AndreaBozzo/ceres-open-data-index huggingface dataset:
20200228_GX1 Science Hub_EHP_FINAL

This dataset contains all underlying data used to generate the figures contained in Gaballah et al. Evaluation of developmental toxicity, developmental neurotoxicity, and tissue dose in zebrafish exposed to GenX and other PFAS. 

This dataset is associated with the following publication:
Gaballah, S., A. Swank, X.M. Howey, J. Sobus, J. Schmid, T. Catron, J. McCord, E. Hines, and M. Strynar. Evaluation of developmental toxicity, developmental neurotoxicity, and tissue dose in zebrafish exposed to GenX and other PFAS. NA. NA (ed.), ENVIRONMENTAL HEALTH PERSPECTIVES. National Institute of Environmental Health Sciences (NIEHS), Research Triangle Park, NC, USA, 128(4): 047005-1 - 047005-22, (2020).

Tags: development-neurotoxicity, dnt, genx, pfas, polyfluorinated-alkyl-substances-pfas, zebrafish
Organization: U.S. Environmental Protection Agency
An automated common algorithm for planetary boundary layer retrievals using aerosol lidars in support of the U.S. EPA Photochemical Monitoring Assessment Program

Ceilometers are devices for measuring and recording the height of clouds using laser based LiDAR technologies. They also can measure the height of planetary boundary layer (PBL), which is the lowest layer in the atmosphere directly influenced by the Earth’s surface. This dataset consists of retrievals from an automated planetary boundary layer (PBL) algorithm. This algorithm is proposed as a common cross-platform method for use with commercially available ceilometers. For additional assistance in access and interpreting the data please contact the listed authors. 

This dataset is associated with the following publication:
Szykman, J., D. Williams, V. Caicedo, R. Delgado, T. Knepp , K. Cavender, and B. Lefer. An automated common algorithm for planetary boundary layer retrievals using aerosol lidars in support of the U.S. EPA Photochemical Monitoring Assessment Program.   Journal of Atmospheric and Oceanic Technology. American Meteorological Society, Boston, MA, USA,  1-51, (2020).

Tags: ensemble-kalman-filter, geos-chem, pm2-5-forecast, wrf-chem, wrf-cmaq
Organization: U.S. Environmental Protection Agency
DLVO Modeling of Spores Dataset

Development of numerical models to predict stormwater-mediated transport of pathogenic spores in the environment depends on an understanding of adhesion forces that dictate detachment after rain events. Zeta potential values were measured for Bacillus globgii and Bacillus thuringiensis kurstaki, two common surrogates used to represent Bacillus anthracis, in synthetic baseline ultrapure water and laboratory stormwater. Zeta potential curves were also determined for materials representative of urban infrastructure (concrete and asphalt). These data were used to predict the interaction energy between the spores and urban materials using Derjaguin-Landau-Verwey-Overbeek (DLVO) modeling. B. globgii and B. thuringiensis kurstaki sourced from Yakibou Inc., were found to have similar zeta potential curves, whereas spores sourced from the U.S. military’s Dugway laboratory were found to diverge. In the ultrapure water, the energy barriers between the spores and the urban materials were tunable through compression of the double layer of the
spores via changes of ionic strength and pH of the water. In the runoff water, charge neutralization dominated surface processes. The cations, metals, and natural organic matter (NOM) in the runoff water contributed to equalizing the zeta potential values for Dugway B. globgii and B. thuringiensis kurstaki, and drastically modified the surface of the concrete and asphalt. All DLVO energy curves using the runoff water were repulsive. The highest energy barrier predicted in this study was for Dugway B. globgii spores interacting with a concrete surface in runoff water, suggesting that this would be the most challenging combination to detach through water-based decontamination. 

This dataset is associated with the following publication:
Mikelonis, A., K. Ratliff, and S. Youn. Laboratory results and mathematical modeling of spore surface interactions in storm water runoff.   JOURNAL OF CONTAMINANT HYDROLOGY. Elsevier Science Ltd, New York, NY, USA, 235: 103707, (2020).

Tags: anthrax, biological, dlvo, stormwater, water-security, zeta-potential
Organization: U.S. Environmental Protection Agency
Calculation of emission factors used in publication of coastal wetland management as a contribution to the US National Greenhouse Gas Inventory

The calculation of emissions factors used to estimate carbon stock changes for coastal wetland areas in the US. Citation information for this dataset can be found in the EDG's Metadata Reference Information section and Data.gov's References section.

Tags: carbon-stock-changes, climate-change, coastal-wetlands, greenhouse-gas-inventory, ipcc-2013-wetlands-supplement, mangroves, revegetation, rewetting, soil-drainage, tidal-marshes, united-nations-framework-convention
Organization: U.S. Environmental Protection Agency
R Code of Simulations

The sims zip file contains R code and accompanying files needed to run the R code. Overall this code demonstrates the R code used in the study is fully functional, documented, and reproducible and that this code could reproduce the simulation results from the study with sufficient computing time. The code as presented is for a single simulated dataset and will produce estimates and confidence intervals produced by all the methods used within the study when run on that one dataset. 

This dataset is associated with the following publication:
Nethery, R., F. Mealli, J. Sacks, and F. Dominici. Evaluation of the Health Impacts of the 1990 Clean Air Act Amendments Using Causal Inference and Machine Learning.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION. Taylor & Francis Group, London,  UK,  1-12, (2020).

Tags: air-quality
Organization: U.S. Environmental Protection Agency
OGI Perfromance Study Dataset

Optical Gas Imaging (OGI) is an important next generation emission measurement (NGEM) technique for finding fugitive industrial emissions (leaks) of methane and volatile organic compounds. The ability of OGI to detect leaks depends on many factors including the skill and training of the OGI operator. This dataset was produced at the Colorado State University Methane Emissions Test and Evaluation Center (METEC) where simulated leaks of various sizes from oil and gas production equipment could be generated.  Dozens of OGI operators from different organizations with various levels of experience participated in a test series to establish their ability to detect leaks under varying conditions using the protocols and procedures they normally employ. This dataset contains the results from this test series.  The associated journal article advances understanding of OGI methods and training using these data. 

This dataset is associated with the following publication:
Zimmerle, D., T. Vaughn, C. Bell, K. Bennett, E. Thoma, J. Dewees, and P. Deshmukh. Detection Limits of Optical Gas Imaging for Natural Gas Leak Detection in Realistic Controlled Conditions August 2020.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY. American Chemical Society, Washington, DC, USA, 54: 18, (2020).

Tags: fugitive-emissions, ldar, ngem, ogi, oil-and-gas
Organization: U.S. Environmental Protection Agency
Dataset for MICRON Nutrient Diffusing Substrate Paper

The data set includes abundance tables obtained after processing 16S rRNA gene sequences and 18S rRNA gene sequences using bioinformatic software.  Sequences were extracted from periphyton samples obtained from nutrient diffusing substrate experiments.  In addition, the data set includes ambient nutrient concentrations and physical water quality parameters from deployment sites.  The data set is zipped with R markdown programs used to generate the publications resulting from the study. 

This dataset is associated with the following publication:
Hagy, J., K. Houghton, D. Beddick, J. James, S. Friedman, and R. Devereux. Quantifying stream periphyton assemblage responses to nutrient amendments with a molecular approach.   Freshwater Science. The Society for Freshwater Science, Springfield, IL,  39(June 2020): 292-308, (2020).

Tags: genomics, nutrients, stream-indicators
Organization: U.S. Environmental Protection Agency
Identifying Trans-Epithelial Effects of Inhaled Chemical Exposures on Stromal-Epithelial Oxidative Stress Dynamics in the Human Airway

Data include: trans-epithelial electrical resistance, FITC-dextran permeability, cell viability and gene expression (RNA and protein). 

This dataset is associated with the following publication:
Faber, S., N. McNabb, P. Ariel, E. Aungst, and S. McCullough. Exposure Effects Beyond the Epithelial Barrier: Trans-Epithelial Induction of Oxidative Stress by Diesel Exhaust Particulates in Lung Fibroblasts in an Organotypic Human Airway Model.   TOXICOLOGICAL SCIENCES. Society of Toxicology, RESTON, VA,  177(1): 140-155, (2020).

Tags: diesel-exhaust, epithelium, fibroblast, lung, new-approach-methodologies, organotypic, oxidative-stress, particulate-matter, trans-epithelial
Organization: U.S. Environmental Protection Agency
MICRON Data (2015-2016) with associated R Markdown code

This data set includes water quality data and microbial community abundance tables for periphyton samples from this project.  The data set also includes extensive R markdown code used to process the data and generate the results included in the report. 

This dataset is associated with the following publication:
Hagy, J., R. Devereux, K. Houghton, D. Beddick, T. Pierce, and S. Friedman. Developing Microbial Community Indicators of Nutrient Exposure in Southeast Coastal Plain Streams using a Molecular Approach. US EPA Office of Research and Development, Washington, DC, USA, 2018.

Tags: genomics, nutrients, stream-indicators
Organization: U.S. Environmental Protection Agency
Commercial imagery for seagrass

Seagrass detection using commercial satellite imagery from WorldView-2 (2 m) and RapidEye (6.5 m). 

This dataset is associated with the following publication:
Coffer, M., B. Schaeffer, R.C. Zimmerman, V. Hill, J. Li, K.A. Islam, and P. Whitman. Performance across WorldView-2 and RapidEye for reproducible seagrass mapping.   REMOTE SENSING OF ENVIRONMENT. Elsevier Science Ltd, New York, NY, USA, 250: 112036, (2020).

Tags: atmospheric-correction, commercial, rapideye, remote-sensing, seagrass, worldview-2
Organization: U.S. Environmental Protection Agency
DriLube VOC Concentrations, Pressure & Vacuum Readings and Metadata

There are 3 main databases. #1 is the VOC concentrations of soil gas and indoor air samples collected over the site. #2 is the pressure readings used to monitor the pressure differential between subslab and indoor air. #3 is the vacuum reading used to monitor effectiveness, strength, and reach of vacuum created during the SVE operation. 

This dataset is associated with the following publication:
Stewart, L., C. Lutes, R. Truesdale, B. Schumacher, J. Zimmerman, and R. Connell. Field Study of Soil Vapor Extraction for Reducing Off‐Site Vapor Intrusion.   Groundwater Monitoring & Remediation. Wiley-Blackwell Publishing, Hoboken, NJ, USA, 40(1): 74-85, (2020).

Tags: mitigation, soil-vapor-extraction, vapor-intrusion
Organization: U.S. Environmental Protection Agency
Age-related differences in pulmonary effects of acute and subchronic episodic ozone exposures in Brown Norway rats

This data set provides the biological endpoints collected from individual animals that culminated into a published paper. 

This dataset is associated with the following publication:
Snow, S., C. Gordon , V. Bass, M. Schladweiler , A. Ledbetter , K. Jarema , P. Phillips , A. Johnstone , and U. Kodavanti. Age-related differences in pulmonary effects of acute and subchronic episodic ozone exposures in Brown Norway rats.   INHALATION TOXICOLOGY. Informa Healthcare USA, New York, NY, USA, 28(7): 313-23, (2016).

Tags: adaptation, age-ozone-pulmonary, age-related-susceptibility, ozone, pulmonary, whole-body-plethysmography
Organization: U.S. Environmental Protection Agency
Identifying Air Pollution Source Impacts in Urban Communities Using Mobile Monitoring

Mobile monitoring data generated using an instrumented electric vehicle. 

This dataset is associated with the following publication:
Deshmukh, P., E. Kimbrough, R. Logan, S. Krabbe, V. Isakov, and R. Baldauf. Identifying Air Pollution Source Impacts in Urban Communities Using Mobile Monitoring.   SCIENCE OF THE TOTAL ENVIRONMENT. Elsevier BV, AMSTERDAM,  NETHERLANDS,  000, (2020).

Tags: black-carbon, kc-traqs, mobile-monitoring, near-source, nitrogen-dioxide, pm2-5, rail, sensors, ultrafine-particulate
Organization: U.S. Environmental Protection Agency
Joint measurements of black carbon and particle mass for heavydutydiesel vehicles using a portable emission measurement system

PEMS-chasing experiments were conducted for twelve heavy-duty diesel vehicles (HDDTs) to evaluate the accuracy of mobile measurement results. Two data processing approaches were integrated to automate the calculations of fuel consumption-based emission factors of nitrogen oxides (NOX). With a total of 245 plume chasing tests conducted, and then averaged by vehicle and road types, we found that the relative errors of vehicle-specific emission factors using an algorithm developed for this project were within approximately ± 20% of the PEMS results for all tested vehicles. Stochastic simulations suggested reasonable results could be obtained using fewer chasing tests per vehicle (e.g., 71% for freeways and 93% for local road, equivalent to two chase tests per vehicle). This study improves the understanding of the accuracy of the mobile chasing method, and provides a practical approach for real-time emission measurements for future scaled-up mobile chasing studies. 

This dataset is associated with the following publications:
Wu, Y., H. Wang, K. Zhang, S. Zhang, R. Baldauf, P. Deshmukh, and R. Snow. Evaluating mobile monitoring of on-road emission factors by comparing concurrent PEMS measurements.   SCIENCE OF THE TOTAL ENVIRONMENT. Elsevier BV, AMSTERDAM,  NETHERLANDS, 736: NA, (2020).
Baldauf, R., X. Zheng, Y. Wu, S. Zhang, K. Zhang, and J. Hao. Joint measurements of black carbon and particle mass for heavydutydiesel vehicles using a portable emission measurement system.   ATMOSPHERIC ENVIRONMENT. Elsevier Science Ltd, New York, NY, USA, 141: 435-442, (2016).

Tags: diesel-emissions, mobile-chase-data, pems, truck-study
Organization: U.S. Environmental Protection Agency
PFBS tissue concentrations and liver gene expression in mice

File contains raw data collected on body and organ weights of mice given PFBS and body burden of the chemical after intervals of several hours, as well as expression of liver candidate genes for nuclear receptors at 24 h post-treatment. 

This dataset is associated with the following publication:
Lau, C., J. Rumpler, K. Das, C. Wood, J. Schmid, M. Strynar, and J. Wambaugh. Pharmacokinetic profile of Perfluorobutane Sulfonate and activation of hepatic nuclear receptor target genes in mice.   TOXICOLOGY. Elsevier Science Ltd, New York, NY, USA, 441: 152522, (2020).

Tags: chemical-contaminant, pfbs, pharmacokinetics, transcriptomics
Organization: U.S. Environmental Protection Agency
Drinking Water Microbiome OTU Abundance Data Set

An abundance matrix (BM_OTU.xlsx) contains rows as OTU, columns as samples, and entries representing the abundance of each OTU as a ratio of all sequences obtained for each individual sample. 

This dataset is associated with the following publication:
Gomez-Alvarez, V., and R. Revetta. Monitoring of Nitrification in Chloraminated Drinking Water Distribution Systems With Microbiome Bioindicators Using Supervised Machine Learning.   Frontiers in Microbiology. Frontiers, Lausanne,  SWITZERLAND, 11: 2254-2267, (2020).

Tags: 16s-rrna, drinking-water, machine-learning, microbiome, nitrification, otu, relative-abundance
Organization: U.S. Environmental Protection Agency
Drinking Water Microbiome Sequence Data Set

The fasta file (BM_OTU.fasta) contain the sequences of the bacterial 16S rRNA-encoding V4 region gene (≈250 nt) for each Operational Taxonomic Unit (OTU). 

This dataset is associated with the following publication:
Gomez-Alvarez, V., and R. Revetta. Monitoring of Nitrification in Chloraminated Drinking Water Distribution Systems With Microbiome Bioindicators Using Supervised Machine Learning.   Frontiers in Microbiology. Frontiers, Lausanne,  SWITZERLAND, 11: 2254-2267, (2020).

Tags: 16s-rrna, drinking-water, machine-learning, microbial-communities, microbiome, nitrification, otu
Organization: U.S. Environmental Protection Agency
Mercury Accumulation in Fall Migrating Raptors through Central North America

The data consist of measured feather concentrations of total mercury (THg) in six species of raptors sampled at Hawk Ridge, Duluth MN between 2009 and 2012.  The species sampled were Sharp-shinned Hawk (Accipiter striatus), Northern Goshawk (Accipiter gentilis), Long-eared Owl (Asio otus), American Kestrel (Falco sparverius), Merlin (Falco columbarius), and Northern Harrier (Circus hudsonius). 

This dataset is associated with the following publication:
Keyel, E., M. Etterson, G. Niemi, D. Evers, C. DeSorbo, J. Hoffman, J. Nichols, Y. Li, and F. Nicoletti. Feather mercury increases with feeding at higher trophic levels in two species of migrant raptors, Merlin (Falco columbarius) and Sharp-shinned Hawk (Accipiter striatus).   The Condor. The Cooper Ornithological Society, Bend, OR, USA, 122: 1-17, (2020).

Tags: birds, hg, raptors
Organization: U.S. Environmental Protection Agency
Ozone-induced dysregulation of neuroendocrine axes requires adrenal-derived stress hormones

This study was performed to determine the role of adrenal-derived stress hormones in mediating brain effects after ozone exposure. Sham and adrenalectomized rats were exposed to air or ozone for 4 hours and within 2 hours after exposure brain regions, hypothalamus and brainstem were isolated and circulating pituitary hormones were analyzed. Global gene expression was analysed in these two brain regions using Illumina mRNA sequencing platform and data were analyzed using various bioinformatics platforms. The resulting data are included in this manuscript. 

This dataset is associated with the following publication:
Henriquez, A., J. House, S. Snow, C. Miller, M. Schladweiler, A. Astriab Fisher, H. Ren, M. Valdez, P. Kodavanti, and U. Kodavanti. Ozone-induced dysregulation of neuroendocrine axes requires adrenal-derived stress hormones.   TOXICOLOGICAL SCIENCES. Society of Toxicology, RESTON, VA,  172(1): 38-50, (2019).

Tags: adrenalectomy, brainstem, hypothalamus, neuroendocrine-hormones, ozone, pituitary
Organization: U.S. Environmental Protection Agency
Expanded coverage of NT-LC-HRMS using atmospheric pressure chemical ionization: A case study with ENTACT mixtures

LC data generated using APCI and ESI for  analysis ENTACT mixtures. 

This dataset is associated with the following publication:
Singh, R.R., A. Chao, K. Phillips, X.R. Xia, D. Shea, J. Sobus, E.L. Schymanski, and E. Ulrich. Expanded coverage of NT-LC-HRMS using atmospheric pressure chemical ionization: A case study with ENTACT mixtures.   Analytical and Bioanalytical Chemistry. Springer, New York, NY, USA, 412(21): 4931–4939, (2020).

Tags: atmospheric-pressure-chemical-ionization-apci, electrospray-ionization-esi, epas-non-targeted-analysis-collaborative-trial-entact, high-resolution-mass-spectrometry-hrms, non-targeted-analysis
Organization: U.S. Environmental Protection Agency
MPAS-A

The document in this data set lists the links to both the released version of the MPAS code, the modified MPAS code and the observational datasets used to evaluate the model updates presented in the publication. High resolution global model output is large and exceeded the limitations of this archive by several orders of magnitude. Thus the document also contains instructions on where the data resides, the data format, and how to obtain these data. 

This dataset is associated with the following publication:
Campbell, P., J. Bash, J. Herwehe, and R. Gilliam. Impacts of tiled land cover characterization in the Model for Predictions Across Scales-Atmosphere (MPAS-A).   JOURNAL OF GEOPHYSICAL RESEARCH-ATMOSPHERES. American Geophysical Union, Washington, DC, USA, 125(15): e2019JD032093, (2020).

Tags: land-use, meteorological-model, mpas, wrf
Organization: U.S. Environmental Protection Agency
Specific Conductivity Stream Network Predictions Eastern Kentucky Watershed Data, Code and HTML

This data is for 60 water quality monitoring sites in the Right Fork of Beaver Creek watershed in Eastern Kentucky where specific conductivity (SC) was measured quarterly for two years from December 2012 to August 2014.  SC was modeled as a function of land use covariates and spatial autocorrelation between sites on the stream network, and by doing so we could compare predictions of the average SC for different portions of the network and identify areas of low and high SC. The htmls files can be opened with a browser such as Internet Explorer or Chrome. 

This dataset is associated with the following publication:
McManus, M., E. DAmico, E. Smith, R. Polinsky, J. Ackerman, and K. Tyler. Variation in stream network relationships and geospatial predictions of watershed conductivity.   Freshwater Science. The Society for Freshwater Science, Springfield, IL,  39(4): 1-18, (2020).

Tags: spatial-autocorrelation, specific-conductivity, stream-networks, water-quality
Organization: U.S. Environmental Protection Agency
Specific Conductivity Stream Network Modeling Eastern Kentucky Watershed Data, Code and Analysis HTMLS

This data is for 60 water quality monitoring sites in the Right Fork of Beaver Creek watershed in Eastern Kentucky where specific conductivity (SC) was measured quarterly for two years from December 2012 to August 2014.  SC was modeled as a function of land use covariates and spatial autocorrelation between sites on the stream network, and by doing so we could compare predictions of the average SC for different portions of the network and identify areas of low and high SC. The htmls files can be opened with a browser such as Internet Explorer or Chrome. 

This dataset is associated with the following publication:
McManus, M., E. DAmico, E. Smith, R. Polinsky, J. Ackerman, and K. Tyler. Variation in stream network relationships and geospatial predictions of watershed conductivity.   Freshwater Science. The Society for Freshwater Science, Springfield, IL,  39(4): 1-18, (2020).

Tags: spatial-autocorrelation, specific-conductivity, stream-networks, water-quality
Organization: U.S. Environmental Protection Agency
Freshwater Science Table S1 Comparison of Spatial Autocovariance Models for Spatial Stream Network Analysis

This data compares spatial autocovariance models used in the modeling and prediction of specific conductivity over 8 sampling periods in an Eastern Kentucky watershed. 

This dataset is associated with the following publication:
McManus, M., E. DAmico, E. Smith, R. Polinsky, J. Ackerman, and K. Tyler. Variation in stream network relationships and geospatial predictions of watershed conductivity.   Freshwater Science. The Society for Freshwater Science, Springfield, IL,  39(4): 1-18, (2020).

Tags: spatial-autocorrelation, specific-conductivity, stream-networks, water-quality
Organization: U.S. Environmental Protection Agency