AndreaBozzo/ceres-open-data-index huggingface dataset:
Updating sea spray aerosol emissions in the Community Multiscale Air Quality (CMAQ) model version 5.0.2

The uploaded data consists of the BRACE Na aerosol observations paired with CMAQ model output, the updated model's parameterization of sea salt aerosol emission size distribution, and the model's parameterization of the sea salt emission factor as a function of sea surface temperature. 

This dataset is associated with the following publication:
Gantt , B., J. Kelly , and J. Bash. Updating sea spray aerosol emissions in the Community Multiscale Air Quality (CMAQ) model version 5.0.2.   Geoscientific Model Development. Copernicus Publications, Katlenburg-Lindau,  GERMANY, 8: 3733-3746, (2015).

Tags: air-quality, base-cations, cmaq, natural-emissions
Organization: U.S. Environmental Protection Agency
Published journal article with data

published journal article. 

This dataset is associated with the following publication:
Schumacher, B., J. Zimmerman, J. Elliot, and G. Swanson. The Effect of Equilibration Time and Tubing Material on Soil Gas Measurements.   SOIL AND SEDIMENT CONTAMINATION: AN INTERNATIONAL JOURNAL. CRC Press LLC, Boca Raton, FL, USA, 25(2): 151-163, (2016).

Tags: equilibration-time, soil-gas, tce, trichloroethylene, tubing-type, volatile-organic-compounds
Organization: U.S. Environmental Protection Agency
Data sets for manuscript titled Unexpected benefits of reducing aerosol cooling effects

These data sets were created using extensive model simulation results from the WRF-CMAQ model, population distributions, and through the use of an health impact assessment model - see manuscript for details. 

This dataset is associated with the following publication:
Xing, J., J. Wang, R. Mathur , J. Pleim , S. Wang, C. Hogrefe , C. Gan, D. Wong , and J. Hao. Unexpected Benefits of Reducing Aerosol Cooling Effects.   ENVIRONMENTAL SCIENCE & TECHNOLOGY. American Chemical Society, Washington, DC, USA, 50(14): 7527–7534, (2016).

Tags: aerosol-direct-effects, air-pollution-exposure, air-quality-climate-interactions, hemispheric-cmaq, wrf-camq
Organization: U.S. Environmental Protection Agency
Exploring Global Exposure Factors Resources URLs

The dataset is a compilation of hyperlinks (URLs) for resources (databases, compendia, published articles, etc.) useful for exposure assessment specific to consumer product use. 

This dataset is associated with the following publication:
Zaleski, R., P. Egeghy, and P. Hakkinen. Exploring Global Exposure Factors Resources for Use in Consumer Exposure Assessments.   International Journal of Environmental Research and Public Health. Molecular Diversity Preservation International, Basel,  SWITZERLAND, 13(7): 744, (2016).

Tags: consumer-behavior, expocast, exposure-assessment, exposure-factors, household-products, time-activity-patterns, urls, web-addresses
Organization: U.S. Environmental Protection Agency
Multi-laboratory survey of qPCR enterococci analysis method performance in U.S. coastal and inland surface waters

Quantitative polymerase chain reaction (qPCR) has become a frequently used technique for quantifying enterococci in recreational surface waters, but there are several methodological options.  Here we evaluated how three method permutations, type of mastermix, sample extract dilution and use of controls in results calculation, affect method reliability among multiple laboratories with respect to sample interference.  Multiple samples from each of 22 sites representing an array of habitat types were analyzed using EPA Method 1611 and 1609 reagents with full strength and five-fold diluted extracts.  The presence of interference was assessed three ways: using sample processing and PCR amplifications controls; consistency of results across extract dilutions; and relative recovery of target genes from spiked enterococci in water sample compared to control matrices with acceptable recovery defined as 50 to 200%.  Method 1609, which is based on an environmental mastermix, was found to be superior to Method 1611, which is based on a universal mastermix. Method 1611 had over a 40% control assay failure rate with undiluted extracts and a 6% failure rate with diluted extracts.  Method 1609 failed in only 11% and 3% of undiluted and diluted extracts analyses.  Use of sample processing control assay results in the delta-delta Ct method for calculating relative target gene recoveries increased the number of acceptable recovery results.  Delta-delta tended to bias recoveries from apparent partially inhibitory samples on the high side which could help in avoiding potential underestimates of enterococci - an important consideration in a public health context.  Control assay and delta-delta recovery results were largely consistent across the range of habitats sampled, and among laboratories.  The methodological option that best balanced acceptable estimated target gene recoveries with method sensitivity and avoidance of underestimated enterococci densities was Method 1609 without extract dilution and using the delta-delta calculation method.  The applicability of this method can be extended by the analysis of diluted extracts to sites where interference is indicated but, particularly in these instances, should be confirmed by augmenting the control assays with analyses for target gene recoveries from spiked target organisms. 

This dataset is associated with the following publication:
Haugland , R., S. Siefring , M. Varma , K. Oshima , M. Sivaganesan , Y. Cao, M. Raith, J. Griffith, S. Weisberg, R. Noble, A.D. Blackwood, J. Kinzelman, T. Anan'eva, R. Bushon, E. Stelzer, V. Harwood, K. Gordon, and C. Sinigalliano. Multi-laboratory survey of qPCR enterococci analysis method performance in U.S. coastal and inland surface waters.   JOURNAL OF MICROBIOLOGICAL METHODS. Elsevier Science Ltd, New York, NY, USA, 123(1): 114-125, (2016).

Tags: enterococci, epa-method-1609, epa-method-1611, interference, performance, qpcr
Organization: U.S. Environmental Protection Agency
IMPACT OF GENETIC STRAIN ON BODY FAT LOSS, FOOD CONSUMPTION, METABOLISM, VENTILATION, AND MOTOR ACTIVITY IN FREE RUNNING FEMALE RATS

Physiologic data associated with different strains of common laboratory rat strains. 

This dataset is associated with the following publication:
Gordon , C., P. Phillips , and A. Johnstone. Impact of Genetic Strain on Body Fat Loss, Food Consumption, Metabolism, Ventilation, and Motor Activity in Free Running Female Rats.   PHYSIOLOGY AND BEHAVIOR. Elsevier Science Ltd, New York, NY, USA, 153: 56-63, (2016).

Tags: body-fat, genetic-strain, metabolism, running-wheel, ventilation
Organization: U.S. Environmental Protection Agency
VIIRS satellite and ground pm2.5 monitoring data

contains all satellite, pm2.5, and meteorological data used in statistical modeling effort to improve prediction of pm2.5. 

This dataset is associated with the following publication:
Schliep, E., A. Gelfand, and D. Holland. Autoregressive Spatially-Varying Coefficient Models for Predicting Daily PM2:5 Using VIIRS Satellite AOT.   Advances in Statistical Climatology, Meteorology and Oceanography. Copernicus Publications, Katlenburg-Lindau,  GERMANY, 1(0): 59-74, (2015).

Tags: pm2-5, prediction, satellite-viirs-data
Organization: U.S. Environmental Protection Agency
Hoffman etal 2016 Fisheries Data

Fish collection data associated with the data analysis presented in  Hoffman et al. 2016. Fisheries 41(1):26-37, DOI: 10.1080/03632415.2015.1114926. 

This dataset is associated with the following publication:
Hoffman , J., J. Schloesser, A. Trebitz , G. Peterson , M. Gutsch , H. Quinlan, and J. Kelly. Sampling design for early detection of aquatic invasive species in Great Lakes ports.   FISHERIES. American Fisheries Society, Bethesda, MD, USA, 41(1): 26-37, (2016).

Tags: aquatic-invasive-species, dna-technology, fish, great-lakes, sampling-design
Organization: U.S. Environmental Protection Agency
Nitrogen Discharge due to Climate Change and Land Cover Change

Simulated model output for the figures in the associated publication. Data are SWAT model simulation results for different scenarios of land-use change and climate change (Temp and Precip, Carbon Dioxide). The results are for two simulated watersheds in the Neuse River basin in North Carolina, USA. These are the raw data used to develop the figures in the paper. 

This dataset is associated with the following publication:
Gabriel , M., C. Knightes , E. Cooter , and R. Dennis. Evaluating relative sensitivity of SWAT-simulated nitrogen discharge to projected climate and land cover changes for two watersheds in North Carolina, USA.   Hydrological Processes. John Wiley & Sons, Ltd., Indianapolis, IN, USA,  online, (2015).

Tags: biogeochemical-cycling, clean-air-act, climate-change, landuse, nitrogen, swat
Organization: U.S. Environmental Protection Agency
DataSet for Passive Containment Journal Article

This data is for Figures 6 and 7 in the journal article.  The data also includes the two EPANET input files used for the analysis described in the paper, one for the looped system and one for the block system. 

This dataset is associated with the following publication:
Grayman, W., R. Murray , and D. Savic. Redesign of Water Distribution Systems for Passive Containment of Contamination.   JOURNAL OF THE AMERICAN WATER WORKS ASSOCIATION. American Water Works Association, Denver, CO, USA, 108(7): 381-391, (2016).

Tags: containment, contamination, district-meter-areas, drinking-water-distribution-system, epanet, homeland-security, modeling, water-quality, water-security
Organization: U.S. Environmental Protection Agency
Global evaluation of ammonia bidirectional exchange and livestock diurnal variation schemes

There is no EPA generated dataset in this study. This dataset is not publicly accessible because: No EPA generated datasets were used in this study. The sole EPA author assisted in the development of the model algorithms and writing portions of the manuscript. It can be accessed through the following means: Modeling and input data can be accessed by contacting the corresponding author of the paper: Daven Henze (daven.henze@colorado.edu)
. Format: None. 

This dataset is associated with the following publication:
Zhu, L., D. Henze, J. Bash , G. Jeong, K. Cady-Pereira, M. Shephard, M. Luo, F. Poulot, and S. Capps. Global evaluation of ammonia bidirectional exchange and livestock diurnal variation schemes.   Atmospheric Chemistry and Physics. Copernicus Publications, Katlenburg-Lindau,  GERMANY, 15: 12823-12843, (2015).

Tags: global-model, inverse-modeling, nh3-emissions, nitrogen-cycle
Organization: U.S. Environmental Protection Agency
Genetic linkage map and comparative genome analysis for the estuarine Atlantic killifish (Fundulus heteroclitus)

Genetic linkage maps are valuable tools in evolutionary biology; however, their availability for wild populations is extremely limited. Fundulus heteroclitus (Atlantic killifish) is a non-migratory estuarine fish that exhibits high allelic and phenotypic diversity partitioned among subpopulations that reside in disparate environmental conditions. An ideal candidate model organism for studying gene-environment interactions, the molecular toolbox for F. heteroclitus is limited. We identified hundreds of novel microsatellites which, when combined with existing microsatellites and single nucleotide polymorphisms (SNPs), were used to construct the first genetic linkage map for this species. By integrating independent linkage maps from three genetic crosses, we developed a consensus map containing 24 linkage groups, consistent with the number of chromosomes reported for this species. These linkage groups span 2300 centimorgans (cM) of recombinant genomic space, intermediate in size relative to the current linkage maps for the teleosts, medaka and zebrafish. Comparisons between fish genomes support a high degree of synteny between the consensus F. heteroclitus linkage map and the medaka and (to a lesser extent) zebrafish physical genome assemblies. 

This dataset is associated with the following publication:
Waits , E., J. Martinson , B. Rinner, S. Morris, D. Proestou, D. Champlin , and D. Nacci. Genetic linkage map and comparative genome analysis for the estuarine Atlantic killifish (Fundulus heteroclitus).   Open Journal of Genetics. Scientific Research Publishing, Inc., Irvine, CA, USA, 6: 28-38, (2016).

Tags: fundulus-heteroclitus, genetic-linkage-map, microsatellite, single-nucleotide-polymorphism-snp, synteny-analysis
Organization: U.S. Environmental Protection Agency
Evaluation of the Efficacy of Methyl Bromide in the Decontamination of Building and Interior Materials Contaminated with Bacillus anthracis Spores

Spreadsheets containing data for recovery of spores from different materials.  Data on the fumigation parameters are also included. 

This dataset is associated with the following publication:
Wood , J., M. Wendling, W. Richter, A. Lastivka, and L. Mickelsen. Evaluation of the Efficacy of Methyl Bromide in the Decontamination of Building and Interior Materials Contaminated with Bacillus anthracis Spores.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY. American Society for Microbiology, Washington, DC, USA,  1-28, (2016).

Tags: bacillus-anthracis, decontamination, methyl-bromide
Organization: U.S. Environmental Protection Agency
Decontamination Data - Blister Agents

Decontamination efficacy data for blister agents on various building materials using various decontamination solutions. 

This dataset is associated with the following publication:
Stone, H., D. See, A. Smiley, A. Ellingson, J. Schimmoeller, and L. Oudejans. Surface Decontamination of Blister Agents Lewisite, Sulfur Mustard and Agent Yellow, a Lewisite and Sulfur Mustard Mixture.   JOURNAL OF HAZARDOUS MATERIALS. Elsevier Science Ltd, New York, NY, USA,  1-5, (2015).

Tags: agent-yellow, blister-agents, chemical-warfare-agents, decontamination, efficacy, lewisite, sulfur-mustard
Organization: U.S. Environmental Protection Agency
CES_EHP_Figure_2

The increasing number of chemicals for which SHEDS probabilistic exposure assessment has been performed over the years. 

This dataset is associated with the following publication:
Egeghy , P., L. Sheldon, K. Isaacs , H. Ozkaynak, M. Goldsmith, J. Wambaugh , R. Judson , and T. Buckley. Computational Exposure Science: An Emerging Discipline to Support 21st-Century Risk Assessment.   ENVIRONMENTAL HEALTH PERSPECTIVES. National Institute of Environmental Health Sciences (NIEHS), Research Triangle Park, NC, USA, 124(6): 697–702, (2016).

Tags: computational-exposure, expocast, exposure-assessment, exposure-modeling, informatics, sheds
Organization: U.S. Environmental Protection Agency
Kanawha River Basin Sediment Data

This data set contains sediment size data collected at research sites using a Wolman Pebble Count method. 

This dataset is associated with the following publication:
Collins , S., M. Thoms, and J. Flotemersch. Hydrogeomorphic zones characterize riverbed sediment patterns within a river network.   River Systems. E. Schweizerbart'sche Verlagsbuchhandlung, Stuttgart,  GERMANY, 21(4): 203-213, (2015).

Tags: functional-process-zones, hydrogeomorphic-characterization, river-type, sediment-count
Organization: U.S. Environmental Protection Agency
Phylogeny and Species Diversity of Gulf of California Oysters

Dataset of DNA sequence data from two mitochondrial loci (COI and 16S) used to infer the phylogeny of oysters in the genus Ostrea along the Pacific coast of North America. This dataset is not publicly accessible because: It's already publicaly available. It can be accessed through the following means: GenBank/NCBI (http://www.ncbi.nlm.nih.gov/). Accession numbers KT317088-KT317610. Format: This dataset is DNA sequence data. It is available in GenBank. Accession numbers KT317088-KT317610. 

This dataset is associated with the following publication:
Raith, M., D. Zacherl, E. Pilgrim , and D. Eernisse. Phylogeny and species diversity of Gulf of California oysters (Ostreidae) inferred from mitochondrial DNA.   American Malacological Bulletin. American Malacological Society, Arlington, VA, USA, 33(2): 263-283, (2016).

Tags: aquatic-invasive-species, dna-barcoding, marcroinvertebrates, ostrea, oyster
Organization: U.S. Environmental Protection Agency
Figure_2_data

Data for Figure 2. 

This dataset is associated with the following publication:
Sarwar, G., D. Kang, K. Foley, D. Schwede, B. Gantt, and R. Mathur. Technical note: Examining ozone deposition over seawater.   ATMOSPHERIC ENVIRONMENT. Elsevier Science Ltd, New York, NY, USA, 141: 255–262, (2016).

Tags: deposition, dimethylsulfide, dissolved-organic-carbon, iodide, ozone
Organization: U.S. Environmental Protection Agency
Data used to generate tables and figures in Holder et al. (2016) Journal of Geophsyical Research: Atmospheres 121, doi:10.1002/2015JD024321

This dataset provides all data used to generate the figures and tables in the article entitled "Particulate matter and black carbon optical properties and emission factors from prescribed fires in the southeastern United States" published in the Journal of Geophysical Research: Atmospheres. 

This dataset is associated with the following publication:
Holder , A., G. Hagler , J. Aurell, M. Hays , and B. Gullett. Particulate matter and black carbon optical properties and emission factors from prescribed fires in the southeastern United States.   JOURNAL OF GEOPHYSICAL RESEARCH-ATMOSPHERES. American Geophysical Union, Washington, DC, USA, 121(7): 3465-3483, (2016).

Tags: aerosol-optical-properties, biomass-burning, black-carbon, brown-carbon, combustion-emissions, fine-particulate-matter, secondary-organic-aerosol
Organization: U.S. Environmental Protection Agency
Characterization of pollutant dispersion near elongated buildings based on wind tunnel simulations-BDW-1

This data set is associated with the results found in the journal article: Perry et al, 2016. Characterization of pollutant dispersion near elongated buildings based on wind tunnel simulations, Atmospheric Environment, 142, 286-295.
The paper presents a wind tunnel study of the effects of elongated rectangular buildings on the dispersion of pollutants from nearby stacks. The study examines the influence of source location, building aspect ratio, and wind direction on pollutant dispersion with the goal of developing improved algorithms within dispersion models. The paper also examines the current AERMOD/PRIME modeling capabilities compared to wind tunnel observations.  Differences in the amount of plume material entrained in the wake region downwind of a building for various source locations and source heights are illustrated with vertical and lateral concentration profiles. These profiles were parameterized using the Gaussian equation and show the influence of building/source configurations on those parameters. When the building is oriented at 45° to the approach flow, for example, the effective plume height descends more rapidly than it does for a perpendicular building, enhancing the resulting surface concentrations in the wake region. Buildings at angles to the wind cause a cross-wind shift in the location of the plume resulting from a lateral mean flow established in the building wake. These and other effects that are not well represented in many dispersion models are important considerations when developing improved algorithms to estimate the location and magnitude of concentrations downwind of elongated buildings. 

This dataset is associated with the following publication:
Perry , S., D. Heist , L. Brouwer, E. Monbureau, and L. Brixey. Characterization of pollutant dispersion near elongated buildings based on wind tunnel simulations.   ATMOSPHERIC ENVIRONMENT. Elsevier Science Ltd, New York, NY, USA, 142: 286-295, (2016).

Tags: building-downwash, dispersion-modeling, wind-tunnel
Organization: U.S. Environmental Protection Agency
Added Value via SPI supplement

Supplement that indicates where to find the source data sets on the EPA system. 

This dataset is associated with the following publication:
Bowden, J., K.D. Talgo, T. Spero , and C. Nolte. Assessing the Added Value of Dynamical Downscaling Using the Standardized Precipitation Index.   ADVANCES IN METEOROLOGY. Hindawi Publishing Corporation, New York, NY, USA, 2016(8432064): 14 pages, (2016).

Tags: dynamical-downscaling, regional-climate-modeling, spi, supplement, wrf
Organization: U.S. Environmental Protection Agency
Macroinvertebrate and organic matter export from headwater tributaries of a Central Appalachian stream

The dataset contains physicochemical and biological data from 12 headwater tributaries of Clemons Fork in Robinson Forest, KY. 

This dataset is associated with the following publication:
Pond , G., K. Fritz , and B. Johnson. Macroinvertebrate and organic matter export from headwater tributaries of a Central Appalachian stream.   HYDROBIOLOGIA. Springer, New York, NY, USA,  1-17, (2016).

Tags: aquatic-insects, central-appalachian-mountains, dispersal, drift, headwater-streams
Organization: U.S. Environmental Protection Agency
Toxicokinetics of PFOS in rainbow trout

This ScienceHub entry was developed for the published paper:  Consoer et al., 2016, Toxicokinetics of perfluorooctane sulfonate in rainow trout (Oncorhynchus mykiss), Environ. Toxicol. Chem. 35:717-727.  Individual rainbow trout were exposed to PFOS by bolus injection (elimination studies) or by adding PFOS to incoming water (branchial uptake studies).  The trout were fitted with indwelling catheters and urinary cannulae to permit periodic collection of blood and urine.  Additional sampling was conducted to evaluate PFOS uptake from and elimination to respired water.  Data obtained from each fish was evaluated using a clearance-volume pharmacokinetic model.  Modeled kinetic parameters were then averaged to develop summary statistics which were used as a basis for interpreting modeled results and making comparisons to a previous study of rainbow trout exposed to perfluorooctanoate (PFOA; Consoer et al., 2014, Aquat. Toxicol. 156:65-73).  The results of this study, combined with that of the previous PFOA study, suggest that PFOA is a substrate for renal transporters in fish while glomerular filtration alone may be sufficient to explain the observed renal elimination of PFOS.  These findings demonstrate that models developed to predict the bioaccumulation of perfluoroalkyl acids by fish must account for differences in renal clearance of individual compounds. 

This dataset is associated with the following publication:
Consoer, D., A. Hoffman , P. Fitzsimmons , P. Kosian , and J. Nichols. Toxicokinetics of perfluorooctane sulfonate in rainbow trout (Oncorhynchus mykiss).   ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY. Society of Environmental Toxicology and Chemistry, Pensacola, FL, USA, 35(3): 717-727, (2016).

Tags: bioaccumulation, fish, perfluorooctane-sulfonate, rainbow-trout, renal-elimination, toxicokinetics
Organization: U.S. Environmental Protection Agency
Data summary of all endpoints measured

qPCR results for Vitellogenin. 

This dataset is associated with the following publication:
Armstrong, B., J. Lazorchak , K. Jensen , H. Haring , M.E. Smith, R. Flick , D. Bencic , and A. Biales. Reproductive effects in fathead minnows (Pimphales promelas) following a 21 d exposure to 17α-ethinylestradiol.   CHEMOSPHERE. Elsevier Science Ltd, New York, NY, USA, 144(1): 366-373, (2015).

Tags: ethinylestradiol, fathead-minnows, reproductive-effects, vitellogenin-gene-and-protein
Organization: U.S. Environmental Protection Agency