AndreaBozzo/ceres-open-data-index huggingface dataset:
Cook et al 2016 data

The data are Excel spreadsheets with detailed physical measurements of 50 mineral fiber samples used for the modeling outlined in the publication. 

This dataset is associated with the following publication:
Cook, P., J.  Swintek, T. Dawson, D. Chapman, M. Etterson , and D. Hoff. Quantitative structure - mesothelioma potency model optimization for complex mixtures of elongated particles in rat pleura: A retrospective study.   JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH - PART B:  CRITICAL REVIEWS. Taylor & Francis, Inc., Philadelphia, PA, USA, 19(5): 266-288, (2016).

Tags: elongated-particles, mesothelioma, rat-pleura
Organization: U.S. Environmental Protection Agency
Asbestosis and iron

None provided. 

This dataset is associated with the following publication:
Ghio, A., J. Soukup, L. Dailey, H. Tong, and J. Richards. The biological effect of asbestos exposure is dependent on changes in iron homeostasis.   INHALATION TOXICOLOGY. Informa Healthcare USA, New York, NY, USA, 28(14): 698-705, (2016).

Tags: particles-and-fibers
Organization: U.S. Environmental Protection Agency
DNA metabarcoding OTU tables

DNA sequence data output with assigned taxonomic IDs. 

This dataset is associated with the following publication:
Hatzenbuhler, C., J.R.  Kelly, J. Martinson, S. Okum, and E. Pilgrim. Sensitivity and accuracy of high-throughput metabarcoding methods for early detection of invasive fish species.   Scientific Reports. Nature Publishing Group,   UK, 7: 1-10 (46393), (2017).

Tags: aquatic-invasive-species, dna-barcoding, great-lakes
Organization: U.S. Environmental Protection Agency
Effects of the antimicrobial contaminant triclocarban, and co-exposure with the androgen 17beta-trenbolone, on reproductive function and ovarian transcriptome of the fathead minnow (Pimephales promelas).

Triclocarban (TCC) is a widely used antimicrobial agent that is routinely detected in surface waters. The present study was designed to examine TCC’s efficacy and mode of action as a reproductive toxicant in fish. Reproductively mature Pimephales promelas were continuously exposed to either 1 or 5 μg TCC/L,  0.5 μg 17β-trenbolone (TRB)/L or a mixture (MIX) of 5 μg TCC and 0.5 μg TRB/L for 22 d and a variety of reproductive and endocrine-related endpoints were examined. The data set includes:
-Concentrations of the test chemicals detected in water and tissues of exposed fish
-Ex vivo production of testosterone and estradiol by gonad tissue placed in culture (ex vivo).
-Plasma concentrations of testosterone, 17beta estradiol, and vitellogenin
-Targeted gene expression measurements examining relative abundance of messenger RNA coding for enzymes involved in steroid synthesis: cholesterol side-chain cleavage
(cyp11a), 17-a-hydroxylase/17,20 lyase (cyp17), aromatase (cyp19a1a), 3b-hydroxysteroid dehydrogenase (3bhsd), 11bhydroxysteroid dehydrogenase (11bhsd), and 17b-hydroxysteroid dehydrogenase (17bhsd) as well as five additional transcripts
measured included steroidogenic acute regulatory protein (star), Vtg receptor (vtgr), follicle-stimulating hormone receptor (fshr), luteinizing hormone receptor (lhr), and
androgen receptor (ar). 
-Ovarian transcriptomics data measured using a 15000 feature oligonucleotide microarray (GEO Platform Accession GPL10259).
-Survival, reproduction, and morphological data.
-. 

This dataset is associated with the following publication:
Villeneuve , D., K. Jensen , J. Cavallin , E. Durhan, N. Garcia-Reyero, M. Kahl , R. Leino, E. Makynen, L. Wehmas, E. Perkins, and G. Ankley. Effects of the anti-microbial contaminant triclocarban and co-exposure with the androgen 17â-trenbolone, on reproductive function and ovarian transcriptome of the fathead minnow (Pimephales promelas).   ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY. Society of Environmental Toxicology and Chemistry, Pensacola, FL, USA, 36(1): :231-242, (2017).

Tags: adverse-outcome-pathway, aquatic-ecosystems, ecotoxicology, endocrine-disruption, screening-and-prioritization
Organization: U.S. Environmental Protection Agency
Derivation and Evaluation of Putative Adverse Outcome Pathways for Effects of Cycylooxygenase inhibitors on Reproductive Processes in Female Fish

Fathead minnows (Pimephales promelas) were exposed to 100 ug/L indomethacin, 200 ug/L ibuprofen, or 20 ug/L celecoxib for 96 h.  Effects on cycloxygenase enzyme activity in ovary, prostaglandin F2alpha concentrations in plasma, 17beta-estradiol concentrations in plasma, and vitellogenin concentrations in plasma were measured. Gene expression in ovary samples was evaluated using a 15,000 probe oligonucleotide microarray. Transcriptomics data (raw data and normalized) are available through the National Center for Biotechnology Information, Gene Expression Omnibus (GEO), accession number GSE72976. Metabolite profiles in liver tissue were measured by proton nuclear magnetic resonance. In addition to these data, the data set also contains identification of differentially expressed genes, pathway enrichment and gene set enrichment analyes, ToxCast data for indomethacin and celecoxib, chemical-gene interaction data derived from the Comparative Toxicogenomics database, and results from Level 1, Level 2, and Level 3 SeqAPASS analyses that examine conservation of target proteins across species (https://seqapass.epa.gov/seqapass/). 

This dataset is associated with the following publication:
Martinovic-Weigelt, D., A. Mehinto, G. Ankley , J. Berninger, T. Collette , J. Davis , N. Denslow, E. Durhan, E. Eid, D. Ekman , K. Jensen , M. Kahl , C. LaLone , Q. Teng , and D. Villeneuve. Derivation and evaluation of putative adverse outcome pathways for the effects of cyclooxygenase inhibitors on reproductive processes in female fish.   TOXICOLOGICAL SCIENCES. Society of Toxicology,    156(2): 344-361, (2017).

Tags: adverse-outcome-pathway, aquatic-ecosystems, ecotoxicology, endocrine-disruption, screening-and-prioritization
Organization: U.S. Environmental Protection Agency
Data For Figures

This dataset contains data presented in the figures of the paper "Semivolatile POA and parameterized total combustion SOA in CMAQv5.2: impacts on source strength and partitioning" published in Atmospheric Chemistry and Physics. It also links to the data archive of field observations. 

This dataset is associated with the following publication:
Murphy, B., M. Woody, J. Jimenez, A.M. Carlton, P. Hayes, S. Liu, N. Ng, L. Russell, A. Setyan, L. Xu, J. Young, R. Zaveri, Q. Zhang, and H. Pye. Semivolatile POA and parameterized total combustion SOA in CMAQv5.2: impacts on source strength and partitioning.   Atmospheric Chemistry and Physics. Copernicus Publications, Katlenburg-Lindau,  GERMANY, 17: 11107-11133, (2017).

Tags: aging, calnex, cares, cmaq, organic-aerosol, particulate-matter, soas, volatility
Organization: U.S. Environmental Protection Agency
Developmental Thyroid Hormone Insufficiency Induces Cortical Brain Malformation and Learning Impairments: A Cross-Fostering Study

thyroid hormone from serum of rats exposed to goitrogen. Morphometry in brain. Behavioral data. 

This dataset is associated with the following publication:
OShaughnessy, K., P. Kosian, J. Ford, W. Oshiro, S. Degitz, and M. Gilbert. Developmental Thyroid Hormone Insufficiency Induces Cortical Brain Malformation and Learning Impairments: A Cross-Fostering Study.   TOXICOLOGICAL SCIENCES. Society of Toxicology, RESTON, VA,  163(1): 101-115, (2018).

Tags: developmental-hypothyroidism, fear-conditioning, heterotopia, thyroid-homone
Organization: U.S. Environmental Protection Agency
Multiplex ELISA MTF-1 and western blot raw data

Multiplex ELisa data, MTF-1 and western blot. 

This dataset is associated with the following publication:
Bruno, M., J. Ross, and Y. Ge. Proteomic Responses of BEAS-2B Cells to Nontoxic and Toxic Chromium: Protein Indicators of Cytotoxicity Conversion.   TOXICOLOGY LETTERS. Elsevier Science Ltd, New York, NY, USA, 264: 59-70, (2016).

Tags: 2d-gel-electrophoresis, apoptosis, cell-growth, chromium, elisa, inflammatory-cytokines, map-kinase, metal-mixtures, mtf-1-akt, proteomics, signaling-proteins
Organization: U.S. Environmental Protection Agency
Effects of Simulated Smog in Rodent Models of Disease Dataset.

The dataset includes the draft main paper and supporting information file to be submitted to the journal, and also excel spread sheets containing the raw data which backs up the processed data used in the paper and supporting information file.
    Data include exposure characterization (temperature, RH, pollutant levels, etc.), physiology data, serum data, lung inflammation data, viral burden data, PCR data, blood data, lung pathology data, and other miscellaneous data.  All the column headings and other relevant definitions and information are included in the data sets, and match the relevant data in the paper to be submitted. 

This dataset is associated with the following publication:
Hargrove, M., S. Snow, R. Luebke, C. Wood, J. Krug, T. Krantz, C. King, C. Copeland, S. McCullough, K. Gowdy, U. Kodavanti, I. Gilmour, and S. Gavett. Effects of Simulated Smog Atmospheres in Rodent Models of Metabolic and Immunologic Dysfunction.   ENVIRONMENTAL SCIENCE & TECHNOLOGY. American Chemical Society, Washington, DC, USA, 52(5): 3062-3070, (2018).

Tags: allergy, bacterial-infection, diabetes, influenza-a, photochemical-reactions, pulmonary-function, pulmonary-injury, smog
Organization: U.S. Environmental Protection Agency
Zhixuan Phosphate Data

The dataset shows two tables for linear combination fitting results of phosphorus speciation generated from two figures. 

This dataset is associated with the following publication:
Zhixuan, Q., A. Shober, K. Scheckel, C. Penn, and K. Turner. Mechanisms of Phosphorus Removal by Phosphorus Sorbing Materials.   JOURNAL OF ENVIRONMENTAL QUALITY. American Society of Agronomy, MADISON, WI, USA, 47(5): 1232-1241, (2018).

Tags: environmental-transport, phosphate-management, phosphate-removal, soil-quality, water-quality
Organization: U.S. Environmental Protection Agency
Data for Haselman et al 2016 Development of the LAGDA: effects of tOP or TB in Xenopus laevis from embryo to juvenile

These data are from two studies conducted to evaluate the performance of the draft Larval Amphibian Growth and Development Assay for incorporation into the U.S. EPA's Endocrine Disruptor Screening Program Tier II testing battery. 4-tert-octylphenol was chosen as an environmental estrogenic compound and 17-beta-trenbolone was chosen as an environmental androgenic compound. Although the effects of these model environmental endocrine disruptors are not novel, these chemicals were used essentially as positive controls to represent each of the potential modes of toxicity that could be encountered by future unknown compounds ordered to be run through the LAGDA in support of risk assessment. Endpoints evaluated were larval growth and metamorphic development, blood thyroid hormone, thyroid histopathology, juvenile growth, juvenile histopathology of the liver, gonads, kidneys and reproductive ducts. 

This dataset is associated with the following publication:
Haselman , J., P. Kosian , J. Korte , A. Olmstead, T. Iguchi, R. Johnson , and S. Degitz. Development of the larval amphibian growth and development assay: Effects of chronic 4-tert-octylphenol or 17ß-trenbolone exposure in Xenopus laevis from embryo to juvenile.   JOURNAL OF APPLIED TOXICOLOGY. John Wiley & Sons, Ltd., Indianapolis, IN, USA, 36(12): 1639-1650, (2016).

Tags: 17-beta-trenbolone, 4-tert-octylphenol, edsp, lagda, xenopus-laevis
Organization: U.S. Environmental Protection Agency
Prior knowledge-based approach for associating contaminants with biological effects: a case study in the St. Croix river basin, MN, WI, USA.

Concentrations of 127 organic chemicals measured in water samples collected from five locations in proximity to two municipal wastewater treatment plants in the St. Croix River basin, MN and WI, USA are included.  Additionally, gene expression in the livers of fathead minnows exposed in situ to the site water for 12 d is included. Gene expression was analyzed by oligonucleotide microarray and raw data are accessible through the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO), accession number GSE81263. Additional analyses performed on those data, including construction of knowledge assembly models from comparison of the detected chemicals data with associated genes from the comparative toxicogenomics database, pathway and gene ontology enrichment analyses performed on the gene expression data, and richness and concordance statistics from a Reverse Causal Reasoning-based statistical approach are included. 

This dataset is associated with the following publication:
Schroeder , A., D. Martinović-Weigelt, G. Ankley , K. Lee, N. Garcia-Reyero, E. Perkins, H. Schoenfuss, and D. Villeneuve. Prior knowledge-based approach for associating contaminants with biological effects: A case study in the St. Croix river basin, MN, WI, USA..   ENVIRONMENTAL POLLUTION. Elsevier Science Ltd, New York, NY, USA, 221: 427-436, (2017).

Tags: adverse-outcome-pathway, aquatic-ecosystems, ecotoxicology, endocrine-disruption, screening-and-prioritization
Organization: U.S. Environmental Protection Agency
Dose-Response Analysis of RNA-Seq Profiles in Archival Formalin-Fixed Paraffin-Embedded Samples.

se of archival resources has been limited to date by inconsistent methods for genomic profiling of degraded RNA from formalin-fixed paraffin-embedded (FFPE) samples. RNA-seq offers a novel way to address this problem. In this study we evaluated transcriptomic dose responses using RNA-seq in paired FFPE and frozen (FROZ) samples from two archival studies in mice, one recent (<2 years old) and the other older (>20 years old). Experimental treatments included di(2-ethylhexyl)phthalate (DEHP) and dichloroacetic acid (DCA) for the <2 and >20 year-old studies, respectively. Total RNA was ribodepleted and sequenced using the Illumina HiSeq platform. In the recent study, FFPE samples showed high concordance in total reads (98% vs FROZ), fold-change values of differentially expressed genes (DEGs) (R2 = 0.99), highly enriched target pathways (90% overlap with FROZ), and benchmark dose estimates for preselected target genes (-2% overall vs FROZ). In contrast, RNA-seq data from older FFPE samples had lower total reads (70% vs FROZ) and poor concordance in global DEGs and pathways. Despite a 99% loss of counts, dose responses were still evident for target genes in FFPE samples and positively correlated with paired FROZ samples. These findings highlight potential variability in the quality of RNA-seq data from FFPE samples. More recent FFPE samples were highly similar to FROZ samples in sequencing quality metrics, DEG profiles, and dose-response parameters, while further methods development is needed for older or lower-quality FFPE samples. This work should help broaden the use of archival resources in both chemical safety and translational science. 

This dataset is associated with the following publication:
Hester, S., V. Bhat, B. Chorley, G. Carswell, W. Jones, L. Wehmas, and C. Wood. Dose-Response Analysis of RNA-Seq Profiles in Archival Formalin-Fixed Paraffin-Embedded (FFPE) Samples..   TOXICOLOGICAL SCIENCES. Society of Toxicology,    154(2): 202-213, (2016).

Tags: dose-response-analysis, rna-seq-archival-ffpe
Organization: U.S. Environmental Protection Agency
SAS code used to analyze data and a datafile with metadata glossary

We compiled macroinvertebrate assemblage data collected from 1995 to 2014 from the St. Louis River Area of Concern (AOC) of western Lake Superior. Our objective was to define depth-adjusted cutoff values for benthos condition classes (poor, fair, reference) to provide tool useful for assessing progress toward achieving removal targets for the degraded benthos beneficial use impairment in the AOC. The relationship between depth and benthos metrics was wedge-shaped. We therefore used quantile regression to model the limiting effect of depth on selected benthos metrics, including taxa richness, percent non-oligochaete individuals, combined percent Ephemeroptera, Trichoptera, and Odonata individuals, and density of ephemerid mayfly nymphs (Hexagenia). We created a scaled trimetric index from the first three metrics. Metric values at or above the 90th percentile quantile regression model prediction were defined as reference condition for that depth. We set the cutoff between poor and fair condition as the 50th percentile model prediction. We examined sampler type, exposure, geographic zone of the AOC, and substrate type for confounding effects. Based on these analyses we combined data across sampler type and exposure classes and created separate models for each geographic zone. We used the resulting condition class cutoff values to assess the relative benthic condition for three habitat restoration project areas. The depth-limited pattern of ephemerid abundance we observed in the St. Louis River AOC also occurred elsewhere in the Great Lakes. We provide tabulated model predictions for application of our depth-adjusted condition class cutoff values to new sample data. 

This dataset is associated with the following publication:
Angradi, T., W. Bartsch, A. Trebitz, V. Brady, and J. Launspach. A depth-adjusted ambient distribution approach for setting numeric removal targets for a Great Lakes Area of Concern beneficial use impairment: Degraded benthos.   JOURNAL OF GREAT LAKES RESEARCH. International Association for Great Lakes Research, Ann Arbor, MI, USA, 43(1): 108-120, (2017).

Tags: benthos, great-lakes-areas-of-concern, reference
Organization: U.S. Environmental Protection Agency
Fox River kindling Bandara et al Summary Data

This study looked at functional endpoints in adult offspring of rats exposed in utero and postnatally to an environmentally relevant mixture of PCBs, Fox River blend. A model of neural plasticity and epilepsy, electrical kindling, was examined. Animals exposed to PCBs had slower kindling rates suggesting impaired plasticity mechanisms, consistent with previous work with PCBs where deficits were seen in another plasticity model, long-term potentiation. 

This dataset is associated with the following publication:
Bandara, S., R. Sadowski, S. Schantz, and M. Gilbert. Developmental Exposure to an Environmental PCB Mixture Delays the Propagation of Kindling in the Amygdala.   NEUROTOXICOLOGY. Elsevier B.V., Amsterdam,  NETHERLANDS,  n/a, (2016).

Tags: childrens-health, developmental-hypothryoidism, neruotoxicity, polyclorinated-biphenyls, thyroid-hormone
Organization: U.S. Environmental Protection Agency
Cardiac effects of acrolein in mice and role of TRPA1

This data shows the heart rate, heart rate variability and cardiac mechanical function of mice exposed to acrolein or ozone. 

This dataset is associated with the following publication:
Kurhanewicz, N., R. McIntosh-Kastrinsky, H. Tong, A. Ledbetter, L. Walsh, A. Farraj, and M. Hazari. TRPA1 mediates changes in heart rate variability and cardiac mechanical function in mice exposed to acrolein.   TOXICOLOGICAL AND APPLIED PHARMICOLOGY. Elsevier Science BV, Amsterdam,  NETHERLANDS, 324: 51-60, (2017).

Tags: acrolein, cardiac, mouse, trpa1
Organization: U.S. Environmental Protection Agency
QT_RR data for effects on diesel exhaust on cardiac conduction

This dataset includes QTc and RR values related to the electrocardiogram of rats exposed to either air or diesel exhaust. 

This dataset is associated with the following publication:
Hazari , M., J. Lancaster, J. Starobin, A. Farraj , and W. Cascio. Diesel exhaust worsens cardiac conduction instability in dobutamine-challenged Wistar-Kyoto and spontaneously hypertensive rats.   Cardiovascular Toxicology. Humana Press Incorporated, Totowa, NJ, USA, 17(2): 120-129, (2017).

Tags: arrhythmia, cardiac, diesel-exhaust, electrocardiogram, qtc, rats
Organization: U.S. Environmental Protection Agency
Nitrogen inputs and stream N concentrations NRSA 2008-2009

This is a combined dataset that includes data for 1966 of the 2008-2009 National Rivers and Streams Assessment watersheds.  The data includes watershed N inputs and stream TN, TON and DIN concentrations. 

This dataset is associated with the following publication:
Bellmore, R., J. Compton, R. Brooks, E. Fox, R. Hill, D. Sobota, D. Thornbrugh, and M. Weber. Nitrogen inputs drive nitrogen concentrations in U.S. streams and rivers during summer low flow conditions.   SCIENCE OF THE TOTAL ENVIRONMENT. Elsevier BV, AMSTERDAM,  NETHERLANDS, 639: 1349-1359, (2018).

Tags: monitoring, n-inputs, nitrogen, rivers, streams, watersheds
Organization: U.S. Environmental Protection Agency
Ecosystem Services Content Analysis Data

Content records of public media. 

This dataset is associated with the following publication:
Weber, M., C. Shannon, P. Ringold, and K. Blocksom. Rivers and Streams in the Media: Evaluating New Sources for Ecosystem Services Content.   Ecology and Society. Resilience Alliance Publications, Waterloo,  CANADA, 22(3): 15, (2017).

Tags: content-analysis, final-ecosystem-services, media, multivariate-analysis-of-variance, nonmetric-multidimensional-scaling, rivers-and-streams
Organization: U.S. Environmental Protection Agency
Data for this project include human subjects PII and cannot be shared.

Data on approximately 2 million births occurring in NJ, OH, and PA from 2000 - 2005. Linked to PM2.5 and ozone concentration estimates from EPA CMAQ fused model. 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: Birth data can be acquired through application to the state health statistics departments of NJ, OH, and PA. Contact author for code. rappazzo.kristen@epa.gov. Format: No data included. 

This dataset is associated with the following publication:
Rappazzo, K., D. Lobdell, L. Messer, C. Poole, and J. Daniels. Comparison of gestational dating methods and implications for exposure-outcome associations: an example with PM2.5 and preterm birth.   JOURNAL OF OCCUPATIONAL AND ENVIRONMENTAL MEDICINE. Lippincott Williams & Wilkins, Philadelphia, PA, USA, 74(2): 138-143, (2017).

Tags: particulate-matter, preterm-birth
Organization: U.S. Environmental Protection Agency