AndreaBozzo/ceres-open-data-index huggingface dataset:
ShahSanjivkumar_HS7-53-05-146_Data-Metadata-Rev_Ftularensis RVPCR Method_Manuscript_20190830

This is a short communication manuscript entitled, “Rapid Viability (RV) PCR Protocol for Detection of Francisella tularensis” to be published in a peer-reviewed journal. This pathogen survives for many days in the environment and water. It is a very slow growing pathogen and can take several days to detect using the traditional microbiological culture methods. Therefore, a high-throughput RV-PCR protocol was developed and optimized by the EPA ORD’s National Homeland Security Research Center (NHSRC) to relatively rapidly detect F. tularensis. The RV-PCR method combines relatively shorter sample enrichment in growth media, and highly specific and sensitive PCR assay-based detection and identification of F. tularensis. Using this method, results can be obtained in 36 hours as compared to several days by the traditional microbiological culture methods. This manuscript contains summarized data from multiple experimental results to show the method performance in various experimental conditions mimicking a real-world interference material. The data has been extracted from the final report for the project on Optimization of a Rapid Viability (RV) PCR Protocol for Detection of Francisella tularensis in water. 

This dataset is associated with the following publication:
Kane, S., S. Shah, and T. Alfaro. Rapid Viability Polymerase Chain Reaction Method for Detection of Francisella tularensis.   JOURNAL OF MICROBIOLOGICAL METHODS. Elsevier Science Ltd, New York, NY, USA, 166: ., (2019).

Tags: biological-agent, detection, francisella-tularensis, indoor-outdoor-contamination, non-spore-forming-biological-agent, rapid-viability-pcr, tularemia, water-samples
Organization: U.S. Environmental Protection Agency
Dietary Lead and Phosphate Interactions Affect Oral Bioavailability of Soil Lead in the Mouse

Dietary Lead and Phosphate Interactions Affect Oral Bioavailability of Soil Lead in the Mouse. This dataset is not publicly accessible because: EPA cannot release personally identifiable information regarding living individuals, according to the Privacy Act and the Freedom of Information Act (FOIA). This dataset contains information about human research subjects. Because there is potential to identify individual participants and disclose personal information, either alone or in combination with other datasets, individual level data are not appropriate to post for public access. Restricted access may be granted to authorized persons by contacting the party listed. It can be accessed through the following means: In the publication and supporting information. Format: These data were generated from US EPA soil samples.  All of the soil samples were provided to NERL for methods development based on the agreement that the specific sample identifiers not be released. 

This dataset is associated with the following publication:
Bradham, K., C. Nelson, G.L. Diamond, W.C. Thayer, K.G. Scheckel, M. Noerpel, K. Herbin-Davis, B. Elek, and D. Thomas. Dietary Lead and Phosphate Interactions Affect Oral Bioavailability of Soil Lead in the Mouse.   ENVIRONMENTAL SCIENCE & TECHNOLOGY. American Chemical Society, Washington, DC, USA, 53(21): 12556-12564, (2019).

Tags: bioavailability, lead, phosphate, soil
Organization: U.S. Environmental Protection Agency
Great Lakes fauna inventory as of 20 May 2019

Dataset is an Excel file with 6 tabs as follows:
1) Changelog: Documentation of additions and changes to file since its creation
2) Citations: Listing of citations with full references used in other 4 tabs
3-6) Fish, Herps, Zoops, Benthos: For each of these 4 groups, a listing where rows are unique taxa and columns are the attributes recorded for them as described in the journal manuscript. 

This dataset is associated with the following publication:
Trebitz, A., M. Sykes, and J. Barge. A reference inventory for aquatic fauna of the Laurentian Great Lakes.   JOURNAL OF GREAT LAKES RESEARCH. International Association for Great Lakes Research, Ann Arbor, MI, USA, 45(6): 1036-1046, (2019).

Tags: biodiversity, great-lakes, species-occurrence, taxonomic-literature
Organization: U.S. Environmental Protection Agency
Assessing Dungeness River BMP Effectiveness Using an Ecological Function Approach

These data sets contain specific biophysical data (information) on the Dungeness River located in Washington State (USA) near Sequim, Washington and very  near the Jamestown S'Klallam Indian Reservation.  Data include water quality, river flow rates, rain fall amounts and other observational data.  The years covered for these data sets are the 1920s to the present. 

This dataset is associated with the following publication:
Hall, E., R. Hall, S. Swanson, W. Yee, D. Kozlowski, M. Philbin, D. Heggem, J. Lin, J. Aron, R. Schafer, D. Guiliano, and E. Wilson. Assessing Dungeness River Functionality and Effectiveness of Best Management Practices (BMPs) Using an Ecological Functional Approach.   American Journal of Environmental Engineering. Scientific & Academic Publishing, Rosemead, CA, USA, 9(2): 36-54, (2019).

Tags: best-management-practices, dugeness-river, ecological-condition-assessment, ecological-health, environmenal-health, proper-functioning-condition, tribal-sustainability, vulnerable-groups, water-quality
Organization: U.S. Environmental Protection Agency
Nichols et al._Biotransformation of PAH mixures by trout liver S9 fractions

This Excel spreadsheet provides data that appear in Tables 1- 2 and Figures 1-4 of the main document, as well as data that appear in Figures S1-S3 of the Supplementary Information. 

This dataset is associated with the following publication:
Nichols, J., M. Ladd, A. Hoffman, and P. Fitzsimmons. Biotransformation of polycyclic aromatic hydrocarbons by trout liver S9 fractions:  Evaluation of competitive inhibition using a substrate depletion approach.   ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY. Society of Environmental Toxicology and Chemistry, Pensacola, FL, USA, 38(12): 2729-2739, (2019).

Tags: bioaccumulation, biotransformation, chemical-mixtures, competitive-inhibition, polycyclic-aromatic-hydrocarbons
Organization: U.S. Environmental Protection Agency
Dissolution of Silver Nanoparticles in Consumer Products: Effects of Particle Size and Capping Agent

The data set contains the details on the characterization of silver nanoparticles suspension, the dissolution of silver nanoparticles in consumer products based on the dissolved mass Ag+ at deionized water and tap water and particle size fluctuations in deionized water and tap. Also contains a comparison of dissolution patterns between silver consumer products and laboratory-synthesized silver nanoparticles. 

This dataset is associated with the following publication:
Radwan, I.M., A. Gitipour, P.M. Potter, D.D. Dionysiou, and S.R. Al-Abed. Dissolution of silver nanoparticles in colloidal consumer products: effects of particle size and capping agent.   Journal of Nanoparticle Research. Springer SBM, New York, NY, USA, 21: 155, (2019).

Tags: capping-agent, consumer-products, dissolution-of-silver-nanoparticles, nanoparticles, particle-size, silver-nanomaterials
Organization: U.S. Environmental Protection Agency
Lead and iron speciation results

The data set comprises of two tables the show the linear combination fitting results for lead and iron speciation in samples collected for the study.  The tables show the names of samples pre- and post-treatment and the relative abundance of various lead and iron species present in each sample. 

This dataset is associated with the following publication:
Kastury, F., E. Smith, E. Doelsh, E. Lombi, M. Donnelley, P. Cmielewski, D.W. Parsons, K.G. Scheckel, D. Paterson, M.D. de Jonge, C. Herde, and A.L. Juhasz. In Vitro, in Vivo, and Spectroscopic Assessment of Lead Exposure Reduction via Ingestion and Inhalation Pathways Using Phosphate and Iron Amendments..   ENVIRONMENTAL SCIENCE & TECHNOLOGY. American Chemical Society, Washington, DC, USA, 53(17): 10329-10341, (2019).

Tags: bioaccessibility-soil, bioavailability, lead-contaminated-soil, lead-immobilzation, synchrotron-speciation
Organization: U.S. Environmental Protection Agency
Assessing the Impact of Wastewater Treatment Plant Effluent on Downstream Drinking Water-Source Quality Using a Zebrafish (Danio Rerio) Liver Cell-Based Metabolomics Approach

The datafile presents the data used to create the figures in the manuscript.  These include: a) Two-component score plots of hydrophilic and lipophilic ZFL cell extracts analyzed with NMR and GC-MS, respectively; b) The t-test filtered difference spectra (exposed minus control) generated from binned 1H NMR spectra (0.5–5.0 ppm in chemical shift) of hydrophilic extracts of ZFL cells; c) Bar chart showing the fold change of 21 annotated metabolites from the lipophilic extracts that exhibited different normalized abundance at one or more of the six sites relative to the control as measured by GC-MS; d) The summed intensity values for significantly changed metabolites from the t-test filtered difference spectra for both hydrophilic  and lipophilic extracts across six sampling sites; and e) Relative normalized abundances for metabolites identified in the cholesterol and fatty acid synthesis pathways from lipophilic ZFL extracts. 

This dataset is associated with the following publication:
Zhen, H., D. Ekman, T. Collette, S. Glassmeyer, M. Mills, E. Furlong, D. Kolpin, and Q. Teng. Assessing the impact of wastewater treatment plant effluent on downstream drinking water-source quality using a zebrafish (Danio Rerio) liver cell-based metabolomics approach.   WATER RESEARCH. Elsevier Science Ltd, New York, NY, USA, 145: 198-209, (2018).

Tags: cell-culture, de-facto-reuse, drinking-water, metabolomics, potable-reuse, source-water, wastewater, wastewater-treatment-plant-effluent, water-quality
Organization: U.S. Environmental Protection Agency
NOx RACT and power plant employment

Data on NOx RACT, ozone nonattainment, and power plant employment, and program files used in:
Glenn Sheriff, Ann E. Ferris, and Ronald J. Shadbegian, "How Did Air Quality Standards Affect Employment at US Power Plants? The Importance of Timing, Geography, and Stringency," Journal of the Association of Environmental and Resource Economists 6, no. 1 (January 2019): 111-149. Citation information for this dataset can be found in the EDG's Metadata Reference Information section and Data.gov's References section.

Tags: clean-air-act, electric-power-utilities, employment, environmental-regulation, nox-ract, ozone-nonattainment
Organization: U.S. Environmental Protection Agency
Salt Marsh Soil Salinity Data

Data used to evaluate the use of apparent conductivity of salt marsh sediments as a rapid alternative to traditional methods of salinity determination that can be used to map soil salinity across a marsh surface. 

This dataset is associated with the following publication:
Mckinney, R., A. Hanson, R. Johnson, and M. Charpentier. Seasonal variation in apparent conductivity and soil salinity at two Narragansett Bay, RI salt marshes.   PeerJ. PeerJ Inc., Corte Madera, CA, USA, 7: e8074, (2019).

Tags: apparent-conductivity, porewater, salt-marsh, soil-salinity
Organization: U.S. Environmental Protection Agency
Nationwide Reconnaissance of Contaminants of Emerging Concern in Source and Treated Drinking Waters of the United States

Files are an overview of all data acquired in the study examining source and treated drinking water. 

This dataset is associated with the following publication:
Glassmeyer , S., E. Furlong, D. Kolpin, A. Batt , B. Benson , S. Boone , O. Conerly , M. Donohue , D. King , M. Kostich , H. Mash , S. Pfaller , K. Schenck , J.E. Simmons , E. Varughese , S. Vesper , E. Villegas , and V. Wilson. Nationwide reconnaissance of contaminants of emerging concern in source and treated drinking waters of the United States.   SCIENCE OF THE TOTAL ENVIRONMENT. Elsevier BV, AMSTERDAM,  NETHERLANDS, 581582: 909-922, (2017).

Tags: drinking-water, microorganisms, per-and-polyfluoroalkyl-substances, pharmaceuticals, source-water
Organization: U.S. Environmental Protection Agency
Exploring the General Equilibrium Costs of Sector-Specific Environmental Regulations

Code and data to replicate simulations used in "Exploring the General Equilibrium Costs of Sector-Specific Environmental Regulations" by Alex Marten, Richard Garbaccio, and Ann Wolverton, in the Journal of the Association of Environmental and Resource Economists. Some of the data used in the modeling is proprietary and cannot be posted. We provide instructions for obtaining the remaining data and creating the datasets in readme.txt. (2019-05-24). Citation information for this dataset can be found in the EDG's Metadata Reference Information section and Data.gov's References section.

Tags: general-equilibrium, regulation, social-costs
Organization: U.S. Environmental Protection Agency
Energy and Emissions Implications of Automated Vehicles in the U.S. Energy System

This data includes model results generated using the MARKAL model and the EPA_US_9r database. Several scenarios involving automated vehicles were modeled. Results include emissions, fuel use, and fuel production under a variety of regimes of vehicle automation. 

This dataset is associated with the following publication:
Dodder, R. Energy and emissions implications of automated vehicles in the U.S. energy system - December 2019.   Transportation Research Part D: Transport and Environment. Elsevier BV, AMSTERDAM,  NETHERLANDS, 77: 132-147, (2019).

Tags: automated-vehicles, energy, energy-modeling, externality, transportation
Organization: U.S. Environmental Protection Agency
(Archives of Toxicology) Recommended approaches in the application of toxicogenomics to derive points of departure for chemical risk assessment

To determine the best way to select predictive groups of genes, we used published microarray data from dose-response studies on six chemicals in rats exposed orally for 5, 14, 28, and 90 days. We evaluated eight approaches for selecting genes for POD derivation and three previously proposed approaches (the lowest pathway BMD, and the mean and median BMD of all genes). This dataset is not publicly accessible because: The research which produced this data was not funded by EPA. The EPA coauthor helped write the manuscript. It can be accessed through the following means: Data generated by other authors. Format: N/A. 

This dataset is associated with the following publication:
Farmahin, R., A. Williams, B. Kuo, N.L. Chepelev, R.S. Thomas, T.S. Burton-Maclaren, I.H. Curran, A. Nong, M.G. Wade, and C.L. Yauk. (Archives of Toxicology) Recommended approaches in the application of toxicogenomics to derive points of departure for chemical risk assessment.   Archives of Toxicology. Springer, New York, NY, USA, 91(5): 2045-2065, (2017).

Tags: expocast, exposure
Organization: U.S. Environmental Protection Agency
(ALTEX) Use of High-throughput in vitro toxicity screening data in cancer hazard evaluations by the IARC Monograph Working Groups

Three recent IARC Working Groups pioneered inclusion of the US Environmental Protection Agency (EPA) ToxCast program high-throughput screening (HTS) data to supplement other mechanistic evidence. In Monograph V110, HTS profiles were compared between perfluorooctanoic acid (PFOA) and prototypical activators across multiple nuclear receptors. For Monograph V112-113, HTS assays were mapped to 10 key characteristics of carcinogens identified by an IARC expert group, and systematically considered as an additional mechanistic data stream. This dataset is not publicly accessible because: The data is generated by external authors from existing public data sources. It can be accessed through the following means: Data is available in existing public data sources. Format: N/A. 

This dataset is associated with the following publication:
Chiu, W., K. Guyton, M. Martin, D. Reif, and I. Rusyn. (ALTEX) Use of High-throughput in vitro toxicity screening data in cancer hazard evaluations by the IARC Monograph Working Groups.   ALTEX. Society ALTEX Edition, Kuesnacht,  SWITZERLAND, 35(1): 51-64, (2018).

Tags: expocast, exposure
Organization: U.S. Environmental Protection Agency
Primary sources of PAHs to Great Lakes tributaries using multiple lines-of-evidence

No data will be attached, all data are provided in either the paper or its supporting information (see tables and supporting information). This dataset is not publicly accessible because: USGS deleveloped and managed all data associated with this paper. It can be accessed through the following means: All data are provided in either the paper or its supporting information (see tables and supporting information. Format: No data will be attached, all data are provided in either the paper or its supporting information (see tables and supporting information). 

This dataset is associated with the following publication:
Baldwin, A.K., S.R. Corsi, S.K. Oliver, P.L. Lenaker, M.A. Nott, M. Mills, G. Norris, and P. Paatero. Primary Sources of Polycyclic Aromatic Hydrocarbons to Streambed Sediment in Great Lakes Tributaries Using Multiple Lines of Evidence.   ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY. Society of Environmental Toxicology and Chemistry, Pensacola, FL, USA, 39(7): 1392-1408, (2020).

Tags: coal-tar-pavement-sealant, polycyclic-aromatic-hydrocarbons-pahs, positive-matrix-factorization-pmf, sediment-toxicity, storm-water-runoff
Organization: U.S. Environmental Protection Agency
Muche et al__Comparison and Evaluation of Gridded Precipitation Datasets in a Kansas Agricultural Watershed using SWAT

The dataset is excel file that contains data for figures in the manuscript. 

This dataset is associated with the following publication:
Muche, M., S. Sinnathamby, R. Parmar, C. Knightes, J. Johnston, K. Wolfe, T. Purucker, M. Cyterski, and D. Smith. Comparison and Evaluation of Gridded Precipitation Datasets in a Kansas Agricultural Watershed Using SWAT.   JOURNAL OF THE AMERICAN WATER RESOURCES ASSOCIATION. American Water Resources Association, Middleburg, VA, USA, 56(3): 486-506, (2020).

Tags: calibration, gridded-precipitation, hydrology, kansas, precipitation, streamflow, swat, watershed-modeling
Organization: U.S. Environmental Protection Agency
Nooksack River Basin N budget

Information used to construct a nitrogen budget for the Nooksack River Watershed.  
The data includes the following four tables: 
Table 1: Annual N Fluxes in the Nooksack River Watershed.
Table 2: Calculated annual fish body mass (kg) in the Nooksack River Watershed.  
Table 3: Mean total nitrogen deposition (kg) of different land uses in the watershed, US portion and Canadian portion. 
Table 4: US portion of the Nooksack River Watershed: crop types, area, annual harvest N, available soil N, annual recommended crop N uptake rates, and proportional contributions of manure and synthetic fertilizer N, respectively.


Tags: balance, nitrogen, nutrients, phosphorus, watersheds
Organization: U.S. Environmental Protection Agency
Cesium Emissions from Laboratory Fires

The data sets contain the raw and reduced data from the instrument measurements including continuous emission monitoring and stack sampling procedure. 

This dataset is associated with the following publication:
Hao, W.M., S. Baker, E. Lincoln, S. Hudson, S. Lee, and P. Lemieux. Cesium Emissions from Laboratory Fires Article.   JOURNAL OF THE AIR & WASTE MANAGEMENT ASSOCIATION. Air & Waste Management Association, Pittsburgh, PA, USA,  49, (2018).

Tags: air-emissions, cesium-partitioning, continuous-emission-monitoring, forest, improvised-nuclear-device, ind, nuclear-power-plant-accident, pm10, pm2-5, radiological-contamination, radiological-dispersal-device, radionuclides, rdd, stack-sampling, wildfire
Organization: U.S. Environmental Protection Agency
Electrolyte Selection for Electrochemical Oxidative Water Treatment Using a Boron-Doped Diamond Anode to Support Site Specific Contamination Incident Response

The dataset contains the raw data for the graphs in the paper. 

This dataset is associated with the following publication:
Phillips, R., R. James, and M. Magnuson. Electrolyte Selection and Microbial Toxicity for Electrochemical Oxidative Water Treatment Using a Boron-doped Diamond Anode to Support Site Specific Contamination Incident Response.   ENVIRONMENTAL SCIENCE & TECHNOLOGY. American Chemical Society, Washington, DC, USA, 197: 135-141, (2017).

Tags: advanced-oxidation-process, boron-doped-diamond-electrode, perfluorinated, pesticide, pfas, treatment, wastewater, water-security
Organization: U.S. Environmental Protection Agency
Gerties Creek Proper Functioning Condition Data Forms

These are Proper Functioning Condition Reach Information Forms filled out during our assessment at Georgina Island.  The forms are from the Technical Reference 1737-15 Second Edition 2015 from BLM, Forest Service and NRCS.  Dickard et al., 2015. 

This dataset is associated with the following publication:
Hall, R., J. Lin, B. Schumacher, K. Charles, and D. Heggem. Ecological risk based assessment used to restore riparian physical functions to a fresh water Creek.   JOURNAL OF ENVIRONMENTAL MANAGEMENT. Elsevier Science Ltd, New York, NY, USA, 221: 63-75, (2018).

Tags: ecological-condition-assessment, ecological-health, environmenal-health, lentic-reach-assessment, lotic-reach-assessment, proper-functioning-condition, tribal-sustainability, vulnerable-groups
Organization: U.S. Environmental Protection Agency
amphibian_dehydration_uptake_data

Bioconcentration data for Glinski DA, Henderson WM, Van Meter RJ, Purucker ST 2017. Effect of hydration status on pesticide uptake in anurans following exposure to contaminated soils. 

This dataset is associated with the following publication:
Glinski, D., M. Henderson, R. Van Meter, and T. Purucker. Effect of hydration status on pesticide uptake in anurans following exposure to contaminated soils.   ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH. Ecomed Verlagsgesellschaft AG, Landsberg,  GERMANY, 25(16): 16192-16201, (2018).

Tags: amphibians, body-burden, dehydration, pesticides, uptake
Organization: U.S. Environmental Protection Agency
Data used in the research titled, "Quantifying the visual-sensory landscapes qualities that contribute to cultural ecosystem services using social media and LiDAR"

Sample1m are the data used to estimate the Negative Binomial models. The validation dataset compares classified photographs with viewshed estimates of visible land use/cover. 

This dataset is associated with the following publication:
VanBerkel, D., P. Tabrizian, M.A. Dorning, L. Smart, D. Newcomb, M. Mehaffey, A. Neale, and R.K. Meentemeyer. Quantifying the visual-sensory landscape qualities that contribute to cultural ecosystem services using social media and LiDAR.   Ecosystem Services. Elsevier Online, New York, NY, USA, 31: 326-335, (2018).

Tags: coastal-scenery, cultural-ecosystem-services, social-media, spatial-analysis
Organization: U.S. Environmental Protection Agency
Data file field studies aerosolized endotoxins biosolids application 2010 and 2012

The dataset consists of columns of values and labels of data collected by air samplers for endotoxin monitoring during the full scale/commercial scale land application of Class B biosolids. The biosolids came from different anaerobic treatment facilities and some material was later treated with lime 24 hours prior to application. 

This dataset is associated with the following publication:
Herrmann , R., R. Grosser, D. Farrar , and B. Brobst. Field studies measuring the aerosolization of endotoxin during the land application of Class B biosolids.  Carmen Galan  AEROBIOLOGIA. Springer, New York, NY, USA, 0(0): 1-18, (2017).

Tags: aerosolized-endotoxin, biosolids, class-b-biosolids, endotoxin, land-application, limulus-amebocyte-lysate
Organization: U.S. Environmental Protection Agency