AndreaBozzo/ceres-open-data-index huggingface dataset:
Photocatalytic C-H activation of Hydrocarbons over VO@g-C3N4

A highly selective and sustainable method has been developed for the oxidation of methyl arenes and their analogues. The VO@g-C3N4 catalyst is very efficient in the C-H activation and oxygen insertion reaction resulting in formation of the corresponding carbonyl compounds and phenols. 

This dataset is associated with the following publication:
Verms, S., R.B.N. Baig, M. Nadagouda, and R. Varma. Photocatalytic C–H Activation of Hydrocarbons over VO@g-C3N4.   ACS Sustainable Chemistry & Engineering. American Chemical Society, Washington, DC, USA, 4(4): 2333-2336, (2016).

Tags: c-h-activation, graphitic-carbon-nitride, heterogeneous-catalysis, photo-catalyst, vanadium-oxide
Organization: U.S. Environmental Protection Agency
USEEIOv1.1 - openLCA

This is a version of the full USEEIO v1.1 model in the openLCA schema serialized as JSON-LD that can be imported into openLCA software (www.openlca.org) v1.5 and more recent versions. 

This dataset is associated with the following publication:
Yang, Y., W. Ingwersen, T. Hawkins, and D. Meyer. USEEIO: A new and transparent United States environmentally extended input-output model.   JOURNAL OF CLEANER PRODUCTION. Elsevier Science Ltd, New York, NY, USA, 158: 308-318, (2017).

Tags: eeio, input-output-data, lca, lci, life-cycle-assessment, life-cycle-inventory-data, openlca, sustainability, useeio
Organization: U.S. Environmental Protection Agency
NLCD - MODIS land cover- albedo dataset for the continental United States

The NLCD-MODIS land cover-albedo database integrates high-quality MODIS albedo observations with areas of homogeneous land cover from NLCD. The spatial resolution (pixel size) of the database is 480m-x-480m aligned to the standardized UGSG Albers Equal-Area projection. The spatial extent of the database is the continental United States. 

This dataset is associated with the following publication:
Wickham, J., M. Nash, and C.A. Barnes. Effect of land cover change on snow free surface albedo across the continental United States.   Global and Planetary Change. Elsevier BV, AMSTERDAM,  NETHERLANDS, 146: 1-9, (2016).

Tags: climate-change, land-cover-change, landsat, radiative-forcing, snow-cover-albedo, snow-free-albedo
Organization: U.S. Environmental Protection Agency
A case study on the use of exposure-activity ratios (EARs) to prioritize sites, chemicals, and bioactivities of concern in Great Lakes waters

As a case study, chemical occurrence data from a 2012 study in the Great Lakes Basin along with the ToxCast™ effects database were used to calculate exposure-activity ratios (EARs) as a prioritization tool. Technical considerations of data processing and use of the ToxCast™ database are presented and discussed. EAR prioritization identified multiple sites, biological pathways, and chemicals that warrant further investigation. Biological pathways were then linked to adverse outcome pathways to identify potential adverse outcomes and biomarkers for use in subsequent monitoring efforts. 

This dataset is associated with the following publication:
Blackwell, B., G. Ankley, S. Corsi, L.A.  DeCicco, K. Houck, R. Judson, S. Li, M. Martin, A. Schroeder, J. Swintek, D. Villeneuve, E. Murphy, and E. Smith. An "EAR" on environmental surveillance and monitoring: A case study on the use of exposure-activity ratios to prioritize sites, chemicals, and bioactivities of concern in Great Lakes waters.   ENVIRONMENTAL SCIENCE & TECHNOLOGY. American Chemical Society, Washington, DC, USA, 51(15): 8713–8724, (2017).

Tags: adverse-outcome-pathway, aquatic-ecosystems, ecotoxicology, endocrine-disruption, exposure-activity-ratio, great-lakes-restoration-initiative, screening-and-prioritization
Organization: U.S. Environmental Protection Agency
First Generation Annotations for the Fathead Minnow (Pimephales promelas) Genome

The fathead minnow (Pimephales promelas) is a laboratory model organism widely used in regulatory toxicity testing and ecotoxicology research. Despite, the wealth of toxicological data for this organism, until recently genome scale information was lacking for the species, which limited the utility of the species for pathway-based toxicity testing and research. As part of a EPA Pathfinder Innovation Project, next generation sequencing was applied to generate a draft genome assembly, which was published in 2016. However, application of those genome-scale sequencing resources was still limited by the lack of available gene annotations for fathead minnow. Here we report on development of a first generation genome annotation for fathead minnow and the dissemination of that information through a web-based browser that makes it easy to search for genes of interest, extract the corresponding sequence, identify intron and exon boundaries and regulatory regions, and align the computationally predicted genes with other supporting evidence. This work greatly enhances the utility of the genome assemblies that were developed and makes it accessible to the ecotoxicology community world-wide, opening up a wide array of new research opportunities with the species. The URL associated with this data set provides access to the genome browser that was developed as well as the current gene models and evidence tracks. 

This dataset is associated with the following publication:
Saari, T., A. Schroeder, G. Ankley, and D. Villeneuve. First generation annotations for the fathead minnow (Pimephales promelas) genome.   ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY. Society of Environmental Toxicology and Chemistry, Pensacola, FL, USA, 36(12): 3436-3442, (2017).

Tags: adverse-outcome-pathway, aquatic-ecosystems, bioinformatics, ecotoxicology, endocrine-disruption, fish, genome, pimephales-promelas, screening-and-prioritization
Organization: U.S. Environmental Protection Agency
Figs1,2,3a

all data is in the netCDF format and zipped. after downloading this data, you need to unzip it first to create original netCDF formatted data. 

This dataset is associated with the following publication:
He, J., T. Glotfelty, K. Yahya, K. Alapaty, and S. Yu. Does temperature nudging overwhelm aerosol radiative effects in regional integrated climate models?.   ATMOSPHERIC ENVIRONMENT. Elsevier Science Ltd, New York, NY, USA, 154: 42-52, (2017).

Tags: aerosol-effects, aerosol-radiative-forcing, climate, nudging
Organization: U.S. Environmental Protection Agency
On the implications of aerosol liquid water and phase separation for organic aerosol mass

This dataset contains data presented in the figures of the paper "On the implications of aerosol liquid water and phase separation for organic aerosol mass" published in Atmospheric Chemistry and Physics. It also links to the data archive of field observations. 

This dataset is associated with the following publication:
Pye, H., B. Murphy, L. Xu, N. Ng, A. Carlton, H. Guo, R. Weber, P. Vasilakos, W. Appel, S. Budisulistiorini, J. Surratt, A. Nenes, W. Hu, J. Jimenez, G. saacman-VanWertz, P. Misztal, and A. Goldstein. On the implications of aerosol liquid water and phase separation for organic aerosol mass.   Atmospheric Chemistry and Physics. Copernicus Publications, Katlenburg-Lindau,  GERMANY, 17: 343-369, (2017).

Tags: aerosol, air-quality, cmaq, organic-aerosol, secondary-organic-aerosol, soa, soas, southeastern-usa, wrf-cmaq
Organization: U.S. Environmental Protection Agency
Significance of dissolved methane in effluents of anaerobically treated low strength wastewater and potential for recovery as an energy product: A review

The data set includes estimations of energy required for processes related to the operation of Anaerobic Membrane Bioreactors. 

This dataset is associated with the following publication:
Crone, B., J. Garland, G. Sorial, and L. Vane. Significance of dissolved methane in effluents of anaerobically treated low strength wastewater and potential for recovery as an energy product: A review.   WATER RESEARCH. Elsevier Science Ltd, New York, NY, USA, 104: 520-531, (2016).

Tags: anaerobic-treatment, energy-and-water
Organization: U.S. Environmental Protection Agency
Detroit Exposure and Aerosol Research Study

The DEARS represents a multipollutant spatial characterization of six neighborhoods and their residents in and around Detroit, Michigan.  Personal, residential indoor, residential outdoor, and ambient monitoring was performed.  Survey information was collected simultaneously with air quality monitoring to provide the means to examine a wide variety of exposure factors on personal exposure. 

This dataset is associated with the following publication:
Logue, J., M. Sherman, M. Lunden, N. Klepeis, R. Williams , C. Croghan , and B. Singer. Development and assessment of a physics-based simulation model to investigate residential PM2.5 infiltration across the US housing stock.   BUILDING AND ENVIRONMENT. Elsevier Science Ltd, New York, NY, USA, 94(1): 21-32, (2015).

Tags: air-quality, ambient, dears, particulate-matter, personal, residential
Organization: U.S. Environmental Protection Agency
Link to paper

Link to the paper. 

This dataset is associated with the following publication:
Naile, J., A.W. Garrison, J. Avants, and J. Washington. Isomers/enantiomers of perfluorocarboxylic acids: Method development and detection in environmental samples.   CHEMOSPHERE. Elsevier Science Ltd, New York, NY, USA, 144: 1722-1728, (2016).

Tags: chiral, enantiomers, enantioselectivity, isomers, perfluorocarboxylic-acids, pfcas, pfoa
Organization: U.S. Environmental Protection Agency
Supporting Information

This is the supporting information for the journal article. 

This dataset is associated with the following publication:
Rankin, K., S. Mabury, T. Jenkins, and J. Washington. A North American and global survey of perfluoroalkyl substances in surface soils: Distribution patterns and mode of occurrence.   CHEMOSPHERE. Elsevier Science Ltd, New York, NY, USA, 161: 333–341, (2016).

Tags: pfoa-pfos-background-soils
Organization: U.S. Environmental Protection Agency
Scenarios for low carbon and low water electric power plant operations: implications for upstream water use

The dataset includes all data used in the creation of figures and graphs in the paper: "Scenarios for low carbon and low water electric power plant operations: implications for upstream water use."   Data includes regional electricity mixes, full life cycle water use, and water use for each life cycle stage.  These encompass a range of scenarios out to 2050, and should not be used as predictions, forecasts or official baselines.  The scenarios and results are for research purposes only, and do not represent current or future U.S. EPA policies or regulations. 

This dataset is associated with the following publication:
Dodder , R., J. Barnwell , and W. Yelverton. Scenarios for low carbon and low water electric power plant operations: implications for upstream water use.   ENVIRONMENTAL SCIENCE & TECHNOLOGY. American Chemical Society, Washington, DC, USA, 50(21): 11460-11470, (2016).

Tags: energy, energy-modeling, energy-system, water
Organization: U.S. Environmental Protection Agency
Volatile and semivolatile organic compounds in laboratory peat fire emissions

Supporting information Tables S3 and S4 list emission factors in g/kg of speciated volatile and particulate organic compounds emitted from peat burning. Peat samples were acquired from Alligator River (AR) and Pocosin Lakes (PL) National Wildlife Refuges. 

This dataset is associated with the following publication:
George , I., R. Black, J. Walker , C. Geron , J. Aurell , M. Hays , W. Preston, and B. Gullett. Volatile and semivolatile organic compounds in laboratory peat fire emissions.   ATMOSPHERIC ENVIRONMENT. Elsevier Science Ltd, New York, NY, USA, 132: 163-170, (2016).

Tags: biomass-burning, particulate-mass, particulate-matter, polycyclic-aromatic-hydrocarbons, smoldering-combustion, volatile-organic-compounds
Organization: U.S. Environmental Protection Agency
Is Skin penetration a determining factor in skin sensitisation potential and potency? Refuting the notion of a LogKow threshold for Skin Sensitisation

t is widely accepted that substances that cannot penetrate through the skin will not be sensitizers. LogKow and molecular weight (MW) have been used to set thresholds for sensitization potential. Highly hydrophilic substances e.g. LogKow ≤ 1 are expected not to penetrate effectively to induce sensitization. To investigate whether LogKow >1 is a true requirement for sensitization, a large dataset of substances that had been evaluated for their skin sensitization potential under Registration, Evaluation, Authorisation and restriction of CHemicals (REACH), together with available measured LogKow values was compiled using the OECD eChemPortal. The incidence of sensitizers relative to non-sensitizers above and below a LogKow of 1 was explored. Reaction chemistry principles were used to explain the sensitization observed for the subset of substances with a LogKow ≤0. 1482 substances were identified with skin sensitization data and measured LogKow values. 525 substances had a measured LogKow ≤ 1, 100 of those were sensitizers. There was no significant difference in the incidence of sensitizers above and below a LogKow of 1. Reaction chemistry principles that had been established for lower MW and more hydrophobic substances were found to be still valid in rationalizing the skin sensitizers with a LogKow ≤ 0. The LogKow threshold arises from the widespread misconception that the ability to efficiently penetrate the stratum corneum is a key determinant of sensitization potential and potency. 

This dataset is associated with the following publication:
Fitzpatrick, J., D. Roberts, and G. Patlewicz. (Journal of Applied Toxicology) Is skin penetration a determining factor in skin sensitisation potential and potency? Refuting the notion of a LogKow threshold for Skin Sensitisation.   JOURNAL OF APPLIED TOXICOLOGY. John Wiley & Sons, Ltd., Indianapolis, IN, USA,  1-11, (2016).

Tags: chemistry-dashboard, dsstox, read-across, skin-sensitization
Organization: U.S. Environmental Protection Agency
Analysis of the Effects of Cell Stress and Cytotoxicity on In Vitro Assay Activity Across a Diverse Chemical and Assay Space

Chemical toxicity can arise from disruption of specific biomolecular functions or through more generalized cell stress and cytotoxicity-mediated processes. Here, concentration-dependent responses of 1063 chemicals including pharmaceuticals, natural products, pesticidals, consumer, and industrial chemicals across a diverse battery of 821 in vitro assay endpoints from 7 high-throughput assay technology platforms were analyzed in order to better distinguish between these types of activities. Both cell-based and cell-free assays showed a rapid increase in the frequency of responses at concentrations where cell stress / cytotoxicity responses were observed in cell-based assays. Chemicals that were positive on at least two viability/cytotoxicity assays within the concentration range tested (typically up to 100 M) activated a median of 12% of assay endpoints while those that were not cytotoxic in this concentration range activated 1.3% of the assays endpoints. The results suggest that activity can be broadly divided into: (1) specific biomolecular interactions against one or more targets (e.g., receptors or enzymes) at concentrations below which overt cytotoxicity-associated activity is observed; and (2) activity associated with cell stress or cytotoxicity, which may result from triggering of specific cell stress pathways, chemical reactivity, physico-chemical disruption of proteins or membranes, or broad low-affinity non-covalent interactions. Chemicals showing a greater number of specific biomolecular interactions are generally designed to be bioactive (pharmaceuticals or pesticidal active ingredients), while intentional food-use chemicals tended to show the fewest specific interactions. The analyses presented here provide context for use of these data in ongoing studies to predict in vivo toxicity from chemicals lacking extensive hazard assessment. 

This dataset is associated with the following publication:
Judson , R., K. Houck , M. Martin , A. Richard , T. Knudsen , I. Shah , S. Little , J. Wambaugh , W. Setzer , P. Kothiya , J. Phuong , D. Filer , D. Smith , D. Reif, D. Rotroff, N. Kleinstreuer, N. Sipes, M. Xia, R. Huang, K. Crofton , and R. Thomas. (Toxicological Sciences) Analysis of the Effects of Cell Stress and Cytotoxicity on In Vitro Assay Activity Across a Diverse Chemical and Assay Space.   TOXICOLOGICAL SCIENCES. Society of Toxicology,     1-47, (2016).

Tags: chemical-safety-for-sustainablity, chemical-safety-research, computational-toxicology, cytotoxicity, high-throughput-toxicology, toxcast
Organization: U.S. Environmental Protection Agency
Using ToxCast data to reconstruct dynamic cell state trajectories and estimate toxicological points of departure.

Background: High-content imaging (HCI) allows simultaneous measurement of multiple cellular phenotypic changes and is an important tool for evaluating the biological activity of chemicals.
Objectives: Our goal was to analyze dynamic cellular changes using HCI to identify the “tipping point” at which the cells did not show recovery towards a normal phenotypic state.
Methods: HCI was used to evaluate the effects of 967 chemicals (in concentrations ranging from 0.4 to 200 μM) on HepG2 cells over a 72-hr exposure period. The HCI end points included p53, c-Jun, histone H2A.x, α-tubulin, histone H3, alpha tubulin, mitochondrial membrane potential, mitochondrial mass, cell cycle arrest, nuclear size, and cell number. A computational model was developed to interpret HCI responses as cell-state trajectories.
Results: Analysis of cell-state trajectories showed that 336 chemicals produced tipping points and that HepG2 cells were resilient to the effects of 334 chemicals up to the highest concentration (200 μM) and duration (72 hr) tested. Tipping points were identified as concentration-dependent transitions in system recovery, and the corresponding critical concentrations were generally between 5 and 15 times (25th and 75th percentiles, respectively) lower than the concentration that produced any significant effect on HepG2 cells. The remaining 297 chemicals require more data before they can be placed in either of these categories.
Conclusions: These findings show the utility of HCI data for reconstructing cell state trajectories and provide insight into the adaptation and resilience of in vitro cellular systems based on tipping points. Cellular tipping points could be used to define a point of departure for risk-based prioritization of environmental chemicals. 

This dataset is associated with the following publication:
Shah , I., W. Setzer , J. Jack, K. Houck , R. Judson , T. Knudsen , J. Liu, M. Martin , D. Reif, A.M. Richard , R.S. Thomas , K. Crofton , D.J. Dix , and R.J. Kavlock. (Envir. Health Perspect.)   Using ToxCast data to reconstruct dynamic cell state trajectories and estimate toxicological points of departure.   ENVIRONMENTAL HEALTH PERSPECTIVES. National Institute of Environmental Health Sciences (NIEHS), Research Triangle Park, NC, USA,  1-33, (2015).

Tags: tipping-points, toxcast, virtual-embryo, virtual-liver, virtual-tissues
Organization: U.S. Environmental Protection Agency
High-throughput screening of chemical effects on steroidogenesis using H295R human adrenocortical carcinoma cells

Disruption of steroidogenesis by environmental chemicals can result in altered hormone levels causing adverse reproductive and developmental effects. A high-throughput assay using H295R human adrenocortical carcinoma cells was used to evaluate the effect of 2060 chemical samples on steroidogenesis via high-performance liquid chromatography followed by tandem mass spectrometry quantification of 10 steroid hormones, including progestagens, glucocorticoids, androgens, and estrogens. The study employed a 3 stage screening strategy. The first stage established the maximum tolerated concentration (MTC; ≥ 70% viability) per sample. The second stage quantified changes in hormone levels at the MTC whereas the third stage performed concentration-response (CR) on a subset of samples. At all stages, cells were prestimulated with 10 µM forskolin for 48 h to induce steroidogenesis followed by chemical treatment for 48 h. Of the 2060 chemical samples evaluated, 524 samples were selected for 6-point CR screening, based in part on significantly altering at least 4 hormones at the MTC. CR screening identified 232 chemical samples with concentration-dependent effects on 17β-estradiol and/or testosterone, with 411 chemical samples showing an effect on at least one hormone across the steroidogenesis pathway. Clustering of the concentration-dependent chemical-mediated steroid hormone effects grouped chemical samples into 5 distinct profiles generally representing putative mechanisms of action, including CYP17A1 and HSD3B inhibition. A distinct pattern was observed between imidazole and triazole fungicides suggesting potentially distinct mechanisms of action. From a chemical testing and prioritization perspective, this assay platform provides a robust model for high-throughput screening of chemicals for effects on steroidogenesis. 

This dataset is associated with the following publication:
Karmaus , A., C. Toole, D. Filer , K. Lewis, and M. Martin. (Toxicological Sciences) High-throughput screening of chemical effects on steroidogenesis using H295R human adrenocortical carcinoma cells.   TOXICOLOGICAL SCIENCES. Society of Toxicology,    150(2): 323-332, (2016).

Tags: cancer, chemical-safety-for-sustainablity, chemical-safety-research, computational-toxicology, high-throughput-toxicology, steroidogenesis, toxcast
Organization: U.S. Environmental Protection Agency
Gene expression and chemical exposure data for larval Pimephales promelas exposed to one of  four pyrethroid pesticides.

Uploaded datasets are detailed exposure information (chemical concentrations and water quality parameters) for exposures conducted in a flow through diluter system with larval Pimephales promelas to four different pyrethroid pesticides.  The GEO submission URL links to the NCBI GEO database and contains gene expression data from whole larvae exposed to different concentrations of the pyrethroids across multiple experiments. 

This dataset is associated with the following publication:
Biales, A., M. Kostich, A. Batt, M. See, R. Flick, D. Gordon, J. Lazorchak, and D. Bencic. Initial Development of a Multigene Omics-Based Exposure Biomarker for Pyrethroid Pesticides.   CRITICAL REVIEWS IN ENVIRONMENTAL SCIENCE AND TECHNOLOGY. CRC Press LLC, Boca Raton, FL, USA, 179(0): 27-35, (2016).

Tags: biomarker, fish, pyrethroids, transcriptomics
Organization: U.S. Environmental Protection Agency