AndreaBozzo/ceres-open-data-index huggingface dataset:
Martin et al_Zebrafish Heart Rate Assay_ All Data

Data file contains heart rate values for each fish by experiment. The data were used to generate figures and tables in the attached manuscript. 

This dataset is associated with the following publication:
Martin, W.K., A. Tennant, R. Conolly, K. Prince, J. Stevens, D. DeMarini, B. Martin, L. Thompson, I. Gilmour, W. Cascio, M. Hays, M. Hazari, S. Padilla, and A. Farraj. High-Throughput Video Processing to Score Heart Rate Responses to Xenobiotics in Wild-type Embryonic Zebrafish per imaging field.   Scientific Reports. Nature Publishing Group, London,  UK, 9(1): 145, (2019).

Tags: fine-particulate-matter, heart-rate, high-throughput, high-througput, video-processing, zebrafish
Organization: U.S. Environmental Protection Agency
Arsenic speciation results

The dataset is a table that shows soil samples with corresponding total arsenic concentrations, arsenic bioavailability values, and linear combination fitting results of synchrotron speciation results. 

This dataset is associated with the following publication:
Stevens, B.N., A.R. Betts, B.W. Miller, K.G. Scheckel, R.H. Anderson, K.D. Bradham, S.W. Casteel, D.J. Thomas, and N.T. Basta. Arsenic Speciation of Contaminated Soils/Solid Wastes and Relative Oral Bioavailability in Swine and Mice.   Soil Systems. MDPI AG, Basel,  SWITZERLAND, 2(2): 27, (2018).

Tags: arsenic, exafs, metal-bioavailability, synchrotron-speciation, xanes
Organization: U.S. Environmental Protection Agency
Metadata for figures in publication "Long Chain Lipid Hydroperoxides Increase the Glutathione Redox Potential Through Glutathione Peroxidase 4

The dataset contains the metadata associated with the figures in the manuscript. 

This dataset is associated with the following publication:
Corteselli, E., E. Gibbs-Flournoy, S. Simmons, P. Bromberg, A. Gold, and J.M. Samet. Long Chain Lipid Hydroperoxides Increase the Glutathione Redox Potential Through Glutathione Peroxidase 4.   Biochimica et Biophysica Acta. Elsevier Science Ltd, New York, NY, USA, 1863(5): 950-959, (2019).

Tags: oxidant-stress
Organization: U.S. Environmental Protection Agency
Phenone rtER binding Vtg_Tapper_A-jm6n_data set 20171002

Phenones and hydroxy benzophenones are widely used as UV radiation filters, and in the manufacturing of insecticides and pharmaceuticals. Understanding the ability of these chemicals to mimic the effects of the steroid estrogen is of interest to the US Environmental Protection Agency and other international environmental organizations. The current study sequentially combined complementary in vitro (outside a living organism) rainbow trout estrogen receptor (rtER) binding and liver slice vitellogenin (Vtg) mRNA induction assays in the context of a defined ER-mediated adverse outcome pathway (AOP). Cyclic phenones, branched phenones, and hydroxybenzophenones bound to rtER with relative potency ranging from no affinity to high binding affinity of 0.11%, and many induced Vtg, an egg yolk protein, gene expression in rt liver slices. In addition, cyclohexylphenylketone which did not bind rtER binding in cytosol was biotransformed within liver tissue to a chemical that induced Vtg expression. Cyclic phenones, branched phenones and hydroxybenzophenones produced estrogen like responses in these rainbow trout in vitro assays. 

This dataset is associated with the following publication:
Tapper, M., J. Denny, J. Serrano, R. Kolanczyk, B. Sheedy, G. Overland, M. Hornung, and P. Schmieder. Phenone, hydroxybenzophenone, and branched phenone estrogen receptor binding and vitellogenin agonism in rainbow trout in vitro models.   Applied In Vitro Toxicology. Mary Ann Liebert, Inc., Larchmont, NY, USA, 5(1): 62-74, (2019).

Tags: aop, endocrine-disruption, estrogen-receptor, in-vitro-assay, vitellogenin-gene-expression
Organization: U.S. Environmental Protection Agency
Resilience of Microbial Communities Sequence Data Set

The EX_Genome_Assemblies.zip file contain the contig sequences (i.e. assembly) of fifteen isolates used for genomic and antibiotic resistance genes (ARG) analysis.

EX_OTU.fasta file contain the sequences of the bacterial 16S rRNA-encoding V4 region gene (≈250 nt) for each Operational Taxonomic Unit (OTU). 

This dataset is associated with the following publication:
Gomez-Alvarez, V., S. Pfaller, J. Pressman, D. Wahman, and R. Revetta. Resilience of microbial communities in a simulated drinking water distribution system subjected to disturbances: role of conditionally rare taxa and potential implications for antibiotic-resistant bacteria.   Environmental Science: Water Research & Technology. Royal Society of Chemistry, Cambridge,  UK, 2: 645-657, (2016).

Tags: 16s-rrna, antibiotic-resistance-genes, biofilm, drinking-water, genomes, microbial-communities, nitrification, otu
Organization: U.S. Environmental Protection Agency
Metropolitan DWDS OTU Abundance Data Set

An abundance matrix (PS_OTU.xlsx) contains rows as OTU, columns as samples, and entries representing the abundance of each OTU as a ratio of all sequences obtained for each individual sample. 

This dataset is associated with the following publication:
Revetta , R., V. Gomez-Alvarez, T. Gerke, J. Santodomingo , and N. Ashbolt. CHANGES IN BACTERIAL COMPOSITION OF BIOFILM IN A METROPOLITAN DRINKING WATER DISTRIBUTION SYSTEM.   JOURNAL OF APPLIED MICROBIOLOGY. Blackwell Publishing, Malden, MA, USA, 121(1): 294-305, (2016).

Tags: biofilm, drinking-water, drinking-water-distribution-system, groundwater, microbial-structure, otu, relative-abundance, surface-water
Organization: U.S. Environmental Protection Agency
Resilience of Microbial Communities Taxonomic Lineage Abundance Data Set

An abundance matrix (EX_taxonomic_lineage.xlsx) contains rows as taxonomic lineage, columns as samples, and entries representing the abundance of each lineage as a ratio of all sequences obtained for each individual sample. 

This dataset is associated with the following publication:
Gomez-Alvarez, V., S. Pfaller, J. Pressman, D. Wahman, and R. Revetta. Resilience of microbial communities in a simulated drinking water distribution system subjected to disturbances: role of conditionally rare taxa and potential implications for antibiotic-resistant bacteria.   Environmental Science: Water Research & Technology. Royal Society of Chemistry, Cambridge,  UK, 2: 645-657, (2016).

Tags: antibiotic-resistance-genes, biofilm, drinking-water, microbial-communities, nitrification, relative-abundance, taxonomy
Organization: U.S. Environmental Protection Agency
Life cycle inventory data of various unit processes in water and wastewater treatment trains and the life cycle impact assessments of different environmental performance categories.

LCI and LCIA for water and wastewater treatment plants. 

This dataset is associated with the following publications:
Xue, X., S. Cashman, A. Gaglione, J. Mosley, L. Weiss, C. Ma, J. Cashdollar, and J. Garland. Holistic Analysis of Urban Water Systems in the Greater Cincinnati Region: (1) Life Cycle Assessment and Cost Implications.   Water Research X. Elsevier B.V., Amsterdam,  NETHERLANDS, 2: 100015, (2019).
Cashman, S., A. Gaglione, J. Mosley, L. Weiss, T. Hawkins, N. Ashbolt, J. Cashdollar , X. Xue, C. Ma , and S. Arden. Environmental and cost life cycle assessment of disinfection options for municipal drinking water treatment. U.S. Environmental Protection Agency, Washington, DC, USA, 2014.
Cashman, S., A. Gaglione, J. Mosley, L. Weiss, N. Ashbolt, T. Hawkins, J. Cashdollar , X. Xue, C. Ma , and S. Arden. Environmental and cost life cycle assessment of disinfection options for municipal wastewater treatment. U.S. Environmental Protection Agency, Washington, DC, USA, 2014.

Tags: drinking-water-systems, energy-expenditure-and-distribution, impact-assessment, lca, lcc, life-cycle-assessment-lca, life-cycle-costing, life-cycle-impact-assessment-method, sustainability-analysis, system-analysis, wastewater-systems, water-systems
Organization: U.S. Environmental Protection Agency
Resilience of Microbial Communities OTU Abundance Data Set

An abundance matrix (EX_OTU.xlsx) contains rows as OTU, columns as samples, and entries representing the abundance of each OTU as a ratio of all sequences obtained for each individual sample. 

This dataset is associated with the following publication:
Gomez-Alvarez, V., S. Pfaller, J. Pressman, D. Wahman, and R. Revetta. Resilience of microbial communities in a simulated drinking water distribution system subjected to disturbances: role of conditionally rare taxa and potential implications for antibiotic-resistant bacteria.   Environmental Science: Water Research & Technology. Royal Society of Chemistry, Cambridge,  UK, 2: 645-657, (2016).

Tags: antibiotic-resistance-genes, biofilm, drinking-water, microbial-communities, nitrification, otu, relative-abundance
Organization: U.S. Environmental Protection Agency
Gene transcription ontogeny of hypothalamic-pituitary-thyroid axis development in early-life stage fathead minnow and zebrafish

Disruption of thyroid hormone signaling is a form of endocrine disruption that is of concern to both human health and ecosystems. Research is being conducted to define the biological targets chemicals may interact with to disrupt thyroid hormone signaling and the stages in development where that disruption can most readily lead to adverse effects. The present data characterize the expression of key genes associated with thyroid hormone signaling and regulation over the course of development for two small fish widely used in aquatic ecotoxicology research. These data provide baseline information that can lead to a more complete understanding of which thyroid disrupting chemicals fish may be susceptible to and at which stages in development. 

This dataset is associated with the following publication:
Vergauwen, L., J. Cavallin, G. Ankley, C. Bars, I. Gabriels, E. Michiels, K. Nelson, J.  Periz-Stanacev, E. Randolph, S. Robinson, T. Saari, A. Schroeder, E. Stinckens, J. Swintek, S. Van Cruchten, E.  Verbueken, D. Villeneuve, and D. Knapen. Gene transcription ontogeny of thyroid-axis development in early-life stage fathead minnow and zebrafish.   Journal of Experimental Biology. The Company of Biologists LIMITED, Cambridge,  UK, 266: 878-1002, (2018).

Tags: adverse-outcome-pathway, aquatic-ecosystems, development, ecotoxicology, endocrine-disruption, screening-and-prioritization
Organization: U.S. Environmental Protection Agency
Metropolitan DWDS Taxonomic Lineage Abundance Data Set

An abundance matrix (PS_taxonomic_lineage.xlsx) contains rows as taxonomic lineage, columns as samples, and entries representing the abundance of each lineage as a ratio of all sequences obtained for each individual sample. 

This dataset is associated with the following publication:
Revetta , R., V. Gomez-Alvarez, T. Gerke, J. Santodomingo , and N. Ashbolt. CHANGES IN BACTERIAL COMPOSITION OF BIOFILM IN A METROPOLITAN DRINKING WATER DISTRIBUTION SYSTEM.   JOURNAL OF APPLIED MICROBIOLOGY. Blackwell Publishing, Malden, MA, USA, 121(1): 294-305, (2016).

Tags: biofilm, drinking-water, drinking-water-distribution-system, groundwater, microbial-structure, relative-abundance, surface-water, taxonomy
Organization: U.S. Environmental Protection Agency
Metropolitan DWDS Sequence Data Set

PS_GenBank.fasta file contain the sequences of the bacterial 16S rRNA-encoding gene for each representative sequence.  The sequence containing four hypervariable regions was amplified using the primer set Eub-8f and 787.

PS_GenBank.xlsx file contains rows as sample and columns as entries representing the accession number (NCBI) deposited in GenBank for each representative sequence (i.e. unique sequences).

PS_OTU.fasta file contain the sequences of the bacterial 16S rRNA-encoding gene for each Operational Taxonomic Unit (OTU). The sequence containing four hypervariable regions was amplified using the primer set Eub-8f and 787. 

This dataset is associated with the following publication:
Revetta , R., V. Gomez-Alvarez, T. Gerke, J. Santodomingo , and N. Ashbolt. CHANGES IN BACTERIAL COMPOSITION OF BIOFILM IN A METROPOLITAN DRINKING WATER DISTRIBUTION SYSTEM.   JOURNAL OF APPLIED MICROBIOLOGY. Blackwell Publishing, Malden, MA, USA, 121(1): 294-305, (2016).

Tags: 16s-rrna, biofilm, drinking-water, drinking-water-distribution-system, groundwater, microbial-communities, microbial-structure, otu, surface-water
Organization: U.S. Environmental Protection Agency
CMAPS Dataset Coarse PM exacerbates allergic airway responses in mice.

The dataset contains the original data relevant for each figure or table in the cleared publication. The excel file has tabs labelled for each figure (Figures 1-4) or table (tables 1-3). Figure 5 in the paper shows representative histology figures, and so is not linked to data other than as representative of table 3 (histology). Table 1 has 3 tabs for PM collection at the CLM site, PM collection at the GTC site, and for chemistry. Table 2 is represented on 1 tab for biochemistry. Table 3 has 2 tabs for the raw histopathology data for the statistics and summary. 

This dataset is associated with the following publication:
Hargrove, M.M., J. Mcgee, E. Gibbs-Flournoy, C. Wood, Y.H. Kim, I. Gilmour, and S. Gavett. Source-Apportioned Coarse Particulate Matter Exacerbates Allergic Airway Responses in Mice.   INHALATION TOXICOLOGY. Informa Healthcare USA, New York, NY, USA, 30(11): 405-415, (2018).

Tags: allergy, emission-sources, particulate-matter
Organization: U.S. Environmental Protection Agency
Edison Big Parking Lot Nutrient data.

The data includes nutrient concentrations for infiltrates, runoff, and rainfall during the monitoring period. 

This dataset is associated with the following publication:
Razzaghmanesh, M., and M. Borst. Long- term effects of three types of permeable pavements on nutrient infiltrate concentrations.   SCIENCE OF THE TOTAL ENVIRONMENT. Elsevier BV, AMSTERDAM,  NETHERLANDS, 670: 893-901, (2019).

Tags: nitrification, nutrients, permeable-pavement-parking-lot, stormwater-runoff, trend-analysis
Organization: U.S. Environmental Protection Agency
Bioaccumulation of highly hydrophobic chemicals by Lumbriculus variegatus

Sediment was dosed with six highly hydrophobic chemicals with estimated log Kows ranging up to 18.3.  Sediment bioaccumulation tests with Lumbriculus variegatus were performed with the dosed sediment.  The attached dataset contains the concentrations in the organisms from the uptake and elimination portions of the test. and supporting data, e.g. lipid contents and weight change for the organisms. 

This dataset is associated with the following publication:
Burkhard, L., T. Lahren, T. Highland, R. Hockett, D. Mount, and T. Norberg-King. Bioaccumulation of highly hydrophobic chemicals by Lumbriculus variegatus.   ARCHIVES OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY. Springer, New York, NY, USA, 76(1): 129-141, (2019).

Tags: bioaccumulation, bioavailability, chemical-uptake, fish-dietary-studies, lumbriculus-variegatus, oligochaete, sediment, sediment-testing
Organization: U.S. Environmental Protection Agency
Measurement of kinetic parameters for biotransformation of PAHs by trout liver S9 fractions: Implications for bioaccumulation assessment

The dataset, which is presented as an Excel spreadsheet, contains all data which is presented as figures in Nichols et al., Measurement of kinetic parameters for biotransformation of polycyclic aromatic hydrocarbons by trout liver S9 fractions: Implications for bioaccumulation assessment, accepted for publication in Applied In Vitro Toxicology 04/2017.  Additional information if provided regarding reaction conditions used to characterize liver S9 fractions and perform PAH depletions studies. 

This dataset is associated with the following publication:
Nichols, J., M. Ladd, and P. Fitzsimmons. Measurement of kinetic parameters for biotransformation of polycyclic aromatic hydrocarbons by trout liver S9 fractions: Implications for bioaccumulation assessment.   Applied In Vitro Toxicology. Mary Ann Liebert, Inc., Larchmont, NY, USA, 4(4): 365-378, (2018).

Tags: bioaccumulation-assessment, biotransformation, fish, in-vitro-in-vivo-extrapolation, liver-s9-fraction, rainbow-trout
Organization: U.S. Environmental Protection Agency
Cardiopulmonary hospitalizations and air quality in counties affected by wildfires, 2008-2010

The final dataset combines cardiopulmonary hospitalization data for those 65 and over using the Medicare Provider Analysis and Review (MEDPAR) files from the Center for Medicare and Medicaid Services (CMS), modeled fine particulate matter (PM2.5) concentrations from the Community Multiscale Air Quality (CMAQ) model, and monitoring site concentrations of PM2.5 from the Air Quality System (AQS). All data are aggregated to the county level and restricted to counties with wildfires recorded between 2008-2010. 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: Due to the presence of PII, limited data are available on request. Format: The data are stored as an R dataset (.RData) on a restricted drive. 

This dataset is associated with the following publication:
Deflorio-Barker, S., J. Crooks, J. Reyes, and A.G. Rappold. Cardiopulmonary effects of fine particulate matter exposure among older adults, during wildfire and non-wildfire periods, in U.S. 2008-2010.   ENVIRONMENTAL HEALTH PERSPECTIVES. National Institute of Environmental Health Sciences (NIEHS), Research Triangle Park, NC, USA, 127(3): 37006, (2019).

Tags: cardiopulmonary, hospitalizations, medicare, wildfire
Organization: U.S. Environmental Protection Agency
Market Sensitivity of Solar-Fossil Hybrid Electricity Generation to Price, Efficiency, Policy, and Fuel Projections

This dataset includes results from the MARKAL model. A technology that generates electricity from a combination of solar and natural gas energy, called ISCC, is evaluated. Results include electricity generation mixes and emissions projections. 

This dataset is associated with the following publication:
Brown, K., and D. Loughlin. Market Sensitivity of Solar-Fossil Hybrid Electricity Generation to Price, Efficiency, Policy, and Fuel Projections.   CLEAN TECHNOLOGIES AND ENVIRONMENTAL POLICY. Springer-Verlag, New York, NY, USA, 21(3): 591-604, (2019).

Tags: energy, energy-modeling, externality
Organization: U.S. Environmental Protection Agency
README_nysdoh

The "dataset" is simply a README file that contains information about the data that EPA provided to the lead authors and where to acquire the data on the EPA high-performance computing system archive.  Those data exceed 1 gigabyte in size, so they are too large to be hosted on ScienceHub. 

This dataset is associated with the following publication:
Zhang, W., T. Spero, C. Nolte, V. Garcia, Z. Lin, P. Romitti, G. Shaw, S. Sheridan, M. Feldkamp, A. Woomert, S. Hwang, S. Fisher, M. Browne, Y. Hao, and S. Lin. Projected Changes in Maternal Heat Exposure During Early Pregnancy and the Associated Congenital Heart Defect Burden in the United States.   Journal of the American Heart Association (JAHA). American Heart Association, Dallas, TX, USA, 8(3): e010995, (2019).

Tags: health-burden, regional-climate-modeling, wrf
Organization: U.S. Environmental Protection Agency
Dataset for Coarse Particulate Organic Matter Connectivity

Datasets include rain, stream discharge, flow duration in ephemeral tributaries, coarse particulate organic matter (leaves and wood) deposition and surrogate (Ginkgo leaves and dowel rods) export in a Central Appalachian catchment in eastern Kentucky, USA. 

This dataset is associated with the following publication:
Fritz, K., G. Pond, B. Johnson, and C. Barton. Coarse particulate organic matter dynamics in ephemeral tributaries of a Central Appalachian stream network.   Ecosphere. ESA Journals,    10(3): e02654, (2019).

Tags: connectivity, deposition, ephemeral-tributary, lag-function, leaf-litter, seasonality, storage, transport, wood
Organization: U.S. Environmental Protection Agency
Data for organotypic stem cell model for human embryonic palatal fusion.

Cleft palate (CP) is a common birth defect, occurring in an estimated 1 in 1000 births worldwide. The secondary palate is formed by paired palatal shelves that grow toward each other, appose, attach and fuse. CP can result from disruption of any of these processes. The palatal shelves basically consist of a mesenchymal tissue core covered with a layer of epithelial cells. One of the mechanisms that can cause CP is failure of fusion, i.e., failure to remove the epithelial seam between the palatal shelves to allow the mesenchyme to merge and form a continuous palate. This process requires complex interactions between mesenchymal and epithelial cells, and signaling components such as growth factors. Epidermal growth factor (EGF) plays an important role in palate growth and differentiation, while it may impede fusion. We developed a 3D organotypic model using human mesenchymal and epithelial stem cells to mimic human embryonic palatal shelves, and tested its functional relevance by monitoring the effects of human EGF (hEGF) on proliferation and fusion. Spheroids were generated from human umbilical-derived mesenchymal stem cells (hMSCs) directed down an osteogenic lineage by culture medium and evaluated for osteogenic differentiation. Heterotypic spheroids, or organoids, were constructed by coating hMSC spheroids with MaxGel™ extracellular matrix solution followed by a layer of human progenitor epithelial keratinocytes (hPEK). Organoids were incubated in co-culture medium with or without hEGF and assessed for cell proliferation and spheroid pairs were assessed for time to fusion. Osteogenic differentiation in hMSC spheroids was highest by day 13. hEGF delayed fusion of heterotypic organoids after 12 and 18 hours of contact.  hEGF increased proliferation in organoids at 4 ng/ml, and proliferation was detected in hPEKs alone on microcarrier beads, suggesting a potential mechanism for delayed fusion by hEGF. Our results show that this model of human palatal fusion consisting of a core of differentiated hMSCs with a hPEK outer layer appropriately mimics the morphology of the developing human palate and responds to hEGF as expected. Future studies will focus on using the organoid model to evaluate the effects of teratogenic chemicals on palatal fusion, and validating the results. 

This dataset is associated with the following publication:
Wolf, C., D. Belair, C. Becker, K. Das, J. Schmid, and B. Abbott. Development of an organotypic stem cell model for the study of human embryonic palatal fusion.   BIRTH DEFECTS RESEARCH PART B:  DEVELOPMENTAL AND REPRODUCTIVE TOXICOLOGY. John Wiley & Sons, Ltd., Indianapolis, IN, USA,  1322-1334, (2018).

Tags: cell-spheroids, cleft-palate, epithelial-cells, fusion, morphogenetic-fusion, organotypic-models, osteogenesis, palate-fusion, stem-cells, stromal-cells
Organization: U.S. Environmental Protection Agency
The dataset is a table showing linear combination fitting results for arsenic and lead in three soils.

Table showing linear combination fitting data for arsenic and lead speciation in three soils. 

This dataset is associated with the following publication:
Kastury, F., E. Smith, R.R. Karna, K.G. Scheckel, and A.L. Juhasz. Methodological factors influencing inhalation bioaccessibility of metal(loid)s in PM2.5 using simulated lung fluid.   ENVIRONMENTAL POLLUTION. Elsevier Science Ltd, New York, NY, USA, 241: 930-937, (2018).

Tags: arsenic, in-vitro-bioaccessibility, lead, lung-toxicity, metal-bioavailability, pm2-5-long-term-exposure, synchrotron-speciation
Organization: U.S. Environmental Protection Agency