AndreaBozzo/ceres-open-data-index huggingface dataset:
The Acute Toxicity of Major Ions to Ceriodaphnia dubia. II. Empirical Relationships in Binary Salt Mixtures

This dataset provides concentration-response data and associated general chemistry conditions for 29 experiments consisting of 209 tests regarding the acute toxicity of binary mixtures of major ions to Ceriodaphnia dubia; it also provides LC50 estimates and the estimated ion mixtures at the LC50 for each toxicity test. 

This dataset is associated with the following publication:
Erickson, R., D. Mount, T. Highland, R. Hockett, D. Hoff, C. Jenson, T. Norberg-King, and K. Peterson. The acute toxicity of major ion salts to Ceriodaphnia dubia.  II.  Empirical relationships in binary salt mixtures.   ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY. Society of Environmental Toxicology and Chemistry, Pensacola, FL, USA, 36(6): 1525-1537, (2017).

Tags: acute-toxicity, binary-salt-mixtures, ceriodaphnia-dubia, freshwater, major-ion-toxicity
Organization: U.S. Environmental Protection Agency
Sorption of cesium onto the mineral phases and cement

Numerical data corresponding to manuscript figures. 

This dataset is associated with the following publication:
Kaminski, M., C. Mertz, J. Jerden, M. Kalensky, N. Kivenas , and M. Magnuson. Sorption of cesium onto the mineral phases and cement of concrete and desorption into simple salt solutions.   JOURNAL OF ENVIRONMENTAL RADIOACTIVITY. Elsevier Science Ltd, New York, NY, USA,  165-171, (2016).

Tags: cement, cesium, concrete, gross-decontamination, ind, indoor-outdoor-decontamination, iwaters, npp, nuclear, nuclear-power-plant, radiological-urban-decontamination, rdd
Organization: U.S. Environmental Protection Agency
Precipitation and stream water stable isotope data from the Marys River, Oregon in water year 2015.

Water stable isotope data collected from a range of streams throughout the Marys River basin in water year 2015, and precipitation data collected within the basin at a range of elevations. 

This dataset is associated with the following publication:
Nickolas, L., C. Segura, and J.R. Brooks. The influence of lithology on surface water sources.   Hydrological Processes. John Wiley & Sons, Ltd., Indianapolis, IN, USA, 31(10): 1913-1925, (2017).

Tags: climate-change, corvallis, geology, lithology, marys-river, oregon, precipitation, river-flow, stable-isotopes, streamflow, water-resources, water-supply
Organization: U.S. Environmental Protection Agency
Identifying Prevalent Chemical Mixtures in the US Population EHP Data

Frequent itemset mining (FIM), a technique used for finding patterns in consumer purchasing behavior, can be applied to data from large-scale biomonitoring studies to identify combinations of chemicals that frequently co-occur in people. As a proof of concept, we applied FIM to biomonitoring data from the National Health and Nutrition Examination Survey. In this way, we identified 90 chemical combinations consisting of relatively few chemicals that occur in at least 30% of the US population, as well as 3 super-combinations consisting of relatively many chemicals that occur in a small but non-negligible proportion of the US population. Thus, we have demonstrated a technique for narrowing a large number of possible chemical combinations down to a much smaller collection of prevalent chemical combinations. 

This dataset is associated with the following publication:
Kapraun, D.F., J.F. Wambaugh, R. Tornero-Velez, and R.W. Setzer. (ENVIRONMENTAL HEALTH PERSPECTIVES) Identifying Prevalent Chemical Mixtures in the US Population.   ENVIRONMENTAL HEALTH PERSPECTIVES. National Institute of Environmental Health Sciences (NIEHS), Research Triangle Park, NC, USA, 125(8): 1-16, (2017).

Tags: biomonitoring, chemical-mixtures, expocast, exposure, frequent-itemset-mining-fim, nhanes
Organization: U.S. Environmental Protection Agency
Datasets used in ORD-018902: Bisphenol A alternatives can effectively substitute for estradiol

Gene Expression Omnibus numbers only. 

This dataset is associated with the following publication:
Mesnage, R., A. Phedonos, M. Arno, S. Balu, C. Corton, and M. Antoniou. Transcriptome profiling reveals bisphenol A alternatives activate estrogen receptor alpha in human breast cancer cells.   TOXICOLOGICAL SCIENCES. Society of Toxicology,    158(2): 431-443, (2017).

Tags: bisphenol-a-alternatives, endocrine-disruption, estrogen-receptor, human-breast-cancer, mcf-7-cell-line
Organization: U.S. Environmental Protection Agency
Potential Wetland Restoration Indicators data for the EnviroAtlas

Data is based on overlap of topographic, soil drainage, and national wetland inventory areas. 

This dataset is associated with the following publication:
Horvath, E., J. Christensen, M. Mehaffey, and A. Neale. Building a Potential Wetland Restoration Indicator for the Contiguous United States..   ECOLOGICAL INDICATORS. Elsevier Science Ltd, New York, NY, USA, 83: 462-473, (2017).

Tags: compound-topographic-index, contiguous-united-states, ecosystem-services, enviroatlas, geographic-information-systems, mapping-methods, national-wetland-inventory, soil-drainage, wetland-restoration
Organization: U.S. Environmental Protection Agency
Data Set for the manuscript entitled, "Sample Processing Approach for Detection of Ricin in Surface Samples."

Figure. 

This dataset is associated with the following publication:
Shah, S., S. Kane, A.M. Erler, and T. Alfaro. Sample Processing Approach for Detection of Ricin in Surface Samples  [HS7.52.04 - 0671].   JOURNAL OF IMMUNOLOGICAL METHODS. Elsevier Science Ltd, New York, NY, USA,  9, (2017).

Tags: biotoxin, indoor-outdoor-decontamination, ricin, sample-processing
Organization: U.S. Environmental Protection Agency
Recreational freshwater fishing drives non-native aquatic species richness patterns at a continental scale

Aim. Mapping the geographic distribution of non-native aquatic species is a critically important precursor to understanding the anthropogenic and environmental factors that drive freshwater biological invasions. Such efforts are often limited to local scales and/or to single species, due to the challenges of data acquisition at larger scales. Here we map the distribution of exotic freshwater species richness across the continental United States and investigate the role of human activity in driving macroscale patterns of aquatic invasion. 

Location. The continental United States.

Methods. We assembled maps of non-native aquatic species richness by compiling occurrence data on exotic animal and plant species from publicly accessible databases. Using a dasymetric model of human population density and a spatially explicit model of recreational freshwater fishing demand we analyzed the effect of these metrics of human influence on the degree of invasion at the watershed scale, while controlling for spatial and sampling bias. We also assessed the effects that a temporal mismatch between occurrence data (collected since 1815) and cross-sectional predictors (developed using 2010 data) may have on model fit. 

Results. Non-native aquatic species richness exhibits a highly patchy distribution, with hotspots in the Northeast, Great Lakes, Florida, and human population centers on the Pacific coast. These richness patterns are correlated with population density, but are much more strongly predicted by patterns of recreational fishing demand. These relationships are strengthened by temporal matching of datasets and are robust to corrections for sampling effort.

Main Conclusions. Distributions of aquatic invasive species across the continental US are better predicted by freshwater recreational fishing than by human population density. This suggests that observed patterns are driven by a mechanistic link between recreational activity and aquatic invasive species richness, and are not merely the outcome of sampling bias associated with human population density. 

This dataset is associated with the following publication:
Davis, A., and J. Darling. Recreational freshwater fishing drives non-native aquatic species richness patterns at a continental scale (journal).   Diversity and Distributions. Blackwell Publishing Limited, Oxford,  UK, 23(6): 692-702, (2017).

Tags: aquatic-invasive-species, biodiversity, enviroatlas, geospatial-analysis, non-indigenous-aquatic-species, non-native-species-richness, populations-density, rarefaction, recreational-water, sampling-effort, threatened-and-endangered-species
Organization: U.S. Environmental Protection Agency
Datasets in Gene Expression Omnibus used in the study ORD-019001: Compensatory changes in CYP expression in three different toxicology mouse models: CAR-null, Cyp3a-null, and Cyp2b9/10/13-null mice.

Accession numbers of microarray data sets used in the analysis. 

This dataset is associated with the following publication:
Kumar, R., L. Mota, E. Litoff, J. Rooney, T. Boswell, E. Courter, C. Henderson, J. Hernandez, C. Corton, D. Moore, and W. Baldwin. Compensatory changes in CYP expression in three different toxicology mouse models: CAR-null, Cyp3a-null, and Cyp2b9/10/13-null mice.   PLoS ONE. Public Library of Science, San Francisco, CA, USA, 12(3): 1-24, (2017).

Tags: constitutive-activated-receptor-car, cyp2b, cyp3a, microarray, microarray-accession-numbers
Organization: U.S. Environmental Protection Agency
HTTK R Package v1.4 - JSS Article on HTTK: R Package for High-Throughput Toxicokinetics

httk: High-Throughput Toxicokinetics

Functions and data tables for simulation and statistical analysis of chemical toxicokinetics ("TK") using data obtained from relatively high throughput, in vitro studies. Both physiologically-based ("PBTK") and empirical (e.g., one compartment) "TK" models can be parameterized for several hundred chemicals and multiple species. These models are solved efficiently, often using compiled (C-based) code. A Monte Carlo sampler is included for simulating biological variability and measurement limitations. Functions are also provided for exporting "PBTK" models to "SBML" and "JARNAC" for use with other simulation software. These functions and data provide a set of tools for in vitro-in vivo extrapolation ("IVIVE") of high throughput screening data (e.g., ToxCast) to real-world exposures via reverse dosimetry (also known as "RTK"). 

This dataset is associated with the following publication:
Pearce , R., C. Strope , W. Setzer , N. Sipes , and J. Wambaugh. (Journal of Statistical Software) HTTK: R Package for High-Throughput Toxicokinetics.   Journal of Statistical Software. American Statistical Association, Alexandria, VA, USA, 79(4): 1-26, (2017).

Tags: expocast, exposure, high-throughput-toxicokinetics, httk, in-vitro-to-in-vivo-extrapolation-ivive, pbpk, pbpk-reverse-dosimetry, physiologically-based-pharmacokinetic-model, toxcast, toxicokinetics
Organization: U.S. Environmental Protection Agency
Nickel proteomics data

The dataset include the following figures and tables: 1)Changes in protein expression of the 14 pathway regulators induced by Ni (II). 2)Hierarchical clustering of 12 differentially expressed or phosphorylated proteins in BEAS-2B cells treated with Ni (II). 3) Relative cell survival (X-axis) vs. protein expression or phosphorylation levels (Y-axis) in BEAS-2B control cells treated with Ni (II) at 4 different concentrations 4)Four representative proteins, PDIA1, ACADM, RUVBL1, PRDX2 identified using 2-DE profiling were either increased or decreased in a concentration responsive manner 5)Networks of proteins showing inter-relationships and pathways which was obtained using IPA 6)Schematic representation of the interplay of the core proteins and cytotoxicity pathways mediated by Ni (II).  7) some supplementary data. 

This dataset is associated with the following publication:
Ge , Y., M. Bruno , N. Coates , K. Wallace , D. Andrews , A. Swank , W. Winnik , and J. Ross. Proteomic Assessment of Biochemical Pathways That Are Critical to Nickel-Induced Toxicity Responses in Human Epithelial Cells.   PLoS ONE. Public Library of Science, San Francisco, CA, USA, 11(9): 1-20, (2016).

Tags: cytotoxicity, dose-response, elisa, human-epithelial-cells, metals, nickel, nickel-proteomic-profile, phosphorylation, protein-expression, proteomics, sys-tems-biology
Organization: U.S. Environmental Protection Agency
County Level Risk scores broken down into three land-types (natural, dual-benefit, and built) as well as three year-ranges (2000-2005, 2005-2010, and 2010-2015).

The data set contains four tables with all U.S. counties.  Three of the data tables are for the 5-year ranges, while the fourth contains the overall risk score.  Within each table is a breakdown of risk by land type (natural, dual-benefit, and built) along with an overall risk score. 

This dataset is associated with the following publications:
Summers, K., L. Harwell, K. Buck, L. Smith, J. Harvey, D. Vivian, J. Bousquin, M. McLaughlin, and S. Hafner. Development of a Climate Resilience Screening Index (CRSI): An Assessment of Resilience to Acute Meteorological Events and Selected Natural Hazards. U.S. Environmental Protection Agency, Washington, DC, USA, 2017.
Buck, K., K. Summers, S. Hafner, L. Harwell, and L. Smith. Development of a Multi-Hazard Landscape for Exposure and Risk Interpretation: The PRISM Approach.   Current Environmental Engineering. Bentham Science Publishers, Ltd., Oak Park, IL, USA, 6(1): 74-94, (2019).

Tags: counties, multiple-stressors, natural-hazards, resilience, risk, technological-hazards
Organization: U.S. Environmental Protection Agency
Stachler et al. 2017 Figure 2 data

Estimated mean log10 concentration of genetic markers for CQQ_056, CPQ_064, HF183/BacR287, and HumM2 genetic markers in nine sewage and two surface water samples. 

This dataset is associated with the following publication:
Stachler, E., C. Kelty, M. Sivaganesan, X. Li, K. Bibby, and O. Shanks. Quantitative CrAssphage PCR Assays for Human Fecal Pollution Measurement.   ENVIRONMENTAL SCIENCE & TECHNOLOGY. American Chemical Society, Washington, DC, USA, 51(16): 9146-9154, (2017).

Tags: crassphage, human-fecal-pollution, microbial-source-tracking, qpcr, water-quality
Organization: U.S. Environmental Protection Agency
Climiate Resilience Screening Index and Domain Scores

CRSI and related-domain scores for all 50 states and 3135 counties in the U.S. This dataset is not publicly accessible because: They are already available within the product. It can be accessed through the following means: Interested audiences can copy the relevant table(s) from the appropriate appendix and copy into another software package, such as Excel, for use. Format: Table-formatted results as appendices within the product (report). 

This dataset is associated with the following publication:
Summers, K., L. Harwell, K. Buck, L. Smith, J. Harvey, D. Vivian, J. Bousquin, M. McLaughlin, and S. Hafner. Development of a Climate Resilience Screening Index (CRSI): An Assessment of Resilience to Acute Meteorological Events and Selected Natural Hazards. U.S. Environmental Protection Agency, Washington, DC, USA, 2017.

Tags: community, crsi, governance, indicators, natural-hazards, resilience
Organization: U.S. Environmental Protection Agency
High-Throughput Dietary Exposure Predictions for Chemical Migrants from Food Contact Substances for Use in Chemical Prioritization

Under the ExpoCast program, United States Environmental Protection Agency (EPA) researchers have developed a high-throughput (HT) framework for estimating aggregate exposures to chemicals from multiple pathways to support rapid prioritization of chemicals. Here, we present methods to estimate HT exposures to chemicals migrating into food from food contact substances (FCS). These methods consisted of combining an empirical model of chemical migration with estimates of daily population food intakes derived from food diaries from the National Health and Nutrition Examination Survey (NHANES). A linear regression model for migration at equilibrium was developed by fitting available migration measurements as a function of temperature, food type (i.e., fatty, aqueous, acidic, alcoholic), initial chemical concentration in the FCS (C0) and chemical properties. The most predictive variables in the resulting model were C0, molecular weight, log Kow, and food type (R2=0.71, p<0.0001). Migration-based concentrations for 1009 chemicals identified via publicly-available data sources as being present in polymer FCSs were predicted for 12 food groups (combinations of 3 storage temperatures and food type). The model was parameterized with screening-level estimates of C0 based on the functional role of chemical in FCS. By combining these concentrations with daily intakes for food groups derived from NHANES, population ingestion exposures of chemical in mg/kg-bodyweight/day (mg/kg-BW/day) were estimated. Calibrated aggregate exposures were estimated for 1931 chemicals by fitting HT FCS and consumer product exposures to exposures inferred from NHANES biomonitoring (R2=0.61, p<0.001); both FCS and consumer product pathway exposures were significantly predictive of inferred exposures. Including the FCS pathway significantly impacted the ratio of predicted exposures to those estimated to produce steady-state blood concentrations equal to in-vitro bioactive concentrations. While these HT methods have large uncertainties (and thus may not be appropriate for assessments of single chemicals), they can provide critical refinement to aggregate exposure predictions used in risk-based chemical priority–setting. 

This dataset is associated with the following publication:
Biryol, D., C. Nicolas, J. Wambaugh, K. Phillips, and K. Isaacs. High-throughput dietary exposure predictions for chemical migrants from food contact substances for use in chemical prioritization.   ENVIRONMENT INTERNATIONAL. Elsevier Science Ltd, New York, NY, USA, 108: 185-194, (2017).

Tags: chemical-prioritization, expocast, exposure, food-contact-substances, food-packaging, high-throughput, sheds
Organization: U.S. Environmental Protection Agency
Tissue disposition of bifenthrin in the rat

Tissue disposition of bifenthrin in the rat and oral and intravenous administration. 

This dataset is associated with the following publication:
Hughes , M., D. Ross , B. Edwards , M. DeVito, and J. Starr. Tissue time course and bioavailability of the pyrethroid insecticide bifenthrin in the Long-Evans rat.   XENOBIOTICA. Taylor & Francis, Inc., Philadelphia, PA, USA, 46(5): 430-438, (2016).

Tags: bifenthrin, bioavailability, disposition, pesticides, pyrethroid, pyrethroids
Organization: U.S. Environmental Protection Agency
This file contains data used to generate figures shown in Phelps et al. Microbial colonization is required for normal neurobehavioral development in zebrafish. Scientific Reports. 2017.

Data used to generate figures shown in Phelps et al. 

This dataset is associated with the following publication:
Phelps, D., N. Brinkman, S. Keely, E. Anneken, T. Catron, D. Betancourt, C. Wood, S. Espenschied, J. Rawls, and T. Tal. Microbial colonization is required for normal neurobehavioral development in zebrafish.   Scientific Reports. Nature Publishing Group, London,  UK, 11(7): 11244, (2017).

Tags: childrens-environmental-health, developmental-neurotoxicity, dnt, microbiome, microbiota, zebrafish
Organization: U.S. Environmental Protection Agency
Bioaerosol concentrations - Figure 3 and Figure 4

Bioaerosol concentrations. 

This dataset is associated with the following publication:
Chattopadhyay, S., S. Perkins, M. Shaw, and T. Nichols. Evaluation of Exposure to Brevundimonas diminuta and Pseudomonas aeruginosa during Showering   [HS7.44.02].   JOURNAL OF AEROSOL SCIENCE. Elsevier Science Ltd, New York, NY, USA, 114: 77-93, (2017).

Tags: bioaerosol-sampler-aerosol-concentration, bioaerosols, brevundimonas-diminuta, exposure-assessment, pathogen, pseudomonas-aeruginosa
Organization: U.S. Environmental Protection Agency
Supplemental information

Supplemental information showing results of inter-comparison between C-PORT, AERMOD and R-LINE dispersion algorithms. 

This dataset is associated with the following publication:
Isakov, V., T. Barzyk, B. Smith, S. Arunachalam , B. Naess , and A. Venkatram. A web-based screening tool for near-port air quality assessments.   ENVIRONMENTAL MODELLING & SOFTWARE. Elsevier Science, New York, NY,   98: 21-34, (2017).

Tags: air-pollution, dispersion-algorithms, dispersion-modeling, emissions, evaluation, exposure, ports
Organization: U.S. Environmental Protection Agency
GMAP Charleston data

GMAP mobile monitoring data from Charleston study and C-PORT results. 

This dataset is associated with the following publication:
Isakov, V., T. Barzyk, B. Smith, S. Arunachalam , B. Naess , and A. Venkatram. A web-based screening tool for near-port air quality assessments.   ENVIRONMENTAL MODELLING & SOFTWARE. Elsevier Science, New York, NY,   98: 21-34, (2017).

Tags: air-pollution, dispersion-modeling, emissions, exposure, ports
Organization: U.S. Environmental Protection Agency
Mixing at double-Tee junctions with unequal pipe sizes in water distribution systems

Pipe flow mixing with various solute concentrations and flow rates at pipe junctions is investigated. The degree of mixing affects the spread of contaminants in a water distribution system. Many studies have been conducted on the mixing at the cross junctions. Yet few have focused on double-Tee junctions of unequal pipe sizes. To investigate the solute mixing at double-Tee junctions with unequal pipe sizes, a series of experiments were conducted in a turbulent regime (Re=12500–50000) with different Reynolds number ratios and connecting pipe lengths. It is found that dimensionless outlet concentrations depended on mixing mechanism at the impinging interface of pipe junctions. Junction with a larger pipe size ratio is associated with more complete mixing. The inlet Reynolds number ratio affects mixing more strongly than the outlet Reynolds number ratio. Furthermore, the dimensionless connecting pipe length in a double-Tee played an important and complicated role in the flow mixing. Based on these results, two-dimensional isopleth maps were developed for the calculation of normalized north outlet concentration. This dataset is not publicly accessible because: The present research is funded by the National Natural Science Foundation of China (No. 51208457 and 51478417), the Major Science and Technology Program for Water Pollution Control and Treatment in China (2012ZX07408-002 and 2012ZX07403-004), and the Fundamental Research Funds for the Central Universities. It can be accessed through the following means: Yang.jeff@epa.gov. Format: Secondary data not available. 

This dataset is associated with the following publication:
Yu, T., H. Qiu, J. Yang, y. shao, and L. Tao. Mixing at double-Tee junctions with unequal pipe sizes in water distribution systems.   Water Science and Technology:  Water Supply. IWA Publishing, London,  UK, 16(6): 1595-1602, (2016).

Tags: double-tee-junctions, solute-mixing, unequal-pipe-sizes, water-distribution-systems
Organization: U.S. Environmental Protection Agency
Supporting data for Suen et al_A-0zpd

Tables, Figures, and Supplemental Materials for doi: 10.1158/1541-7786.MCR-16-0084. 

This dataset is associated with the following publication:
Suen, A., W. Jefferson, C. Wood, E. Padilla-Banks, V. Bae-Jump, and C. Williams. SIX1 Oncoprotein as a Biomarker in a Model of Hormonal Carcinogenesis and in Human Endometrial Cancer..   Molecular Cancer Research. American Association for Cancer Research, Inc., Philadelphia, PA, USA, 14(9): 849-858, (2016).

Tags: biomarker, diethylstilbestrol, estrogen, estrogenic-chemicals, oncofetal, uterine-cancer
Organization: U.S. Environmental Protection Agency