contains the following units:  survival rates are fraction surviving per year and fecundity rates are eggs per year. 

This dataset is associated with the following publication:
Miller, D., B. Clark, and D. Nacci. A multidimensional density dependent matrix population model for assessing risk of stressors to fish populations.   ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY. Elsevier Science Ltd, New York, NY, USA, 201: 1-8, (2020).

Tags: density-dependence, ecological-risk-assessment, matrix-models, population-ecology
Organization: U.S. Environmental Protection Agency
County-Level Human Well-Being Index and Domain Scores (2000-2010) plus EQI data set (2000-2005)

The HWBI_Draft_1 is an internal map service being prepared for public release (early FY18). This map services contains mean county-level HWBI, domain, indicators and service scores related to research efforts completed in 2014. The EQI map service is a publically accessible map services that contains average county-level results for 2000-2005. 

This dataset is associated with the following publication:
Harwell, L., L. Smith, and K. Summers. Modified HWBI Model(s) Linking Service Flows to Well-Being Endpoints: Accounting for Environmental Quality. U.S. Environmental Protection Agency, Washington, DC, USA, 2017.

Tags: composite-index, eqi, hwbi, indicators
Organization: U.S. Environmental Protection Agency
Sustainable Strategy Utilizing Biomass: Visible-Light-Mediated Synthesis of gamma-Valerolactone

A novel sustainable approach to valued g-valerolactone was investigated.
This approach exploits the visible-light-mediated conversion of biomass-derived levulinic acid by using a bimetallic catalyst on a graphitic carbon nitride, AgPd@g-C3N4. 

This dataset is associated with the following publication:
Verma, S., R.B.N. Baig, M. Nadagouda , and R. Varma. Sustainable Strategy Utilizing Biomass: Visible-Light-Mediated Synthesis of γ-Valerolactone.   ChemCatChem. Wiley-VCH, WEINHEIM,  GERMANY, 8(4): 872, (2016).

Tags: biomass, biomass-heterogeneous-catalysis-levulinic-acid, earth-abundant-materials, heterogeneous-catalysis, levulinic-acid, sustainable-materials-management, valerolactone
Organization: U.S. Environmental Protection Agency
Decadal DSMs of Apollo Bay, Victoria, Australia, 1946, 66, 71, 77 and 86

Decadal DSMs, photomosaics and point clouds of of Apollo Bay, Victoria, Australia, created through Structure-from-Motion (SfM) technique applied to historical aerial photography taken in May 1946, Mar 1966, Jan 1971, Feb 1977 and Mar 1986.

These datasets were originally generated to quantify decadal volumetric changes along sandy beaches of the iconic Great Ocean Road, in Australia. Results of this study, as well as further details of these datasets were published elsewhere (Carvalho, R. C. et al. Quantifying decadal volumetric changes along sandy beaches using improved historical aerial photographic models and contemporary data. Earth Surface Processes and Landforms, 2021).



Organization: OpenTopography
High Resolution Topography of the  Bolokenu-Aqikekuduk (Dzhungarian) Fault

This dataset comprises two high-resolution structure-from-motion (SfM) models (<0.5 m/pixel) surveyed by a small four-rotor unmanned drones along the active right-lateral strike-slip Bolokenu -Aqikekuduk (Dzhungarian) Fault  in the northern Tian Shan. The flight height of unmanned drones was set from 100 to 150 m based on the different target areas. The images were processed with Agisoft Photoscan Pro software. 

Organization: OpenTopography
A state-of-the-science review of chemical and non-chemical stressors found in the built and natural environments and how they may impact American Indian/Alaska Native children’s health and well-being: Dataset

Data gathered from 35 published references (until 2016) targeting built and natural environment stressors for American Indian/Alaska Native children. 

This dataset is associated with the following publication:
Barros, N., N. Tulve, D. Heggem, and K. Bailey. Review of built and natural environment stressors impacting American-Indian/Alaska-Native children.   REVIEWS ON ENVIRONMENTAL HEALTH. Freund Publishing House Limited, Tel Aviv,  ISRAEL, 33(4): 349–381, (2018).

Tags: american-indian-alaska-native, built-environment, children, natural-environment, state-of-the-science-review, stressors
Organization: U.S. Environmental Protection Agency
Enhancements to AERMOD’s Building Downwash Algorithms based on Wind-Tunnel and Embedded-LES Modeling -BDW-2

This data set is associated with the results found in the journal article: Monbureau et al, 2018. Enjancements to AERMOD's building downwash algorithms based on wind-tunnel and Embedded-LES modeling. Atmospheric Environment, https://doi.org/10.1016/j.atmosenv.2018.02.022. 
The goal of this study is to improve AERMOD's ability to accurately model important and complex building downwash scenarios by incorporating knowledge gained from a recently completed series of wind tunnel studies and complementary large eddy simulations of flow and dispersion around simple structures for a variety of building dimensions, stack locations, stack heights, and wind angles. This study presents three modifications to the building downwash algorithm in AERMOD that improve the physical basis and internal consistency of the model, and one modification to AERMOD's building pre-processor to better represent elongated buildings in oblique winds. These modifications are demonstrated to improve the ability of AERMOD to model observed ground-level concentrations in the vicinity of a building for the variety of conditions examined in the wind tunnel and numerical studies. 

This dataset is associated with the following publication:
Monbureau, E., D. Heist, S. Perry, L. Brouwer, H. Foroutan , and W. Tang. Enhancements to AERMOD's building downwash algorithms based on wind-tunnel and Embedded-LES modeling.   ATMOSPHERIC ENVIRONMENT. Elsevier Science Ltd, New York, NY, USA, 179: 321-330, (2018).

Tags: building-downwash, cfd, dispersion-modeling, wind-tunnel
Organization: U.S. Environmental Protection Agency
"MS-Ready” structures for non-targeted high-resolution mass spectrometry screening studies

The dataset(s) supporting the conclusions of this article are available via the CompTox Chemistry Dashboard Downloads Page (https://comptox.epa.gov/dashboard/downloads) and MS-Ready GitHub repository (https://github.com/kmansouri/MS-ready). The MetFrag functionality is available through the web interface (https://msbi.ipb-halle.de/MetFragBeta/) and the command line version (http://c-ruttkies.github.io/MetFrag/projects/metfragcl/). All additional data supporting the conclusions of this article are included within the article and its additional files. 

This dataset is associated with the following publication:
McEachran, A., K. Mansouri, C. Grulke, E. Schymanski, C. Ruttkies, and A. Williams. “MS-Ready” structures for non-targeted high-resolution mass spectrometry screening studies.   Journal of Cheminformatics. Springer, New York, NY, USA, 10(45): 1-16, (2018).

Tags: actor, database-searching, high-resolution-mass-spectrometry-hrms, structure-curation, structure-identification
Organization: U.S. Environmental Protection Agency
Informing Future Risks of Record‐Level Rainfall in the United States

One supplemental file, one link to a repository where the complete matlab code can be found to reproduce the study (41 files). Citation information for this dataset can be found in the EDG's Metadata Reference Information section and Data.gov's References section.

Tags: climate-change, clustering, extreme-rainfall, extreme-value-analysis, record-precipitation
Organization: U.S. Environmental Protection Agency
Pensacola watershed case study

This data set contains the spatial layers that were input into ecosystem services models (Maps.zip), including the A2 and B1 landuse change scenarios, and the polygon boundaries for the Pensacola watershed.  This dataset also includes the future climate data (ClimateData.csv) used in scenarios.  Model output for 20 stochastic runs of each A2 and B1 scenario is included in three files: 1) the calculated ES metrics that were used to calculate ES indicators (ESMetrics_CountyYearly.xlsx), 2) the scaled ES indicators used as input into HWBI regression models (ESIndicators_CountyYearly.xlsx), and 3) the calculated HWBI Domain and composite scores (HWBIDomains_CountyYearly.xlsx). 

This dataset is associated with the following publication:
Yee, S., E. Paulukonis, C. Simmons, M. Russell, R. Fulford, L. Harwell, and L. Smith. Projecting effects of land use change on human well-being through changes in ecosystem services.   ECOLOGICAL MODELLING. Elsevier Science BV, Amsterdam,  NETHERLANDS, 440(109358): 20, (2021).

Tags: ecosystem-services, forecasting, human-well-being-index, land-use-change, relationship-functions
Organization: U.S. Environmental Protection Agency
Sustainability Index _MSAs

Calculation of average sustainability in US Metropolitan and Micropolitan areas. Three domains of sustainability are measured: economic, social, and environmental. 

This dataset is associated with the following publication:
Buck, K., K. Summers, and L. Smith. Investigating the relationship between environmental quality, socio-spatial segregation and the social dimension of sustainability in US urban areas.   Sustainable Cities and Society. Elsevier B.V., Amsterdam,  NETHERLANDS, 67(102732): 11, (2021).

Tags: community, economic-analysis, environmental-quality, neighborhoods, resilience, segregation, social-economical-status, sustainability, vulnerability
Organization: U.S. Environmental Protection Agency
HWBI Domain and Services Metrics for Puerto Rico 2000-2017

This data set provides the compile metrics for HWBI domains and services for Puerto Rico from 2000-2017, as well as the downscaled and scaled metrics and aggregated indicators used for statistical analyses. 

This dataset is associated with the following publication:
Yee, S. Contributions of Ecosystem Services to Human Well-being in Puerto Rico.   Sustainability. MDPI AG, Basel,  SWITZERLAND, 12(22): 38, (2020).

Tags: ecosystem-services, human-well-being, spatial-interpolation
Organization: U.S. Environmental Protection Agency
Segregation_Indices_2015

There are two excel data sheets with index values for each of the five minority groups assessed. In addition, there are two zip files with shapefiles containing the same index values. 

This dataset is associated with the following publication:
Buck, K., K. Summers, and L. Smith. Investigating the relationship between environmental quality, socio-spatial segregation and the social dimension of sustainability in US urban areas.   Sustainable Cities and Society. Elsevier B.V., Amsterdam,  NETHERLANDS, 67(102732): 11, (2021).

Tags: community, neighborhoods, resilience, segregation, vulnerability
Organization: U.S. Environmental Protection Agency
Human Well-Being Domain and Composite Scores 2000-2017

This data set contains the average census tract-scale scores, from 2000-2013, for the composite HWBI, each domain within the HWBI, each indicator within domains, and each metric within indicators.  Domain and composite scores at the beginning and end of the study period (2000, 2013) are also given. 

This dataset is associated with the following publication:
Yee, S., E. Paulukonis, and K. Buck. Downscaling a human well-being index for environmental management and environmental justice applications in Puerto Rico.   Applied Geography. ELSEVIER, AMSTERDAM,  HOLLAND, 123: 14, (2020).

Tags: human-well-being, spatial-interpolation
Organization: U.S. Environmental Protection Agency
Peripheral Metabolic Effects of Ozone Exposure in Healthy and Diabetic Rats on Normal or High-Cholesterol Diet

In this study, using male Wistar and Wistar-derived Goto-Kakizaki (GK) rats, which exhibit a non-obese type-2 diabetes phenotype, we investigated whether two key metabolic stressors, type-2 diabetes and a high-cholesterol atherogenic diet, exacerbate ozone-induced metabolic effects. Rats were fed a normal control diet (ND) or high-cholesterol diet (HCD) for 12 weeks starting at 4 week-age and then exposed to filtered air or 1.0-ppm ozone (6h/day) for 1 or 2 days. Metabolic responses were analyzed at the end of each day and after an 18-hour recovery period following the 2-day exposure. 

This dataset is associated with the following publication:
Snow, S., A. Henriquez, A. Fisher, B. Vallanat, J. House, M.C. Schladweiler, C. Wood, and U. Kodavanti. Peripheral Metabolic Effects of Ozone Exposure in Healthy and Diabetic Rats on Normal or High-Cholesterol Diet.   TOXICOLOGY AND APPLIED PHARMACOLOGY. Academic Press Incorporated, Orlando, FL, USA, 415(115427): 1, (2021).

Tags: adipose-tissue, liver, metabolic-response, ozone, type-2-diabetes-rat-model, western-high-cholesterol-diet
Organization: U.S. Environmental Protection Agency
Diets Enriched with Coconut, Fish, and Olive Oil Modify Peripheral Metabolic Effects of Ozone in Rats

In this study male Wistar Kyoto rats maintained on diets enriched with coconut, fish or olive oil were compared with animals receiving normal diet for 8 weeks. After 8 weeks of dietary regimen, and while on respective diets, animals were exposed to air or 0.8 ppm ozone for 4 hours per day for 2 consecutive days and necropsies were performed post air or ozone exposure within 2 hours. Body weights, food consumption and body composition were assessed during dietary regimen. At necropsy, livers were stained for lipids, serum lipids and metabolic hormones were assessed, and liver, muscle and adipose tissues are assessed for gene expression using targeted Illumina sequencing for selected genes. Based on reviewers comments during revision period, circulating n-3, n-6, n-9 and unsaturated fatty acids were assessed in the serum through collaboration with Jenifer I. Fenton and Travis Goeden, Michigan State University where samples were shipped for analysis of these lipids using mass spectrometry. These data were incorporated in the manuscript (Table 1) and part of figure 3. 

This dataset is associated with the following publication:
Snow, S., A. Henriquez, W. Cheng, A. Fisher, B. Vallanat, M. Angrish, J. Richards, M.C. Schladweiler, C. Wood, H. Tong, and U. Kodavanti. Diets Enriched with Coconut, Fish, and Olive Oil Modify Peripheral Metabolic Effects of Ozone in Rats.   TOXICOLOGY AND APPLIED PHARMACOLOGY. Academic Press Incorporated, Orlando, FL, USA, 410(1): 115337, (2020).

Tags: adipose-tissue, circulating-fatty-acids, fish-oil-enriched-diet, liver, muscle, olive-oil-enriched-diet, ozone
Organization: U.S. Environmental Protection Agency
Pulmonary and Vascular Effects of Acute Ozone Exposure in Diabetic Rats Fed an Atherogenic Diet

In this study, we investigated effects of inhaled ozone exposure and high-cholesterol diet (HCD) in healthy Wistar and Wistar-derived Goto-Kakizaki (GK) rats, a non-obese model of type 2 diabetes. Male rats (4-week old) were fed normal diet or HCD for 12 weeks and then exposed to filtered air or 1.0 ppm ozone (6hrs/day) for 1 or 2 days. We examined pulmonary, vascular, hematology, and inflammatory responses after each exposure plus an 18-hr recovery period. 

This dataset is associated with the following publication:
Snow, S., A. Henriquez, L. Thompson, C. Fisher, M.C. Schladweiler, C. Wood, and U. Kodavanti. Pulmonary and Vascular Effects of Acute Ozone Exposure in Diabetic Rats Fed an Atherogenic Diet.   TOXICOLOGY AND APPLIED PHARMACOLOGY. Academic Press Incorporated, Orlando, FL, USA, 415(115430): 1, (2021).

Tags: pulmonary-injury, systemic-inflammation, type-2-diabetes-rat-model, vasocontraction, western-high-cholesterol-diet
Organization: U.S. Environmental Protection Agency
Fish bio-energetics model metadata

The Oregon stream temperatures used in Fig. 1 were sourced from 58 sites monitored by the Oregon Department of Environmental Quality and 17 sites monitored by The United States Geological Survey. These data are publicly available at https://www.oregon.gov/deq/wq/Pages/WQdata.aspx and https://waterdata.usgs.gov/nwis/sw, respectively. The water temperature data used in Figs. 2–4 are posted on GitHub at https://github.com/chris3jordan/Growth-Potential.
The code for processing water temperature and growth potential data for Figs. 2–4 is posted on GitHub at https://github.com/chris3jordan/Growth-Potential. The code for the numerical simulation is posted on GitHub at https://github.com/aimeefullerton/growth_regime_IBM. 

This dataset is associated with the following publication:
Armstrong, J.B., A.H. Fullerton, C.E. Jordan, J. Ebersole, J.R. Bellmore, I. Arismendi, B. Penaluna, and G.H. Reeves. The importance of warm habitat to the growth regime of cold-water fishes.   Nature Climate Change. Nature Publishing Group, New York, NY, USA,  00994, (2021).

Tags: recovery, refugia, resilience, water-quality, wildfire
Organization: U.S. Environmental Protection Agency
Migration corridor simulation - for second paper

The model scenario and associated outputs of the case study used to illustrate the migration corridor simulation model demonstrating fish fitness outcomes. 

This dataset is associated with the following publication:
Snyder, M., N. Schumaker, J. Dunham, M. Keefer, P. Leinenbach, A. Brookes, J. Palmer, J. Wu, D. Keenan, and J. Ebersole. Assessing contributions of coldwater refuges to reproductive migration corridor conditions for adult salmon and steelhead trout in the Columbia River, USA.   Journal of Ecohydraulics. Taylor & Francis Group, London,  UK,  1855086, (2020).

Tags: cold-water-refuge, migration, salmon, trout
Organization: U.S. Environmental Protection Agency