AndreaBozzo/ceres-open-data-index huggingface dataset:
Data from Tiered High-Throughput Screening Approach to Identify Thyroperoxidase Inhibitors within the ToxCast Phase I and II Chemical Libraries

High-throughput screening for potential thyroid-disrupting chemicals requires a system of assays to capture multiple molecular-initiating events (MIEs) that converge on perturbed thyroid hormone (TH) homeostasis. Screening for MIEs specific to TH-disrupting pathways is limited in the U.S. Environmental Protection Agency ToxCast screening assay portfolio. To fill 1 critical screening gap, the Amplex UltraRed-thyroperoxidase (AUR-TPO) assay was developed to identify chemicals that inhibit TPO, as decreased TPO activity reduces TH synthesis. The ToxCast phase I and II chemical libraries, comprised of 1074 unique chemicals, were initially screened using a single, high concentration to identify potential TPO inhibitors. Chemicals positive in the single-concentration screen were retested in concentration-response. Due to high false-positive rates typically observed with loss-of-signal assays such as AUR-TPO, we also employed 2 additional assays in parallel to identify possible sources of nonspecific assay signal loss, enabling stratification of roughly 300 putative TPO inhibitors based upon selective AUR-TPO activity. A cell-free luciferase inhibition assay was used to identify nonspecific enzyme inhibition among the putative TPO inhibitors, and a cytotoxicity assay using a human cell line was used to estimate the cellular tolerance limit. Additionally, the TPO inhibition activities of 150 chemicals were compared between the AUR-TPO and an orthogonal peroxidase oxidation assay using guaiacol as a substrate to confirm the activity profiles of putative TPO inhibitors. This effort represents the most extensive TPO inhibition screening campaign to date and illustrates a tiered screening approach that focuses resources, maximizes assay throughput, and reduces animal use. 

This dataset is associated with the following publication:
Paul-Friedman, K., E.D. Watt , M.W. Hornung , J.M. Hedge , R.S. Judson , K.M. Crofton , K.A. Houck , and S.O. Simmons. (TOXICOLOGICAL SCIENCES) Tiered High-Throughput Screening Approach to Identify Thyroperoxidase Inhibitors within the ToxCast Phase I and II Chemical Libraries.   TOXICOLOGICAL SCIENCES. Society of Toxicology,     1-59, (2016).

Tags: chemical-safety-for-sustainablity, chemical-safety-research, endocrine-disruption, high-throughput-toxicology, thyroperoxidase, toxcast
Organization: U.S. Environmental Protection Agency
Computational Modeling and Simulation of Genital Tubercle Development

Hypospadias is a developmental defect of urethral tube closure that has a complex etiology involving genetic and environmental factors, including anti-androgenic and estrogenic disrupting chemicals; however, little is known about the morphoregulatory consequences of androgen/estrogen balance during genital tubercle (GT) development. Computer models that predictively model sexual dimorphism of the GT may provide a useful resource to translate chemical-target bipartite networks and their developmental consequences across the human-relevant chemical universe. Here, we describe a multicellular agent-based model of genital tubercle (GT) development that simulates urethrogenesis from the sexually-indifferent urethral plate stage to urethral tube closure. The prototype model, constructed in CompuCell3D, recapitulates key aspects of GT morphogenesis controlled by SHH, FGF10, and androgen pathways through modulation of stochastic cell behaviors, including differential adhesion, motility, proliferation, and apoptosis. Proper urethral tube closure in the model was shown to depend quantitatively on SHH- and FGF10-induced effects on mesenchymal proliferation and epithelial apoptosis—both ultimately linked to androgen signaling. In the absence of androgen, GT development was feminized and with partial androgen deficiency, the model resolved with incomplete urethral tube closure, thereby providing an in silico platform for probabilistic prediction of hypospadias risk across combinations of minor perturbations to the GT system at various stages of embryonic development. 

This dataset is associated with the following publication:
Leung , M.C.K., S. Hutson, A. Seifert, R. Spencer, and T. Knudsen. (REPRODUCTIVE TOXICOLOGY) Computational Modeling and Simulation of Genital Tubercle Development.   REPRODUCTIVE TOXICOLOGY. Elsevier Science Ltd, New York, NY, USA,  1-11, (2016).

Tags: childrens-environmental-health, reproductive-development, reproductive-effects, tipping-points, virtual-embryo, virtual-liver, virtual-tissues
Organization: U.S. Environmental Protection Agency
NLCD - MODIS land cover- albedo dataset for the continental United States

The NLCD-MODIS land cover-albedo database integrates high-quality MODIS albedo observations with areas of homogeneous land cover from NLCD. The spatial resolution (pixel size) of the database is 480m-x-480m aligned to the standardized UGSG Albers Equal-Area projection. The spatial extent of the database is the continental United States. 

This dataset is associated with the following publication:
Wickham , J., C.A. Barnes, and T. Wade. Combining NLCD and MODIS to Create a Land Cover-Albedo Dataset for the Continental United States.   REMOTE SENSING OF ENVIRONMENT. Elsevier Science Ltd, New York, NY, USA, 170(0): 143-153, (2015).

Tags: climate-change, land-cover-change, landsat, radiative-forcing, snow-cover-albedo, snow-free-albedo
Organization: U.S. Environmental Protection Agency
Pacific Ocean buoy temperature date - TAO/TRITON database & National Buoy Data Center database

Pacific Ocean buoy temperature data. 

This dataset is associated with the following publication:
Carbone, F., M. Landis, C.N. Gencarelli, A. Naccarato, F. Sprovieri, F. De Simone, I.M. Hedgecock, and N. Pirrone. Sea surface temperature variation linked to elemental mercury concentrations measured on Mauna Loa.   GEOPHYSICAL RESEARCH LETTERS. American Geophysical Union, Washington, DC, USA,  online, (2016).

Tags: ocean-evation
Organization: U.S. Environmental Protection Agency
Systems Toxicology of Male Reproductive Development: Profiling 774 Chemicals for Molecular Targets and Adverse Outcomes

Background: Trends in male reproductive health have been reported for increased rates of testicular germ cell tumors, low semen quality, cryptorchidism, and hypospadias, which have been associated with prenatal environmental chemical exposure based on human and animal studies.

Objective: In the present study we aimed to identify significant correlations between environmental chemicals, molecular targets, and adverse outcomes across a broad chemical landscape with emphasis on developmental toxicity of the male reproductive system.

Methods: We used U.S. EPA’s animal study database (ToxRefDB) and a comprehensive literature analysis to identify 774 chemicals that have been evaluated for adverse effects on male reproductive parameters, and then used U.S. EPA’s in vitro high-throughput screening (HTS) database (ToxCastDB) to profile their bioactivity across approximately 800 molecular and cellular features. 

Results: A phenotypic hierarchy of testicular atrophy, sperm effects, tumors, and malformations, a composite resembling the human testicular dysgenesis syndrome (TDS) hypothesis, was observed in 281 chemicals. A subset of 54 chemicals with male developmental consequences had in vitro bioactivity on molecular targets that could be condensed into 156 gene annotations in a bipartite network. 

Conclusion: Computational modeling of available in vivo and in vitro data for chemicals that produce adverse effects on male reproductive end points revealed a phenotypic hierarchy across animal studies consistent with the human TDS hypothesis. We confirmed the known role of estrogen and androgen signaling pathways in rodent TDS, and importantly, broadened the list of molecular targets to include retinoic acid signaling, vascular remodeling proteins, G-protein coupled receptors (GPCRs), and cytochrome P450s. 

This dataset is associated with the following publication:
Leung , M., J. Phuong , N. Baker , N. Sipes , G. Klinefelter , M. Martin , K. McLaurin, W. Setzer , S. Darney , R. Judson , and T. Knudsen. (ENVIRONMENTAL HEALTH PERSPECTIVES) Systems Toxicology of Male Reproductive Development: Profiling 774 Chemicals for Molecular Targets and Adverse Outcomes.   ENVIRONMENTAL HEALTH PERSPECTIVES. National Institute of Environmental Health Sciences (NIEHS), Research Triangle Park, NC, USA,  1-47, (2015).

Tags: childrens-environmental-health, reproductive-effects, tipping-points, virtual-embryo, virtual-liver, virtual-tissues
Organization: U.S. Environmental Protection Agency
Evaluation of food-relevant chemicals in the ToxCast high-throughput screening program

Thousands of chemicals are directly added to or come in contact with food, many of which have undergone little to no toxicological evaluation. The landscape of the food-relevant chemical universe was evaluated using cheminformatics, and subsequently the bioactivity of food-relevant chemicals across the publicly available ToxCast highthroughput screening program was assessed. In total, 8659 food-relevant chemicals were compiled including direct food additives, food contact substances, and pesticides. Of these food-relevant chemicals, 4719 had curated structure definition files amenable to defining chemical fingerprints, which were used to cluster chemicals using a selforganizing map approach. Pesticides, and direct food additives clustered apart from one another with food contact substances generally in between, supporting that these categories not only reflect different uses but also distinct chemistries. Subsequently, 1530 food-relevant chemicals were identified in ToxCast comprising 616 direct food additives, 371 food contact substances, and 543 pesticides. Bioactivity across ToxCast was filtered for cytotoxicity to identify selective chemical effects. Initiating analyses from strictly chemical-based methodology or bioactivity/cytotoxicity-driven evaluation presents unbiased approaches for prioritizing chemicals. Although bioactivity in vitro is not necessarily predictive of adverse effects in vivo, these data provide insight into chemical properties and cellular targets through which foodrelevant chemicals elicit bioactivity. 

This dataset is associated with the following publication:
Karmaus , A., D. Filer , M. Martin , and K. Houck. (FOOD AND CHEMICAL TOXICOLOGY) Evaluation of food-relevant chemicals in the ToxCast high-throughput screening program.   FOOD AND CHEMICAL TOXICOLOGY. Elsevier Science Ltd, New York, NY, USA, 92: 188-196, (2016).

Tags: chemical-safety-for-sustainablity, chemical-safety-research, computational-toxicology, food-additive, food-contact-substance, high-throughput-screening, high-throughput-toxicology, pesticide, toxcast
Organization: U.S. Environmental Protection Agency
CERAPP: Collaborative Estrogen Receptor Activity Prediction Project

Data from a large-scale modeling project called CERAPP (Collaborative Estrogen Receptor Activity Prediction Project) demonstrating using predictive computational models on high-throughput screening data to screen thousands of chemicals against the estrogen receptor. 

This dataset is associated with the following publication:
Mansouri , K., A. Abdelaziz, A. Rybacka, A. Roncaglioni, A. Tropsha, A. Varnek, A. Zakharov, A. Worth, A. Richard , C. Grulke , D. Trisciuzzi, D. Fourches, D. Horvath, E. Benfenati , E. Muratov, E.B. Wedebye, F. Grisoni, G.F. Mangiatordi, G.M. Incisivo, H. Hong, H.W. Ng, I.V. Tetko, I. Balabin, J. Kancherla , J. Shen, J. Burton, M. Nicklaus, M. Cassotti, N.G. Nikolov, O. Nicolotti, P.L. Andersson, Q. Zang, R. Politi, R.D. Beger , R. Todeschini, R. Huang, S. Farag, S.A. Rosenberg, S. Slavov, X. Hu, and R. Judson. (Environmental Health Perspectives)  CERAPP: Collaborative Estrogen Receptor Activity Prediction Project.   ENVIRONMENTAL HEALTH PERSPECTIVES. National Institute of Environmental Health Sciences (NIEHS), Research Triangle Park, NC, USA,  1-49, (2016).

Tags: chemistry-dashboard, dsstox, endocrine-disruption, estrogen-receptor, qsar, read-across, toxcast
Organization: U.S. Environmental Protection Agency
Linking high resolution mass spectrometry data with exposure and toxicity forecasts to advance high-throughput environmental monitoring

There is a growing need in the field of exposure science for monitoring methods that rapidly screen environmental media for suspect contaminants. Measurement and analysis platforms, based on high resolution mass spectrometry (HRMS), now exist to meet this need. Here we describe results of a study that links HRMS data with exposure predictions from the U.S. EPA's ExpoCast™ program and in vitro bioassay data from the U.S. interagency Tox21 consortium. Vacuum dust samples were collected from 56 households across the U.S. as part of the American Healthy Homes Survey (AHHS). Sample extracts were analyzed using liquid chromatography time-of-flight mass spectrometry (LC–TOF/MS) with electrospray ionization. On average, approximately 2000 molecular features were identified per sample (based on accurate mass) in negative ion mode, and 3000 in positive ion mode. Exact mass, isotope distribution, and isotope spacing were used to match molecular features with a unique listing of chemical formulas extracted from EPA's Distributed Structure-Searchable Toxicity (DSSTox) database. A total of 978 DSSTox formulas were consistent with the dust LC–TOF/molecular feature data (match score ≥ 90); these formulas mapped to 3228 possible chemicals in the database. Correct assignment of a unique chemical to a given formula required additional validation steps. Each suspect chemical was prioritized for follow-up confirmation using abundance and detection frequency results, along with exposure and bioactivity estimates from ExpoCast and Tox21, respectively. Chemicals with elevated exposure and/or toxicity potential were further examined using a mixture of 100 chemical standards. A total of 33 chemicals were confirmed present in the dust samples by formula and retention time match; nearly half of these do not appear to have been associated with house dust in the published literature. Chemical matches found in at least 10 of the 56 dust samples include Piperine, N,N-Diethyl-m-toluamide (DEET), Triclocarban, Diethyl phthalate (DEP), Propylparaben, Methylparaben, Tris(1,3-dichloro-2-propyl)phosphate (TDCPP), and Nicotine. This study demonstrates a novel suspect screening methodology to prioritize chemicals of interest for subsequent targeted analysis. The methods described here rely on strategic integration of available public resources and should be considered in future non-targeted and suspect screening assessments of environmental and biological media. 

This dataset is associated with the following publication:
Rager, J.E., M. Strynar , S. Liang, R.L. McMahen, A. Richard , C.M. Grukle, J. Wambaugh , K. Isaacs , R. Judson , A. Williams , and J. Sobus. Linking high resolution mass spectrometry data with exposure and toxicity forecasts to advance high-throughput environmental monitoring.   ENVIRONMENT INTERNATIONAL. Elsevier Science Ltd, New York, NY, USA, 88: 269-280, (2016).

Tags: non-targeted-suspect-screening-exposome-expocast-toxcast-dust
Organization: U.S. Environmental Protection Agency
EPA True NO2 ground site measurements – multiple sites, TCEQ ground site measurements of meteorological and air pollution parameters – multiple sites ,GeoTASO NO2 Vertical Column

EPA True NO2 ground site measurements – multiple sites - http://www-air.larc.nasa.gov/cgi-bin/ArcView/discover-aq.tx-2013; TCEQ ground site measurements of meteorological and air pollution parameters – multiple sites - http://www-air.larc.nasa.gov/cgi-bin/ArcView/discover-aq.tx-2013; GeoTASO NO2 Vertical Column - http://www-air.larc.nasa.gov/cgi-bin/ArcView/discover-aq.tx-2013?FALCON=1. 

This dataset is associated with the following publication:
Nowlan, C., X. Lu, J. Leitch, K. Chance, G. González Abad, C. Lu, P. Zoogman, J. Cole, T. Delker, W. Good, F. Murcray, L. Ruppert, D. Soo, M. Follette-Cook, S. Janz, M. Kowalewski, C. Loughner, K. Pickering, J. Herman, M. Beaver, R. Long, J. Szykman, L. Judd, P. Kelley, W. Luke, X. Ren, and J. Al-Saadi. Nitrogen dioxide observations from the Geostationary Trace gas and Aerosol Sensor Optimization (GeoTASO) airborne instrument: Retrieval algorithm and measurements during DISCOVER-AQ Texas 2013.   Atmospheric Measurement Techniques. Copernicus Publications, Katlenburg-Lindau,  GERMANY, 9(6): 2647-2668, (2016).

Tags: air-quality-from-space, column-density, geotaso, nitrogen-dioxide, true-no2
Organization: U.S. Environmental Protection Agency
SEQUENCING AND DE NOVO DRAFT ASSEMBLIES OF A FATHEAD MINNOW (Pimpehales promelas) reference genome

The dataset provides the URLs for accessing the genome sequence data and two draft assemblies as well as fathead minnow genotyping data associated with estimating the heterozygosity of the in-bred line. 

This dataset is associated with the following publication:
Burns, F., L. Cogburn, G. Ankley , D. Villeneuve , E. Waits , Y. Chang, V. Llaca, S. Deschamps, R. Jackson, and R. Hoke. Sequencing and De novo Draft Assemblies of the Fathead Minnow (Pimphales promelas)Reference Genome.   ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY. Society of Environmental Toxicology and Chemistry, Pensacola, FL, USA, 35(1): 212-217, (2016).

Tags: adverse-outcome-pathway, aquatic-ecosystems, computational-toxicology, genome, pathfinder-innovation-project
Organization: U.S. Environmental Protection Agency
Titanium-based zeolitic imidazolate framework for chemical fixation of carbon dioxide

A titanium-based zeolitic imidazolate framework (Ti-ZIF) with high surface area and porous morphology has been synthesized and its application as a recyclable catalyst is demonstrated in the synthesis of cyclic carbonate via cycloaddition of carbon dioxide and epoxide in aqueous media. 

This dataset is associated with the following publication:
Varma, R., S. Verma, R.B.N. Baig, and M. Nadagouda. Titanium-based zeolitic imidazolate framework for chemical fixation of carbon dioxide.   GREEN CHEMISTRY. Royal Society of Chemistry, Cambridge,  UK, 18: 4855-4858, (2016).

Tags: carbon-dioxide, chemical-fixation, earth-abundant-materials, sustainable-materials-management, zeolitic-imidazolate-framework
Organization: U.S. Environmental Protection Agency
Aerobic oxidation of alcohols in visible light on Pd-grafted Ti cluster

The titanium cluster with the reduced band gap has been synthesized having the palladium nanoparticles over the surface, which not only binds to the atmospheric oxygen but also catalyzes the oxidation of alcohols under visible light. 

This dataset is associated with the following publication:
Verma, S., R.B.N. Baig, M. Nadagouda, and R. Varma. Aerobic oxidation of alcohols in visible light on Pd-grafted Ti cluster.   TETRAHEDRON. Elsevier Science Ltd, New York, NY, USA, 73(38): 5577-5580, (2017).

Tags: aerial-oxidation, earth-abundant-materials, heterogeneous-catalysis, palladium-nanoparticle, sustainable-materials-management, titanium-cluster
Organization: U.S. Environmental Protection Agency
A photoactive bimetallic framework for direct aminoformylation of nitroarenes

A bimetallic catalyst, AgPd@g-C3N4, synthesized by reducing silver and palladium salts over graphitic carbon nitride (g-C3N4), enables the concerted reductive formylation of aromatic nitro compounds under photo-chemical conditions using formic acid, which serves the dual role of a hydrogen source and a formylating agent. 

This dataset is associated with the following publication:
Baig, R.B.N., S. Verma, M. Nadagouda , and R. Varma. A photoactive bimetallic framework for direct aminoformylation of nitroarenes.   GREEN CHEMISTRY. Royal Society of Chemistry, Cambridge,  UK, 18(4): 1019-1022, (2016).

Tags: aminoformylation, bimetallic-framework, earth-abundant-materials, nitroarenes, sustainable-materials-management
Organization: U.S. Environmental Protection Agency
Visible light mediated upgrading of biomass to biofuel

AgPd@g-C3N4, comprising heterogenized Ag and Pd
nanoparticles on graphitic carbon nitride, g-C3N4, has been
synthesized and used for the upgrading of biofuel as exemplified
by the hydrodeoxygenation of lignin-derived vanillin under
photochemical conditions using formic acid. The bimetallic
framework is found to be highly active due to the synergistic
effects of Ag and Pd with the graphitic carbon nitride support and
their mutual interaction. 

This dataset is associated with the following publication:
Varma , R., M. Nadagouda , S. Verma, and R.B. Nasir Baig. Visible light mediated upgrading of biomass to biofuel.   Energy & Environmental Science. RSC Publishing, Cambridge,  UK, 18(5): 1327-1333, (2016).

Tags: biofuel-production, biomass-upgrade, earth-abundant-materials, sustainable-materials-management, visible-light
Organization: U.S. Environmental Protection Agency
Magnetically separable Fe3O4@DOPA–Pd: a heterogeneous catalyst for aqueous Heck reaction

Magnetically separable Fe3O4@DOPA–Pd catalyst has been synthesized via anchoring of palladium over dopamine-coated magnetite via co-ordinate interaction
and the catalyst is utilized for expeditious Heck coupling in aqueous media. 

This dataset is associated with the following publication:
Baig, N., J. Leazer , and R. Varma. Magnetically Separable Fe3O4@DOPA-Pd: A Heterogeneous Catalyst for Aqueous Heck Reaction.   CLEAN TECHNOLOGIES AND ENVIRONMENTAL POLICY. Springer-Verlag, New York, NY, USA, 17(7): 2073-2077, (2015).

Tags: heck-reaction, heterogeneous-catalyst, magnetically-separable
Organization: U.S. Environmental Protection Agency
Oxidative esterification via photocatalytic C-H activation

Direct oxidative esterification of alcohol via photocatalytic C–H activation has been developed using VO@g-C3N4 catalyst; an expeditious esterification of alcohols occurs under neutral conditions using visible light as the source of energy. 

This dataset is associated with the following publication:
Varma , R., S. Verma, R.B.N. Baig, C. Han, and M. Nadagouda. Oxidative esterification via photocatalytic C-H activation.   GREEN CHEMISTRY. Royal Society of Chemistry, Cambridge,  UK, 18: 251-254, (2015).

Tags: earth-abundant-materials, oxidative-esterification, photocatalytic-c-h-activation, sustainable-materials-management, visible-light
Organization: U.S. Environmental Protection Agency
Nanoparticle-organic pollutant interaction dataset

Dataset presents concentrations of organic pollutants, such as polyaromatic hydrocarbon compounds, in water samples. Water samples of known volume and concentration were allowed to equilibrate with known mass of nanoparticles. The mixture was then ultracentrifuged and sampled for analysis. 

This dataset is associated with the following publication:
Sahle-Demessie, E., A. Zhao, C. Han, B. Hann, and H. Grecsek. Interaction of engineered nanomaterials with hydrophobic organic pollutants..   Journal of Nanotechnology. Hindawi Publishing Corporation, New York, NY, USA, 27(28): 284003, (2016).

Tags: engineered-nanoparticles-np, enmpollutant-adsorption, hydrophobic-pollutant-adsorption, hydrophobic-pollutants, partitioning-coefficient, polyaromatic-hydrocarbon, tga, tga-gc-ms
Organization: U.S. Environmental Protection Agency
Nanomaterials - pollutant interaction

Concentrations of different polyaromatic hydrocarbons in water before and after interaction with nanomaterials. The results show the capacity of engineer nanomaterials for adsorbing different organic pollutants. 

This dataset is associated with the following publication:
Sahle-Demessie, E., A. Zhao, C. Han, B. Hann, and H. Grecsek. Interaction of engineered nanomaterials with hydrophobic organic pollutants..   Journal of Nanotechnology. Hindawi Publishing Corporation, New York, NY, USA, 27(28): 284003, (2016).

Tags: adsorption-tga-gc-ms, engineered-nanomaterials, engineered-nanoparticles-np, enmpollutant-adsorption, hydrophobic-pollutant-adsorption, hydrophobic-pollutants, partitioning-coefficient, tga, tga-gc-ms
Organization: U.S. Environmental Protection Agency