AndreaBozzo/ceres-open-data-index huggingface dataset:
Defining the Taxonomic Domain of Applicability for Mammalian-Based High-Throughput Screening Assays

Final Data SeqAPASS v3.0.zip contains datasets from Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS) tool versions 3.0 for all 497 proteins evaluated using Level 1 (primary amino acid sequence comparisons) and Level 2 (functional domain(s) sequence comparisons) to understand conservation of HTS targets across species. Each folder is labeled by the protein accession (identification number and SeqAPASS version), with subfolders containing Level 1 and Level 2 output from the SeqAPASS tool.
SeqAPASS v3.0 Data in Assay Groups.zip Contains all SeqAPASS data sorted by ToxCast Assay Group (as described in manuscript materials and methods). The original SeqAPASS data for each assay group are found in the folders titled Cell Adhesion, Cytochrome P450, Cytokine, DNA Binding, Esterase, G protein-coupled receptor, Growth Factor, Hydrolase, Ion Channel, Kinase, Lyase, Methyltransferase, Nuclear Receptor, Oxidoreductase, Phophatase, Protease, Protease Inhibitor, and Transporter. The Data_L1_Output folders and Data_L2_Output folders provide summaries of the Level 1 and Level 2 data comparing across datasets (See manuscript Supplemental Data, Legend for further details). 

This dataset is associated with the following publication:
LaLone, C., D. Villeneuve, J. Doering, B. Blackwell, T. Transue, C. Simmons, J. Swintek, S. Degitz, A. Williams, and G. Ankley. Defining the taxonomic domain of applicability for mammalian-based high-throughput screening assays..   ENVIRONMENTAL SCIENCE & TECHNOLOGY. American Chemical Society, Washington, DC, USA, 52(23): 13960-13971, (2018).

Tags: adverse-outcome-pathway, cross-species-extrapolation, ecotoxicology, endocrine-disruptor-screening-program, high-throughput-screening, honey-bee, networks, screening-and-prioritization, steroidogenesis, thyroid-axis
Organization: U.S. Environmental Protection Agency
CADETS Results by Site 050918

Measured, continuous, and intermittent Allegheny River conductivity by site. 

This dataset is associated with the following publication:
Brown, K., G. Norris, K. Kovalcik, A. Kamal, K. Patnode, and M. Landis. Signal Decomposition of Conductivity Sensor Measurements on the Allegheny River, Pennsylvania.   JOURNAL OF ENVIRONMENTAL ENGINEERING. American Society of Civil Engineers  (ASCE), Reston, VA, USA, 144(10): 04018103, (2018).

Tags: allegheny-river, conductivity, frequency, water-sensor
Organization: U.S. Environmental Protection Agency
ScienceHub Supplement

The study created 45 3-year regional climate simulations by downscaling historical reanalysis data using the WRF model.  The simulations are not an ensemble, but rather are explorations of various nudging strategies to elucidate and recommend best practices.  The data available with this research effort are a suite of 2D fields of hourly data in WRF I/O API (built upon netCDF) for each simulation and for the full 3-year study period.  There are additional post-processed and statistical data that were generated and archived for this effort.  Metadata associated with each simulation are in standard netCDF format. 

This dataset is associated with the following publication:
Spero, T., C. Nolte, M. Mallard, and J. Bowden. A Maieutic Exploration of Nudging Strategies for Regional Climate Applications Using the WRF Model.   JOURNAL OF APPLIED METEOROLOGY AND CLIMATOLOGY. American Meteorological Society, Boston, MA, USA, 57: 1883-1906, (2018).

Tags: dynamical-downscaling, nudging, regional-climate-modeling, wrf
Organization: U.S. Environmental Protection Agency
Dry Dep Comp_Wu et al_2018

Datasets present results of comparisons of five commonly dry deposition algorithms for ozone and sulfur dioxide, including diurnal patterns in deposition velocities, leaf-level processes such as stomatal conductance, and sensitivity to use of modeled versus measured meteorology. 

This dataset is associated with the following publication:
Wu, Z., D. Schwede, R. Vet, J. Walker, M. Shaw, R. Staebler, and L. Zhang. Evaluation and Intercomparison of Five North American Dry Deposition Algorithms at a Mixed Forest Site.   Journal of Advances in Modeling Earth Systems. John Wiley & Sons, Inc., Hoboken, NJ, USA, 10(7): 1571-1586, (2018).

Tags: air-surface-exchange, bidirectional-flux, deposition, dry-deposition, micrometeorology, model-evaluation, nitrogen, ozone, sulfur
Organization: U.S. Environmental Protection Agency
Evolution of the US energy system and related emissions under varying social and technological development paradigms Dataset

This data is associated with the manuscript "Evolution of the US energy system and related emissions under varying social and technological development paradigms: Plausible scenarios for use in robust decision making" which will be submitted to Environmental Science & Technology (ES&T). The research considers how the US energy system might evolve under four possible scenarios, including different technologies and different emission outcomes. 

This dataset is associated with the following publication:
Brown, K., T. Hottle, R. Bandyopadhyay, S. Babaee, R. Dodder, O. Kaplan, C. Lenox, and D. Loughlin. Evolution of the US energy system and related emissions under varying social and technological development paradigms: Plausible scenarios for use in robust decision making.   ENVIRONMENTAL SCIENCE & TECHNOLOGY. American Chemical Society, Washington, DC, USA,  8027-8038, (2018).

Tags: air-quality, energy, energy-modeling, externality, markal, scenario-planning, scenarios
Organization: U.S. Environmental Protection Agency
Soil organic matter and amphibian exposure dataset

Dataset containing experimental data and R scripts used for data analyses. 

This dataset is associated with the following publication:
Van Meter, R., D. Glinski, M. Henderson , and T. Purucker. Soil organic matter content effects on dermal pesticide bioconcentration in American toads (Bufo americanus)..   ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY. Society of Environmental Toxicology and Chemistry, Pensacola, FL, USA, 35(11): 2734–2741, (2016).

Tags: amphibians, dermal-exposure, pesticides, soil-organic-matter
Organization: U.S. Environmental Protection Agency
Plasma Standards

Digital droplet PCR fluorsence amplitude values from which plasmid copy concentrations of DNA standards were determined as described in D-EMMD-MEB-018-SOP-01and Journal article. Summary of  stability testing results also provided. 

This dataset is associated with the following publication:
Sivaganesan, M., M. Varma, S. Siefring, and R. Haugland. Quantification of plasmid DNA standards for U.S. EPA fecal indicator bacteria qPCR methods by droplet digital PCR analysis.   JOURNAL OF MICROBIOLOGICAL METHODS. Elsevier Science Ltd, New York, NY, USA, 152: 135-142, (2018).

Tags: digital-droplet-pcr, dna-standards, draft-method-c, epa-methods-1609-1, epa-methods-1611-1, qpcr
Organization: U.S. Environmental Protection Agency
Ballast water exchange and invasion risk posed by intra-coastal vessel traffic: An evaluation using high throughput sequencing

Dataset including all data for samples analyzed in Darling et al. 2018 Environmental Science & Technology. Includes OTU counts for all samples, taxonomic assignments for all OTUs, variables associated with vessels, and family-level counts across all vessels (used for indicator analysis). File also includes metadata describing all variables. 

This dataset is associated with the following publication:
Darling, J., J. Martinson, Y. Gong, S. Okum, E. Pilgrim, K. Pagenkopp Lohan, J. Carney, and G. Ruiz. Ballast Water Exchange and Invasion Risk Posed by Intracoastal Vessel Traffic: An Evaluation Using High Throughput Sequencing.   ENVIRONMENTAL SCIENCE & TECHNOLOGY. American Chemical Society, Washington, DC, USA, 52(17): 9926-9936, (2018).

Tags: ballast-water, ballast-water-exchange, high-throughput-sequencing, invasive-species, metabarcoding
Organization: U.S. Environmental Protection Agency
Metals removal from mine influenced water

The primary objective of this study was to evaluate the long-term effectiveness of a chitin (crushed crab shells) substrate compared to traditional ligneous (wood chips, hay, and manure) substrates on Zn, other metals (Al, Cu, Fe, Cd, Mn), and sulfate removal in MIW under anaerobic column bioreactor conditions. The secondary objective includes the evaluation of aeration and neutralization water pretreatment on the removal of the mentioned contaminants. 

This dataset is associated with the following publication:
Pinto, P., S. Al-Abed, and J. McKernan. Comparison of the efficiency of chitinous and ligneous substrates in metal and sulfate removal from mining-influenced water.   JOURNAL OF ENVIRONMENTAL MANAGEMENT. Elsevier Science Ltd, New York, NY, USA, 227(1): 321-328, (2018).

Tags: acid-mine-drainage, anaerobic-bioreactors, manganese, sulfate-reducing-bacteria, sulfate-reduction-rate, zinc
Organization: U.S. Environmental Protection Agency
Evaluation of Formaldehyde Column Observations by Pandora Spectrometers

Data collected for this research provides information on mixing heights, surface and column formaldehyde during the KORUS-AQ field campaign and over two research sites in South Korea. 

This dataset is associated with the following publication:
Spinei, E., A. Whitehill, A. Fried, M. Tiefengraber, T. Knepp, S. Herndon, J. Herman, M. Muller, N. Abuhassan, A. Cede, D. Richter, J. Walega, J. Crawford, J. Szykman, L. Valin, D. Williams, R. Long, R. Swap, Y. Lee, N. Nowak, and B. Poche. The first evaluation of formaldehyde column observations by improved Pandora spectrometers during the KORUS-AQ field study.   Atmospheric Measurement Techniques. Copernicus Publications, Katlenburg-Lindau,  GERMANY, 11(9): 4943-4961, (2018).

Tags: column-formaldehyde, formaldehyde-columns, korus-aq, mixing-heights, pandora, satellite-validation, surface-formaldehyde
Organization: U.S. Environmental Protection Agency
CAIRSENSE-Denver

The databases contain continuous sensor information as well as time stamped equivalent reference data. 

This dataset is associated with the following publication:
Feinberg, S., R. Williams, G. Hagler, J. Rickard, R. Brown, D. Garver, G. Harshfield, P. Stauffer, E. Mattson, R. Judge, and S. Garvey. Long-term evaluation of air sensor technology under ambient conditions in Denver, Colorado.   Atmospheric Measurement Techniques. Copernicus Publications, Katlenburg-Lindau,  GERMANY, 11(8): 4605-4615, (2018).

Tags: cairsense, performance-evaluations, sensors
Organization: U.S. Environmental Protection Agency
Human health impact of non-potable reuse of distributed wastewater and greywater treated by membrane bioreactors

This dataset contains simulated annual probabilities of infection for non-potable indoor use of greywater or wastewater treated by membrane bioreactors and chlorine disinfection.  The .zip file contains .csv files for each combination of source water and pathogen; see readme file (read me file.txt) for data dictionary and file naming convention. 

This dataset is associated with the following publication:
Schoen, M., M. Jahne, and J. Garland. Human health impact of non-potable reuse of distributed wastewater and greywater treated by membrane bioreactors (Microbial Risk Analysis).   Microbial Risk Analysis. Elsevier B.V., Amsterdam,  NETHERLANDS, 9: 72-81, (2018).

Tags: decentralized-systems, greywater, log-reduction-target, microbial-risk-assessment, non-potable, pathogens, potable, qmra, wastewater, water-reuse, waterborne-pathogens
Organization: U.S. Environmental Protection Agency
Placeholder

Placeholder. This dataset is not publicly accessible because: This manuscript is based on literature review. No analysis was performed and there is no data associated with this product. It can be accessed through the following means: This manuscript is based on literature review. No analysis was performed and there is no data associated with this product. Format: This manuscript is based on literature review. No analysis was performed and there is no data associated with this product. 

This dataset is associated with the following publication:
Briski, E., F. Chan, J. Darling, V. Lauringson, H. MacIsaac, A. Zhan, and S. Bailey. Beyond propagule pressure: importance of selection during the transport stage of biological invasions.   FRONTIERS IN ECOLOGY AND THE ENVIRONMENT. Ecological Society of America, Ithaca, NY, USA, 16(6): 345-353, (2018).

Tags: genetic-diversity, invasion-process, selection, transport
Organization: U.S. Environmental Protection Agency
Clarksburg green infrastructure data

This data set includes 5-minute time series runoff and precipitation data of neighborhood catchments with a variety of stormwater control measures, and definition of individual precipitation-runoff events and associated runoff metrics. Also included are geospatial data that delineates the neighborhood catchments with their land use/land cover and stormwater infrastructure. 

This dataset is associated with the following publication:
Woznicki, S., K. Hondula, and T. Jarnagin. Effectiveness of landscape‐based green infrastructure for stormwater management in suburban catchments.   Hydrological Processes. John Wiley & Sons, Ltd., Indianapolis, IN, USA, 32(15): 2346-2361, (2018).

Tags: best-management-practices, green-infrastructure, maryland, stormwater-control-measures, stormwater-management, urbanization, usa
Organization: U.S. Environmental Protection Agency
Dataset of Measurements of parameters controlling the emissions of organophoshpate flame retardants in indoor environments

The data presented in this data file is a product of a journal publication. The dataset contains measurements of mass transfer, material/air, and surface/air partition coefficients and emission concentrations of OPFRs in chambers and diffusion tubes. It also contains modeling data. 

This dataset is associated with the following publication:
Liang, Y., X. Liu, and M. Allen. Measurements of Parameters Controlling the Emissions of Organophosphate Flame Retardants in Indoor Environments.   ENVIRONMENTAL SCIENCE & TECHNOLOGY. American Chemical Society, Washington, DC, USA,  5821-5829, (2018).

Tags: chamber-testing, material-air-partition, material-phase-diffusion, organophosphorus-flame-retardants-opfrs, semivolatile-organic-compounds-svocs, surface-air-partition
Organization: U.S. Environmental Protection Agency
Suspect Screening Analysis of Chemicals in Consumer Products

A suspect screening analysis method is presented to rapidly characterize chemicals in 100 consumer products -- whether they be formulations (shampoos, paints), articles (upholsteries, shower curtains), or foods (cereals) – and therefore supports broader efforts to prioritize chemicals based on potential human health risks. A two-dimensional gas chromatography-time of flight/mass spectrometry method was used to screen for chemicals in selected products. Analysis yielded 4270 unique chemical signatures across the products, with 1602 signatures tentatively identified using the National Institute of Standards and Technology 2008 spectral database. Chemical standards confirmed the presence of 119 compounds. Of the 1602 chemicals, 1404 were not present in a public database of known consumer product chemicals. 

This dataset is associated with the following publication:
Phillips, K., A. Yau, K. Favela, K. Isaacs, A. McEachran, C. Grulke, A. Richard, A. Williams, J. Sobus, R. Thomas, and J. Wambaugh. Suspect Screening Analysis of Chemicals in Consumer Products.   ENVIRONMENTAL SCIENCE & TECHNOLOGY. American Chemical Society, Washington, DC, USA, 52(5): 3125-3135, (2018).

Tags: consumer-products, expocast, exposure, gas-chromatography-mass-spectrometry-gc-ms
Organization: U.S. Environmental Protection Agency
Rapid Experimental Estimates of Physicochemical Properties

We have performed high-throughput experimental estimates of five physicochemical properties for a set of 200 chemicals to evaluate the consistency with previous measurements, factors impacting consistency and experimental success, and the applicability domain of the new data in relation to previously measured data and predictive models. 

This dataset is associated with the following publication:
Nicolas, C., K. Mansouri, K. Phillips, C. Grulke, A. Richard, A. Williams, J. Rabinowitz, K. Isaacs, A. Yau, and J. Wambaugh. (ENVIRONMENTAL SCIENCE and TECHNOLOGY) Rapid Experimental Estimates of Physicochemical Properties to Inform Models and Testing.   ENVIRONMENTAL SCIENCE & TECHNOLOGY. American Chemical Society, Washington, DC, USA, 636: 901-909, (2018).

Tags: expocast, exposure, physicochemical-properties, qsar-modeling, quantitative-structure-activity-relationship-qsar
Organization: U.S. Environmental Protection Agency
HTTK R Package v1.7 - Evaluation and Calibration of High-Throughput Predictions of Chemical Distribution to Tissues

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., W. Setzer, J. Davis, and J. Wambaugh. Evaluation and Calibration of High-Throughput Predictions of Chemical Distribution to Tissues.   JOURNAL OF PHARMACOKINETICS AND PHARMACODYNAMICS. Springer, New York, NY, USA, 44(6): 549-565, (2017).

Tags: expocast, exposure, high-throughput-toxicokinetics, httk, in-vitro-to-in-vivo-extrapolation-ivive, pbpk-reverse-dosimetry, r-package, toxcast
Organization: U.S. Environmental Protection Agency
Differentiating Pathway-Specific From Nonspecific Effects in High-Throughput Toxicity Data: A Foundation for Prioritizing Adverse Outcome Pathway Development

Previous work identified a ‘cytotoxic burst’ (CTB) phenomenon wherein large numbers of the ToxCast assays begin to respond at or near test chemical concentrations that elicit cytotoxicity, and a statistical approach to defining the bounds of the CTB was developed. To focus AOP development on the molecular targets corresponding to ToxCast assays indicating pathway-specific effects, we conducted a meta-analysis to identify which assays most frequently respond at concentrations below the CTB.  A preliminary list of potentially important, target-specific assays was determined by ranking assays by the fraction of chemical hits below the CTB compared to the number of chemicals tested.  Additional priority assays were identified using a diagnostic-odds-ratio approach which gives greater ranking to assays with high specificity but low responsivity. Combined, the two prioritization methods identified several novel targets (e.g., peripheral benzodiazepine and progesterone receptors) to prioritize for AOP development, and affirmed the importance of a number of existing AOPs aligned with ToxCast targets (e.g., thyroperoxidase, estrogen receptor, aromatase). 

This dataset is associated with the following publication:
Fay, K., J. Swintek, D. Villeneuve, S. Edwards, M. Nelms, B. Blackwell, and G. Ankley. Differentiating pathway-specific from non-specific effects in high-throughput toxicity data: A foundation for prioritizing adverse outcome pathway development.   TOXICOLOGICAL SCIENCES. Society of Toxicology, RESTON, VA,  163(2): 500-515, (2018).

Tags: adverse-outcome-pathway, aquatic-ecosystems, computational-toxicology, ecotoxicology, endocrine-disruption, screening-and-prioritization, toxcast
Organization: U.S. Environmental Protection Agency
2009 USVI

EPA conducted a small regional coral reef assessment at 13 stations selected to represent a range of human influence around Charlotte Amalie (CA) Port in St. Thomas.  Sites were selected to represent an east-west gradient of human disturbance with CA at its center. In order to minimize habitat differences, all locations were selected in close proximity to land and at a similar depth (5-9 m). Multiple biological assemblages were measured, including stony corals, sponges and gorgonians, fish, and invertebrates. 

This dataset is associated with the following publication:
Oliver, L., W. Fisher, L. Fore, A. Smith, and P. Bradley. Assessing Land Use, Sedimentation and Water Quality Stressors as Predictors of Coral Reef Condition in St. Thomas, U.S. Virgin Islands.   ENVIRONMENTAL MONITORING AND ASSESSMENT. Springer, New York, NY, USA, 190: 213, (2018).

Tags: biocriteria, coral-reef-condition, probability-based-sampling, puerto-rico, reef-assessments, stony-coral, usvi
Organization: U.S. Environmental Protection Agency
Intergenerational responses of wheat to CeO2 nanoparticles, growth and nutrient contents

The intergenerational impact of engineered nanomaterials in plants is a key knowledge gap in the literature. A soil microcosm study was performed to assess the effects of multi-generational exposure of wheat (Triticum aestivum L.) to cerium oxide nanoparticles (CeO2-NPs). Seeds from plants that were exposed to 0, 125, and 500 mg CeO2-NPs/kg soil (Ce-0, Ce-125 or Ce-500, respectively) in first generation (S1) were cultivated in factorial combinations of Ce-0, Ce-125 or Ce-500 to produce second generation (S2) plants. The factorial combinations for first/second generation treatments in Ce-125 were S1-Ce-0/S2-Ce-0, S1-Ce-0/S2-Ce-125, S1-Ce-125/S2-Ce-0 and S1-Ce-125/S2-Ce-125, and in Ce-500 were S1-Ce-0/S2-Ce-0, S1-Ce-0/S2-Ce-500, S1-Ce-500/S2-Ce-0 and S1-Ce-500/S2-Ce-500. Agronomic, elemental, isotopic, and synchrotron X-ray fluorescence (XRF) and X-ray absorption near-edge spectroscopy (XANES) data were collected on second generation plants. Results showed that plants treated during the first generation only with either Ce-125 or Ce-500 (e.g. S1-Ce-125/S2-Ce-0 or S1-Ce-500/S2-Ce-0) had reduced accumulation of Ce (61 or 50%), Fe (49 or 58%) and Mn (34 or 41%) in roots, and δ15N (11 or 8%) in grains compared to the plants not treated in both generations (i.e. S1-Ce-0/S2-Ce-0). Plants treated in both generations with Ce-125 (i.e. S1-Ce-125/S2-Ce-125) produced grains that had lower Mn, Ca, K, Mg and P relative to plants treated in the second generation only (i.e. S1-Ce-0/S2-Ce-125). In addition, synchrotron XRF elemental chemistry maps of soil/plant thin-sections revealed limited transformation of CeO2-NPs with no evidence of plant uptake or accumulation. The findings demonstrated that first generation exposure of wheat to CeO2-NPs affects the physiology and nutrient profile of the second generation plants. However, the lack of concentration-dependent responses indicate that complex physiological processes are involved which alter uptake and metabolism of CeO2-NPs in wheat. 

This dataset is associated with the following publication:
Rico, C., M. Johnson, M. Marcus, and C. Andersen. Intergenerational responses of wheat (Triticum aestivum L.) to cerium oxide nanoparticles exposure.   Environmental Science: Nano. RSC Publishing, Cambridge,  UK, 4: 700-711, (2017).

Tags: ammonium-nitrate, engineered-nanomaterials-enms, intergenerational-effects, isotope, isotopic-discrimination, nitrogen
Organization: U.S. Environmental Protection Agency