AndreaBozzo/ceres-open-data-index huggingface dataset:
Doc Title:  Adult Hippocampal Neurogenesis is Impaired by Transient Developmental Thyroid Hormone Disruption

Severe thyroid hormone (TH) deprivation during development impairs neurogenesis throughout the brain. The hippocampus also maintains a capacity for neurogenesis throughout life which is reduced in adult-onset hypothyroidism. This study examined hippocampal volume in the neonate and adult hippocampal neurogenesis after developmental and adult-onset TH insufficiency. Pregnant rat dams were administered 0, 3, or 10 ppm of propylthiouracil (PTU) via drinking water from gestational day (GD) 6 until weaning. PTU at the high dose reduced body, brain, hippocampal weights on postnatal day (PN) 14, 21 and 78. Sub-regional analysis revealed decrements in hippocampal volumes at 10 but not 3 ppm PTU on PN23. In Experiment 2, one pair of adult male offspring of 0 and 3ppm-teated dams was placed on 3 ppm PTU from PN60, while a 2nd pair remained on control water. Adult neurogenesis was assessed by bromodeoxyuridine (BrdU, 50mg/kg, ip, 2X daily, X5 days) starting on PN90. Brains from animals perfused 1 and 28 days later were processed for immunohistochemistry. Although no volume changes were seen in neonates at 3ppm, thinning of the granule cell layer emerged in adulthood. Developmental TH insufficiency reduced BrdU+ve cells at 1-day with no further reduction at 28-days post-BrdU, indicative of a selective effect on cell proliferation. This was supported by fewer cells staining for the proliferative marker, Ki67. Adult only PTU did not impair neurogenesis or exacerbate effects seen with developmental exposure. A reduced capacity for neurogenesis may contribute to cognitive deficits evident in adults following moderate degrees of developmental TH insufficiency. 

This dataset is associated with the following publication:
Gilbert, M., J. Goodman, J. Gomez, A. Johnstone, and R. Ramos. Adult Hippocampal Neurogenesis is Impaired by Transient and Moderate Developmental Thyroid Hormone Disruption.   TOXICOLOGICAL SCIENCES. Society of Toxicology,     9-21, (2017).

Tags: brain, chemical-safety-for-sustainablity, developmental-neurotoxicity, hippocampus, neurogenesis, thyroid, thyroid-hormone-insufficiency
Organization: U.S. Environmental Protection Agency
Wehmas et al. 94-04 Toxicol Sci: Datasets for manuscript

Dataset includes overview text document (accepted version of manuscript) and tables, figures, and supplementary materials. Supplementary tables provide summary data underlying figures, as noted in the text. 

This dataset is associated with the following publication:
Wehmas, L., A. Deangelo, S. Hester, B. Chorley, G. Carswell, G. Olson, M. George, J. Carter, S. Eldridge, A. Fisher, B. Vallanat, and C. Wood. Metabolic Disruption Early in Life is Associated With Latent Carcinogenic Activity of Dichloroacetic Acid in Mice.   TOXICOLOGICAL SCIENCES. Society of Toxicology,    159(2): 354-365, (2017).

Tags: carcinogenesis, dichloroacetic-acid, early-life-exposure, liver, metabolism
Organization: U.S. Environmental Protection Agency
Cockle Emergence Lab Experiment (2017)

To identify the factors of green macroalgae (GMA) accumulation that cause cockles to rapidly emerge from the sediment, we conducted a series of laboratory experiments to isolate the effects of anoxia, surficial pressure/barrier, GMA presence, and the interaction of GMA presence and a surficial pressure/barrier on the emergence behavior of buried cockles.  We quantified the emergence response of cockles in each of these five treatments with six replicates (emergent proportion of cockles tank-1) per treatment (n = 30 tanks).  After the start of each trial, subjects were examined at 0.5, 1, 2, 4, 6, and 8 hrs for changes in burial depth; those that were partially or completely exposed at the sediment surface were considered to have exhibited an emergence response. 

This dataset is associated with the following publication:
Lewis, N., and T. DeWitt. Effect of Green Macroalgal Blooms on the Behavior, Growth, and Survival of Cockles (Clinocardium nuttallii) in Pacific NW Estuaries.   MARINE ECOLOGY PROGRESS SERIES. Inter-Research, Luhe,  GERMANY, 582: 105-120, (2017).

Tags: behavior, burial, cockle, ecosystem-services, eutrophication, green-macroalgae, gull, nutrient-enrichment, oregon, ulva-spp
Organization: U.S. Environmental Protection Agency
Gull Foraging Field Survey Data (2015)

We conducted a predation study to determine whether emergence from the sediment affected cockle survival or physiological condition.  We performed a field survey of the gull population from May-August 2015 in the same low-mid intertidal range of Idaho Flat that other field experiments were conducted.  Surveyed gulls were observed in order to determine diet composition.  This dataset contains all data collected during that field survey. 

This dataset is associated with the following publication:
Lewis, N., and T. DeWitt. Effect of Green Macroalgal Blooms on the Behavior, Growth, and Survival of Cockles (Clinocardium nuttallii) in Pacific NW Estuaries.   MARINE ECOLOGY PROGRESS SERIES. Inter-Research, Luhe,  GERMANY, 582: 105-120, (2017).

Tags: behavior, burial, cockle, ecosystem-services, eutrophication, green-macroalgae, gull, nutrient-enrichment, oregon, ulva-spp
Organization: U.S. Environmental Protection Agency
Cockle Temperature Exposure Lab Experiment (2016)

We carried out a lab experiment in which we exposed cockles to a range of air temperatures to simulate the physiological rigors of exposure to sunlight and air at the sediment surface during daytime low tides.  Cockles were subjected to twelve different temperature (6, 14, 21, 30, 34, 38 ± 1.0 °C) x time (2, 4 hrs) treatments within temperature-controlled chambers, representing the temperature and exposure durations regularly observed on Yaquina Bay mid-intertidal flats during daytime low tides in the summer.  This dataset contains all data collected during that lab experiment. 

This dataset is associated with the following publication:
Lewis, N., and T. DeWitt. Effect of Green Macroalgal Blooms on the Behavior, Growth, and Survival of Cockles (Clinocardium nuttallii) in Pacific NW Estuaries.   MARINE ECOLOGY PROGRESS SERIES. Inter-Research, Luhe,  GERMANY, 582: 105-120, (2017).

Tags: behavior, burial, cockle, ecosystem-services, eutrophication, green-macroalgae, gull, nutrient-enrichment, oregon, ulva-spp
Organization: U.S. Environmental Protection Agency
Cockle/Green Macroalgae Field Survey Data (2014)

To quantify any spatial or temporal variability in cockle densities with respect to in situ GMA biomass in Yaquina Bay, OR, we conducted field surveys during consecutive daytime low tides (<0.46 m MLLW) in both June and August 2014, which provided a comparison between early and late summer.  This dataset contains all data collected during those field surveys. 

This dataset is associated with the following publication:
Lewis, N., and T. DeWitt. Effect of Green Macroalgal Blooms on the Behavior, Growth, and Survival of Cockles (Clinocardium nuttallii) in Pacific NW Estuaries.   MARINE ECOLOGY PROGRESS SERIES. Inter-Research, Luhe,  GERMANY, 582: 105-120, (2017).

Tags: behavior, burial, cockle, ecosystem-services, eutrophication, green-macroalgae, gull, nutrient-enrichment, oregon, ulva-spp
Organization: U.S. Environmental Protection Agency
Cockle Field Caging Experiment Data (2014)

To determine whether differences in cockle density or qualitative burial depth observed during the 2014 field survey were affected by green macroalgal (GMA) mats, we conducted a field caging experiment whereby cockles were subjected to the presence or absence of simulated GMA mats for 12 weeks (July-September 2014).  This dataset contains all data collected during that field experiment. 

This dataset is associated with the following publication:
Lewis, N., and T. DeWitt. Effect of Green Macroalgal Blooms on the Behavior, Growth, and Survival of Cockles (Clinocardium nuttallii) in Pacific NW Estuaries.   MARINE ECOLOGY PROGRESS SERIES. Inter-Research, Luhe,  GERMANY, 582: 105-120, (2017).

Tags: behavior, burial, cockle, ecosystem-services, eutrophication, green-macroalgae, gull, nutrient-enrichment, oregon, ulva-spp
Organization: U.S. Environmental Protection Agency
Extending the Community Multiscale Air Quality (CMAQ) Modeling System to Hemispheric Scales

Hemispheric scale simulations with CMAQ and the Weather Research and Forecasting model are performed for multiple years. Model capabilities for a range of applications including episodic long-range pollutant transport, long-term trends in air pollution across the Northern Hemisphere, and air pollution-climate interactions are evaluated through detailed comparison with available surface, aloft, and remotely sensed observations. 

This dataset is associated with the following publication:
Mathur, R., J. Xing, R. Gilliam, G. Sarwar, C. Hogrefe, J. Pleim, G. Pouliot, S. Roselle, T. Spero, D. Wong, and J. Young. Extending the Community Multiscale Air Quality (CMAQ) Modeling System to Hemispheric Scales: Overview of Process Considerations and Initial Applications.   Atmospheric Chemistry and Physics. Copernicus Publications, Katlenburg-Lindau,  GERMANY, 17: 12449-12474, (2017).

Tags: background-pollution, hemispheric-cmaq, long-range-transport, wrf
Organization: U.S. Environmental Protection Agency
Evaluation of air pollutant emissions projections from the GCAM-USA integrated assessment model

This dataset contains 2010 emissions of nitrogen oxides, sulfur dioxide, and fine particulate matter by sector and state as modeled using the GCAM-USA integrated assessment model, in comparison to the 2011 National Emissions Inventory (NEI).  In addition, the dataset includes 2025 projections from both GCAM-USA and the NEI.
The dataset includes data underlying the figures and tables in the following journal article:
Wenjing Shi et al. (2017), Projecting state-level air pollutant emissions using an integrated assessment model: GCAM-USA.  Applied Energy, in review. 

This dataset is associated with the following publication:
Shi, W., Y. Ou, S. Smith, C. Ledna, C. Nolte, and D. Loughlin. Projecting state-level air pollutant emissions using an integrated assessment model: GCAM-USA..   Applied Energy. Elsevier B.V., Amsterdam,  NETHERLANDS, 208: 511-521, (2017).

Tags: air-quality, emissions, gcam-usa, integrated-assessment-modeling
Organization: U.S. Environmental Protection Agency
Data for MSM example application for MSM manuscript

Input data used by the MSM and HSPF for QMRA application to the Manitowoc Basin. 

This dataset is associated with the following publication:
Whelan, G., K. Kim, R. Parmar, G. Laniak, K. Wolfe, M. Galvin, M. Molina, Y. Pachepsky, P. Duda, R. Zepp, L. Prieto, J. Kinzelman, G.T. Kleinheinz, and M. Bouchard. Capturing microbial sources distributed in a mixed-use watershed within an integrated environmental modeling workflow.   ENVIRONMENTAL MODELLING AND SOFTWARE. Elsevier Science Ltd, New York, NY, USA, 99: 126-146, (2018).

Tags: integrated-environmental-modeling, manure, pathogens, qmra, risk-assessment, watershed-modeling
Organization: U.S. Environmental Protection Agency
Association rule mining data for census tract chemical exposure analysis

Chemical concentration, exposure, and health risk data for U.S. census tracts from National Scale Air Toxics Assessment (NATA). 

This dataset is associated with the following publication:
Huang, H., R. Tornero-Velez, and T. Barzyk. Associations between socio-demographic characteristics and chemical concentrations contributing to cumulative exposures in the United States.   Journal of Exposure Science and Environmental Epidemiology. Nature Publishing Group, London,  UK, 27(6): 544-550, (2017).

Tags: combined-effects, cumulative-risks, environmental-justice, multiple-stressors, rule-mining
Organization: U.S. Environmental Protection Agency
CMAQ predicted concentration files

model predicted concentrations. 

This dataset is associated with the following publication:
Muñiz-Unamunzaga, M., R. Borge, G. Sarwar, B. Gantt, D. de la Paz, C. Cuevas, and A. Saiz-Lopez. The influence of ocean halogen and sulfur emissions in the air quality of a coastal megacity: The case of Los Angeles.   SCIENCE OF THE TOTAL ENVIRONMENT. Elsevier BV, AMSTERDAM,  NETHERLANDS, 610(611): 1536-1545, (2018).

Tags: air-quality, cmaq, dms, halogens, los-angeles, marine-natural-emissions, urban-air-quality
Organization: U.S. Environmental Protection Agency
Digitized Onondaga Lake Dissolved Oxygen Concentrations and Model Simulated Values using Bayesian Monte Carlo Methods

The dataset is lake dissolved oxygen concentrations obtained form plots published by Gelda et al. (1996) and lake reaeration model simulated values using Bayesian Monte Carlo methods (Chaudhary and Hantush, 2017). The data also includes measured (Gelda et al., 1996 and references therein) versus estimated liquid film transfer coefficient values (KL) by Chaudhary and Hantush (2017). 

This dataset is associated with the following publication:
Chaudhary, A., and M. Hantush. Bayesian Monte Carlo and Maximum Likelihood Approach for Uncertainty Estimation and Risk Management:  Application to Lake Oxygen Recovery Model.  Mark van Loosdrecht  WATER RESEARCH. Elsevier Science Ltd, New York, NY, USA, 108: 301-311, (2017).

Tags: 95-confidence-interval, bayesian-statistics, liquid-film-transfer-coefficient, margin-of-safety, markov-chain-monte-carlo, model-calibration, monte-carlo-method, observed-dissolved-oxygen-concentration, simulated-dissolved-oxygen-concentration, tmdl, uncertainty-estimation, water-quality-management
Organization: U.S. Environmental Protection Agency
Data for Macrophyte Community Response to Nitrogen Loading and Thermal Stressors in Rapidly Flushed Mesocosm Systems

Data represent response variables from a series of mesocosm experiments to assess how estuarine macrophyte communities respond to nitrogen loading under two different thermal regimes. 

This dataset is associated with the following publication:
Kaldy, J., C. Brown, W. Nelson, and M. Frazier. Macrophyte Community Response to Nitrogen Loading and Thermal Stressors in Rapidly Flushed Mesocosm Systems.   JOURNAL OF EXPERIMENTAL MARINE BIOLOGY AND ECOLOGY. Elsevier Science Ltd, New York, NY, USA, 497: 107-119, (2017).

Tags: eutrophication, macroalgae, nutrient-pollution-index, nutrients, seagrass, temperature, wasting-disease, zostera-japonica, zostera-marina
Organization: U.S. Environmental Protection Agency
Barrierless Reactions with Loose Transition States Govern the Yields and Lifetimes of Organic Nitrates Derived from Isoprene

The attached extensive computational chemistry dataset was succinctly presented by Piletic et al. (Journal of Physical Chemistry A, 2017, DOI: 10.1021/acs.jpca.7b08229) and involves detailed electronic structure (density functional theory - DFT) and kinetic calculation (master equation formalism) outputs for the reactions of isoprene peroxy radical isomers with NOx.  The first three tabs describe the potential energy surfaces (PESs) of the beta and delta hydroxy-peroxy isoprene isomers reacting with NO to produce NO2, HONO and organic nitrates.  Microcanonical rate constants and organic nitrate yield data are presented in the fourth and fifth tabs.  The PESs for the reactions of the E and Z delta hydroxy-peroxy isoprene isomers is given in the sixth tab while the seventh tab shows the PES data for the reaction of the hydroxyl radical with several organic nitrates. 

This dataset is associated with the following publication:
Piletic, I., E. Edney, and L. Bartolotti. Barrierless Reactions with Loose Transition States Govern the Yields and Lifetimes of Organic Nitrates Derived from Isoprene.   JOURNAL OF PHYSICAL CHEMISTRY A. American Chemical Society, Washington, DC, USA, 121(43): 8306-8321, (2017).

Tags: air-quality, atmospheric-chemistry, chemical-mechanisms, cmaq, computational-chemistry, hono, isoprene, nox, organic-nitrate, ozone-concentrations, pm2-5
Organization: U.S. Environmental Protection Agency
Near-Port Air Quality Assessment Utilizing a Mobile Monitoring Approach

Near-Port Air Quality Assessment Utilizing a Mobile Monitoring Approach. 

This dataset is associated with the following publication:
Steffens, J., S. Kimbrough, R. Baldauf, V. Isakov, R. Brown, A. Powell, and P. Deshmukh. Near-Port Air Quality Assessment Utilizing a Mobile Monitoring Approach.   Atmospheric Pollution Research. Turkish National Committee for Air Pollution Research and Control, Izmir,  TURKEY, 8(6): 1023-1030, (2017).

Tags: air-quality, mobile-monitoring, near-source, ports
Organization: U.S. Environmental Protection Agency
Effects of energy system changes on CO2 projections for the United States_data tables with data dictionary

Dataset that corresponds to paper titled Effects of recent energy system changes on CO2 projections for the United States. 

This dataset is associated with the following publication:
Lenox, C., and D. Loughlin. Effects of recent energy system changes on CO2 projections for the United States.   CLEAN TECHNOLOGIES AND ENVIRONMENTAL POLICY. Springer-Verlag, New York, NY, USA, 19(9): 2277-2290, (2017).

Tags: air-quality, energy, greenhouse-gas, markal, modeling, systems-analyses
Organization: U.S. Environmental Protection Agency
Production, emissions and economic as well as historical marketing data for the pulp and paper industries in the United States

The pulp & paper sector database contains the entire population of integrated and non-integrated pulp and paper mills (approx. 663 mills) and their products in the U.S. Ion this database, all paper products in the modeling framework are grouped into eight major categories: 1) containerboard, 2) boxboard and other board, 3) packaging and industrial paper, 4) corrugating medium, 5) newsprint, 6) tissue, 7) coated printing and writing paper, and 8) uncoated printing and writing paper. The inputs data contain industry-specific data, market-specific data, and optimization parameters. Data outputs include optimized mitigation options and optimized economic parameters of products. The input data that are specific to the pulp and paper industry characterize the following aspects of individual facilities: unit-level production for each category of products, capacity, production cost (material, operations, and maintenance costs) (RISI 2011), capital cost, fuel types and cost, information about emissions sources (boilers, recovery furnaces, and lime kilns), mitigation technologies (emission controls), energy efficiency measures, and fuel emission intensities. The data related to mitigation technologies provide information regarding applicable air pollution control technologies, their costs, and their emission control characteristics. Similarly, data related to measures intended to increase energy efficiency provide information regarding applicable energy efficiency measures, their costs, and their characteristics. The market data consist of historical and projected nationwide commodity consumption, discount rates, cost of electricity, escalation rates, economic life of technologies, and import and export quantities and prices. 

This dataset is associated with the following publication:
Bhander , G., and W. Jozewicz. Universal industrial sectors integrated solutions module
for the pulp and paper industry.   Nordic Pulp & Paper Research Journal. Mid Sweden University, Sundsvall,  SWEDEN, 32(3): 375-385, (2017).

Tags: economic-analysis, emissions-analysis, environmental-analysis, historical-projected-data, industry-specific-data, market-specific-data, mitigation-options-and-cost, mitigation-technologies, modeling, multi-pollutant-assessment, pulp-and-paper-sector
Organization: U.S. Environmental Protection Agency
Air and Soil Data Files from Sumas Study

The data are summarized in the manuscript, but users may wish to apply them from these files. 

This dataset is associated with the following publication:
Wroble, J., T. Frederick, A. Frame, and D. Vallero. Comparison of soil sampling and analytical methods for asbestos at the Sumas Mountain Asbestos Site—Working towards a toolbox for better assessment.   PLoS ONE. Public Library of Science, San Francisco, CA, USA, 12(7): e0180210, (2017).

Tags: asbestos, asbestos-in-air, contaminated-soil, naturally-occurring-asbestos, sediment, transmission-electronic-microscopy-tem
Organization: U.S. Environmental Protection Agency
Effects of Na and Ca on particle size; Effect of filtering on UV absorbance

Effects of Na and Ca on particle size; Effect of filtering on UV absorbance. 

This dataset is associated with the following publication:
Bouchard, D., C. Knightes, X. Chang, and B. Avant. Simulating Multiwalled Carbon Nanotube Transport in Surface Water Systems Using the Water Quality Analysis Simulation Program (WASP).   ENVIRONMENTAL SCIENCE & TECHNOLOGY. American Chemical Society, Washington, DC, USA, 51(19): 11174–11184, (2017).

Tags: carbon-nanotubes, mwcnts, nanomaterials, wasp8, water-quality-modeling
Organization: U.S. Environmental Protection Agency
Data for Assessing background levels of specific conductivity using weight of evidence 508 compliant

Data contains sampling station locations with physical and chemical data.
Data: stations 508.xlsx (Ohio dataset), env.bio70 508.xlsx (WV biological station dataset). 

This dataset is associated with the following publication:
Cormier, S., L. Zheng, G. Suter, and C. Flaherty. Assessing background levels of specific conductivity using weight of evidence.   SCIENCE OF THE TOTAL ENVIRONMENT. Elsevier BV, AMSTERDAM,  NETHERLANDS, 628-629: 1637-1649, (2018).

Tags: applicability, background, chemistry, conductivity, ohio, regional, stream, water-quality, weight-of-evidence, west-virginia
Organization: U.S. Environmental Protection Agency
Datasets in Gene Expression Omnibus used in the study ORD-020382: Evaluation of estrogen receptor alpha activation by glyphosate-based herbicide constituents

GEO accession number of the microarray study. 

This dataset is associated with the following publication:
Mesnage, R., A. Phedonos, M. Biserni, M. Arno, S. Balu, C. Corton, R. Ugarte, and M. Antoniou. Evaluation of estrogen receptor alpha activation by glyphosate-based herbicide constituents.   FOOD AND CHEMICAL TOXICOLOGY. Elsevier Science Ltd, New York, NY, USA, 108: 30-42, (2017).

Tags: breast-cancer, estrogen-receptor, glyphosate, mcf-7-cells
Organization: U.S. Environmental Protection Agency
Data contributed by EPA/ORD/NERL/CED researchers to the manuscript "Advanced Error Diagnostics of the CMAQ and CHIMERE modeling systems within the AQMEII3 Model Evaluation Framework"

This dataset contains the data contributed by EPA/ORD/NERL/CED researchers to the manuscript "Advanced Error Diagnostics of the CMAQ and CHIMERE modeling systems within the AQMEII3 Model Evaluation Framework" led by Dr. Efisio Solazzo of the European Commission's Joint Research Center. 

This dataset is associated with the following publication:
Solazzo, E., C. Hogrefe, A. Colette, M. Garcia-Vivanco, and S. Galmarini. Advanced error diagnostics of the CMAQ and Chimere modelling systems within the AQMEII3 model evaluation framework.   Atmospheric Chemistry and Physics. Copernicus Publications, Katlenburg-Lindau,  GERMANY, 17: 10435-10465, (2017).

Tags: air-quality-model-evaluation, error-apportionment, error-persistence, ozone-diurnal-cycle, spectral-decomposition
Organization: U.S. Environmental Protection Agency
Human BDCM Mulit-Route PBPK Model

This data set contains the code for the BDCM human multi-route model written in the programming language acsl.  The final published manuscript is provided since it contains all the model parameters and data (from published literature). 

This dataset is associated with the following publication:
Kenyon , E., T.L. Leavens, C. Eklund , and R. Pegram. Development and Application of a Human PBPK Model for Bromodichloromethane (BDCM) to Investigate Impacts of Multi-Route Exposure.   JOURNAL OF APPLIED TOXICOLOGY. John Wiley & Sons, Ltd., Indianapolis, IN, USA, 36(9): 1095-1111, (2015).

Tags: acslx, bromodichloromethane, disinfection-byproducts, model-code, multi-route, pbpk, physiologically-based-pharmacokinetic-model
Organization: U.S. Environmental Protection Agency