AndreaBozzo/ceres-open-data-index huggingface dataset:
Emergy accounting of Greater Cincinnati water and wastewater systems

All the data used to generate figures and tables, the background data such as unit emergy value library are in the dataset. 

This dataset is associated with the following publication:
Arden, S., C. Ma, and M. Brown. Holistic Analysis of Urban Water Systems in the Greater Cincinnati Region: (2) Resource Use Profiles by Emergy Accounting Approach - journal needs to be Water Research X.   Water Research X. Elsevier B.V., Amsterdam,  NETHERLANDS, 2: 100012, (2019).

Tags: emergy, integrated-urban-water-management, resource-efficiency, sustainability, system-analysis
Organization: U.S. Environmental Protection Agency
Phage Data

Phage Data. 

This dataset is associated with the following publication:
Zepp, R., M. Cyterski, K. Wong , O. Georgacopoulos, B. Acrey, G. Whelan, R. Parmar, and M. Molina. Biological Weighting Functions for Evaluating the Role of Sunlight-Induced Inactivation of Coliphages at Selected Beaches and Nearby Tributaries.   ENVIRONMENTAL SCIENCE & TECHNOLOGY. American Chemical Society, Washington, DC, USA, 52(22): 13068-13076, (2018).

Tags: drinking-water, great-lakes, microbial-fate-and-transport, recreational-waters
Organization: U.S. Environmental Protection Agency
FIB concentrations, rate of release from manure, FIB transport, daily flow, non-point source

FIB concentrations, rate of release from manure, FIB transport, daily flow, non-point source. 

This dataset is associated with the following publication:
Kim, K., G. Whelan, M. Molina, R. Parmar, K. Wolfe, M. Galvin, P. Duda, R. Zepp, J. Kinzelman, G. Kleinheinz, and M. Borchardt. Using Integrated Environmental Modeling to Assess Sources of Microbial Contamination in Mixed-Use Watersheds.   JOURNAL OF ENVIRONMENTAL QUALITY. American Society of Agronomy, MADISON, WI, USA, 47(5): 1103-1114, (2018).

Tags: integrated-environmental-modeling, manure, pathogens, qmra, risk-assessment, source-apportionment, watershed-modeling
Organization: U.S. Environmental Protection Agency
Florida cattle decay study

Fecal contamination of recreational waters with cattle manure can pose a risk to public health due to the potential presence of various zoonotic pathogens. Fecal indicator bacteria (FIB) have a long history of use in the assessment. However, FIB quantification provides no information about pollution sources. Microbial source tracking (MST) genetic markers have been developed in response to a need to identify pollution sources, yet factors that influence host-identifier target decay once discharged into the environment are often poorly understood, especially for agriculture fecal waste sources. Here, we investigate the influence of water type (freshwater versus marine) and select environmental parameters (indigenous microbiota, ambient sunlight) on the decay of FIB and MST genetic markers originating from cattle manure. Experiments were conducted in situ using a submersible aquatic mesocosm containing dialysis bags filled with a mixture of cattle manure and ambient water. Culturable FIB (E. coli and enterococci) were enumerated by membrane filtration and the concentration of general fecal indicator bacteria (GenBac3, Entero1a, and EC23S857) and MST (Rum2Bac, CowM2, and CowM3) genetic markers were estimated by qPCR. Water type was the most significant factor influencing the decay of cattle manure indicator bacteria (three-way ANOVA, p: 0.006 to < 0.001), although the magnitude of the effect differed among microbial targets and over time. The presence of indigenous microbiota and exposure to sunlight were both significantly correlated (three-way ANOVA, p: 0.044 to < 0.001) with decay of enterococci and CowM2, while E. coli, EC23S857, Rum2Bac, and CowM3 (three-way ANOVA, p: 0.044 <0.001) were significantly impacted by either sunlight or indigenous microbiota. Findings indicate the extended persistence (>144 hours) of both cultivated FIB and genetic markers in marine and freshwater water types. Findings suggest that multiple environmental stressors are important determinants of FIB and MST marker persistence, but their magnitude can vary across different indicators. Selective exclusion of natural aquatic microbiota and/or sunlight typically resulted in extended survival, but the effect was minor and limited to select microbial targets. 

This dataset is associated with the following publication:
Korajkic, A., B. McMinn, N. Ashbolt, M. Sivaganesan, V. Harwood, and O. Shanks. Extended persistence of general and cattle-associated fecal indicators in marine and freshwater environment.   SCIENCE OF THE TOTAL ENVIRONMENT. Elsevier BV, AMSTERDAM,  NETHERLANDS, 650(1): 1292-1302, (2018).

Tags: abiotic-factors, biotic-factors, decay, fecal-indicator-bacteria, microbial-source-tracking-markers, pathogens
Organization: U.S. Environmental Protection Agency
Method Comparison Manuscript

Coliphage are alternative fecal indicators that may be suitable surrogates for viral pathogens, but a majority of standard detection methods utilize insufficient sample volumes (1-100 mL) for routine detection in environmental waters. Here we compare three somatic and F+ coliphage enumeration methods based on a paired measurement from 1L samples collected from the Great Lakes region (n=74). Methods include: 1) a dead-end hollow fiber ultrafilter combined with single agar layer plaque assay (D-HFUF-SAL); 2) a modified SAL (M-SAL); and 3) a direct membrane filtration (DMF) technique. Overall, D-HFUF-SAL outperformed all other methods as it yielded the lowest frequency of non-detects [(ND); 10.8%] and the highest average coliphage concentrations (2.51 ± 1.02 log10 plaque forming unit/liter (PFU/L) and 0.79 ± 0.71 log10 PFU/L for somatic and F+, respectively). M-SAL yielded 29.7% ND and average concentrations of 2.26 ± 1.15 log10 PFU/L (somatic) and 0.59 ± 0.82 log10 PFU/L (F+). DMF performed worse compared to D-HFUF-SAL and M-SAL methods (ND of 65.6%; average somatic coliphage concentration 1.52 ± 1.32 log10 PFU/L, with no F+ detected), indicating this procedure is unsuitable for 1L surface water sample volumes. This study represents an important step toward the use of a coliphage method for recreational water quality criteria purposes. 

This dataset is associated with the following publication:
McMinn, B., E. Rhodes, E. Huff, P. Wanjugi, M. Ware, S. Nappier, M. Cyterski, O. Shanks, K. Oshima, and A. Korajkic. Comparison of somatic and F+ coliphage enumeration methods with large volume surface water samples.   JOURNAL OF VIROLOGICAL METHODS. Elsevier Science Ltd, New York, NY, USA, 261: 63-66, (2018).

Tags: coliphage, culture-based-methods, method-comparison
Organization: U.S. Environmental Protection Agency
Wetland Figures/Tables Dataset

Data sets for all figures and tables in the manuscript. 

This dataset is associated with the following publication:
McMinn, B., S. Klemm, A. Korajkic, K. Wyatt, M. Herrmann, R. Haugland, J. Lu, E. Villegas, and C. Frye. A constructed wetland for treatment of an impacted waterway and the influence of native waterfowl on its perceived effectiveness..   ECOLOGICAL ENGINEERING. Elsevier Science Ltd, New York, NY, USA, 128: 48-56, (2019).

Tags: fecal-indicator, microbial-source-tracking, wetland
Organization: U.S. Environmental Protection Agency
Data for Measures of abdominal obesity, metabolic dysfunction, and metabolic syndrome in United States adolescents: exploratory analysis using the National Health and Nutrition Examination Survey (NHANES) 2011-2014 data

NHANES data from the 2011-2014 survey years. Specific to adolescents. Ancillary data related to metabolic syndrome and other covariates. 

This dataset is associated with the following publication:
Gaston, S., N. Tulve, and T. Ferguson. Abdominal obesity, metabolic dysfunction, and metabolic syndrome in U.S. adolescents: National Health and Nutrition Examination Survey 2011–2016.   ANNALS OF EPIDEMIOLOGY. Elsevier Science Ltd, New York, NY, USA, 30: 30-36, (2019).

Tags: adolescents, metabolic-syndrome, nhanes
Organization: U.S. Environmental Protection Agency
Scenario Output Table

Output from three different scenarios generated using stormwater management planning support software to reduce occurrence of combined sewer overflow events through the use of green infrastructure. 

This dataset is associated with the following publication:
Fu, X., H. Goddard, X. Wang, and M. Hopton. Development of a scenario-based stormwater management planning support system for reducing combined sewer overflows (CSOs).   JOURNAL OF ENVIRONMENTAL MANAGEMENT. Elsevier Science Ltd, New York, NY, USA, 236: 571-580, (2019).

Tags: green-infrastructure, scenario-planning, stormwater-management
Organization: U.S. Environmental Protection Agency
Investigating the role of distributed energy in the industrial and commercial sectors in the U.S. to attain greenhouse gas reductions goals

The dataset presents the metadata going into Figures presented in the manuscript. 

This dataset is associated with the following publication:
Kaplan, O., and J. Witt. What is the role of distributed energy resources under scenarios of greenhouse gas reductions? A specific focus on combined heat and power systems in the industrial and commercial sectors.   Applied Energy. Elsevier B.V., Amsterdam,  NETHERLANDS, 235: 83-94, (2018).

Tags: air-pollution, chp, energy-modeling, greenhouse-gases, industrial-sector
Organization: U.S. Environmental Protection Agency
Dataset for Summertime organic carbon absorption and sources at a southeastern U.S. location - dominance of secondary organic aerosol

The data tables in this file were used to generate the figures in the manuscript, "Summertime organic carbon absorption and sources at a southeastern U.S. location - dominance of secondary organic aerosol". Light-absorbing organic carbon, i.e. brown carbon, has been intensively investigated in atmospheres impacted by biomass burning impacted atmospheres. However, other brown carbon sources have been rarely studied in ambient aerosols. This data set includes forty-five PM2.5 filter samples that were collected in Research Triangle Park (RTP), NC, USA from June 1st to July 15th, 2013. The bulk carbonaceous components, including organic carbon, elemental carbon, water soluble organic carbon, and an array of organic molecular markers were measured; an ultraviolet (UV)/visible  (Vis) spectrometer was used to measure the light absorption of methanol and water extractable organic carbon. A complete description of how the data was acquired and and analyzed is provided in the manuscript.  A description of each parameter presented is provided in the file in the Data Dictionary. 

This dataset is associated with the following publication:
Xie, M., X. Chen, A. Holder, M. Hays, M. Lewandowski, J. Offenberg, T. Kleindienst, and M. Jaoui. Summertime organic carbon absorption and sources at a southeastern U.S. location – dominance of secondary organic aerosol.   ENVIRONMENTAL POLLUTION. Elsevier Science Ltd, New York, NY, USA, 244: 38-46, (2018).

Tags: aerosol-optical-properties, black-carbon, brown-carbon, combustion-emissions, fine-particulate-matter, secondary-organic-aerosol
Organization: U.S. Environmental Protection Agency
Transport of Nanohybrids Dataset

Characterization of nanohybrids using TEM, XPS, zeta potential measurement, UV-Vis spectrometry. Modeling results of nanohybrids transport. 

This dataset is associated with the following publication:
Wang, D., Y. Jin, C. Park, J. Heo, X. Bai, N. Aich, and C. Su. Modeling the Transport of the "New Horizon" Reduced Graphene Oxide—Metal Oxide Nanohybrids in Water-Saturated Porous Media.   ENVIRONMENTAL SCIENCE & TECHNOLOGY. American Chemical Society, Washington, DC, USA, 52: 4610-4622, (2018).

Tags: and-rgo-zinc-oxide-zno-nanohybrids, column-transport-test, reduced-graphene-oxide-rgo-magnetite-fe3o4, rgo-titanium-dioxide-tio2
Organization: U.S. Environmental Protection Agency
Data for 3D Organoid Model Assessment of Influence of Chemicals on Morphogenetic Fusion.

Organogenesis in the embryo involves cell differentiation and organization events that are unique to each tissue and organ and are susceptible to developmental toxicants. Animal models are the gold standard for identifying putative teratogens, but the limited throughput of developmental toxicological studies in animals coupled with the limited concordance between animal and human teratogenicity motivates a different approach. In vitro organoid models can mimic the cellular architecture and phenotype of many tissues and organs, and the three-dimensional (3D) architecture of organoids presents an opportunity to study developmental human toxicology. Common themes during development like the involvement of epithelial-mesenchymal transition and tissue fusion present an opportunity to develop in vitro models to study cell and tissue morphogenesis. We previously described organoids composed of human stem and progenitor cells that recapitulated the cellular features of palate fusion, and here we further characterized the model by examining pharmacological inhibitors targeting known palatogenesis and epithelial morphogenesis pathways as well as twelve cleft palate teratogens identified from rodent models. Organoid survival was dependent on signaling through EGF, IGF, HGF, and FGF pathways, and organoid fusion was disrupted by inhibition of BMP signaling. We observed concordance between the effects of EGF, FGF, and BMP inhibitors on organoid fusion and epithelial cell migration in vitro, suggesting that organoid fusion is dependent on epithelial morphogenesis. Three of the twelve putative cleft palate teratogens studied here significantly disrupted in vitro fusion, including theophylline, triamcinolone, and valproic acid. Tributyltin chloride and all-trans retinoic acid (ATRA) were cytotoxic to fusing organoids.  The study herein demonstrates the utility of the in vitro fusion assay for identifying chemicals that disrupt human organoid survival and morphogenesis in a scalable format amenable to toxicology screening. 

This dataset is associated with the following publication:
Belair, D., C. Wolf, S. Moorefield, C. Wood, C. Becker, and B. Abbott. A Three-Dimensional Organoid Culture Model to Assess the Influence of Chemicals on Morphogenetic Fusion..   TOXICOLOGICAL SCIENCES. Society of Toxicology, RESTON, VA,   394-408, (2018).

Tags: cell-spheroids, epithelial-cells, extracellular-matrix, mesenchymal-cells, morphogenetic-fusion, osteogenesis, palate-fusion, pharmacological-inhibitors, stromal-cells, teratogens, tissue-engineering
Organization: U.S. Environmental Protection Agency
Datasets used in ORD-023413: Frequent Modulation of the Sterol Regulatory Element Binding Protein (SREBP) by Chemical Exposure in the Livers of Rats

Datasets used in ORD-023413: Frequent Modulation of the Sterol Regulatory Element Binding Protein (SREBP) by Chemical Exposure in the Livers of Rats. 

This dataset is associated with the following publication:
Corton, C. Frequent modulation of the sterol regulatory element binding protein (SREBP) by chemical exposure in the livers of rats.   Computational Toxicology. Elsevier B.V., Amsterdam,  NETHERLANDS, 10: 113-129, (2019).

Tags: cholesterol-synthesis, fatty-acid-synthesis, fatty-liver-disease, gene-expression-omnibus-accession-numbers, hepatic-steatosis, microarray, sterol-regulatory-element-binding-protein
Organization: U.S. Environmental Protection Agency
The role of soil and house dust physicochemical properties in the post ingestion bioaccessibility of sorbed polychlorinated biphenyls

This file presents physicochemical properties of soils, house dusts, PCBs, and the bioaccessibility values calculated from the analysis of PCBs in the soils, house dusts, and synthetic digestive fluids. Bioaccessibility values were calculated using the ratio of the analyte in the sediment relative to that in the digestive fluids. The first tab in the excel spreadsheet is the data dictionary and contains the meta data (column headings and fields).  The second tab contains the soil/dust/PCB physicochemical properties and the associated bioaccessibility values. 

This dataset is associated with the following publication:
Shen, H., W. Li, S. Graham, and J. Starr. The role of soil and house dust physicochemical properties in determining the post ingestion bioaccessibility of sorbed polychlorinated biphenyls.   CHEMOSPHERE. Elsevier Science Ltd, New York, NY, USA, 217: 1-8, (2019).

Tags: bioaccessibility-soil, house-dust, ingestion, physicochemical-properties, polychlorinated-biphenyls
Organization: U.S. Environmental Protection Agency
Bioaccessibility of fipronil sorbed to soils and house dusts

Bioaccessibility values for fipronil determined using 37 paired soil and dust samples. Values for the physicochemical properties of the soils and dusts used to model the bioaccessibility data. 

This dataset is associated with the following publication:
Starr , J., W. Li, S. Graham , K. Bradham , D. Stout , A. Williams , and J. Sylva. Using paired soil and house dust samples in an in vitro assay to assess the post ingestion bioaccessibility of sorbed fipronil.   JOURNAL OF HAZARDOUS MATERIALS. Elsevier Science Ltd, New York, NY, USA, 312: 141-149, (2016).

Tags: bioaccessibility, fipronil, house-dusts, ingestion, soils
Organization: U.S. Environmental Protection Agency
Variability of pyrethroid and pyrethroid degradate concentrations on hard surface kitchen flooring in occupied residences.

Concentrations of pyrethroids and pyrethroid degradates in surface wipe samples collected from occupied residences. 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: Restricted access may be granted to authorized persons by contacting the party listed. 
James Starr
Research Physical Scientist
USEPA/ORD/NERL/EMMD/PHCB
MD D205-05
109 TW Alexander Dr.
RTP, NC 27711. Format: These data are from a human study. The study design was approved by the US EPA’s Human Subjects Research Review Official and the University of North Carolina’s Institutional Review Board (study number 09-0741). 

This dataset is associated with the following publication:
Starr, J., S. Graham, W. Li, A. Gemma, and M. Morgan. Variability of pyrethroid concentrations on hard surface kitchen flooring in occupied housing.   INDOOR AIR. Blackwell Publishing, Malden, MA, USA, 28(5): 665-675, (2018).

Tags: indoor, pyrethorid-degrates, pyrethorids, wipe-sampling
Organization: U.S. Environmental Protection Agency
CatronTara_A-brvd_MB2Dataset_20180221

This file contains data used to generate figures shown in Catron et al. Characterization of host toxicity and microbiota disruption in larval zebrafish following developmental exposure to BPA and BPA alternatives. 

This dataset is associated with the following publication:
Catron, T., S. Keely, N. Brinkman, T. Zurlinden, C. Wood, J. Wright, D. Phelps, E. Wheaton, A. Kvasnicka, S. Gaballah, R. Lamendella, and T. Tal. Host Developmental Toxicity of BPA and BPA Alternatives Is Inversely Related to Microbiota Disruption in Zebrafish.   TOXICOLOGICAL SCIENCES. Society of Toxicology, RESTON, VA,  167(2): 468-483, (2019).

Tags: bisphenol-a-bpa, developmental-toxicity, microbiome, zebrafish
Organization: U.S. Environmental Protection Agency
PCBs in Caulk report 07132010

A method was developed to determine the levels of polychlorinated biphenyls (PCBs) in caulk and window glazing. This method was tested on a combination of 36 samples of caulk and glazing materials from older buildings in the northeastern area of the United States. 

This dataset is associated with the following publication:
Osemwengie, L., and J. Morgan. PCBs in Older Buildings: Measuring PCB Levels in Caulk and Window Glazing Materials in Older Buildings.   Environments. MDPI AG, Basel,  SWITZERLAND, 6(2): 15, (2019).

Tags: arochlor, caulking-materials, gas-chromatography, old-buildings, pcbs, pressurized-liquid-extraction-ple
Organization: U.S. Environmental Protection Agency
Transformation of Silver Nanoparticle Consumer Products during Simulated Usage and Disposal

The data set contains the details on the silver speciation in silver nanoparticle consumer products and the transformation of the silver during their usage and disposal. Synthetic stomach fluid and wastewater sludge are used to create a model for the lifecycle of silver nanoparticle dietary supplements. 

This dataset is associated with the following publication:
Potter, P., J. Navratilova, K. Rogers, and S. Al-Abed. Transformation of silver nanoparticle consumer products during simulated usage and disposal.   Environmental Science: Nano. RSC Publishing, Cambridge,  UK, 6(2): 592-598, (2019).

Tags: capping-agent, consumer-products, environmental-fate-and-transformation, particle-size, silver-nanoparticles
Organization: U.S. Environmental Protection Agency
Theoretical Study of Isoprene Peroxy Radical 1-5 Hydrogen Shift Reactions that Regenerate HOx Radicals and Produce Highly Oxidized Molecules

The attached extensive computational chemistry dataset involves detailed electronic structure (density functional theory - DFT) and kinetic calculation (master equation formalism) outputs for the reactions of isoprene and first generation oxidants with the hydroxyl radical. There are a total of 9 tabs in the Excel spreadsheet.  The first two tabs provide the potential energy surfaces (PESs) of the isoprene+OH and isopOOH+OH (1st generation oxidant) reactions.  The PESs are zero-point energy corrected and obtained at the M062x/maug-cc-pVTZ level of DFT.  The third tab provides the reaction barriers for first and second generation 1,5-hydrogen atom shifts for two different isoprene peroxy radical isomers with several different DFT methods.  The fourth and fifth tabs provide microcanonical rate constants for the reactions of isoprene and isopOOH with OH respectively. The remaining tabs give the rate constants for the 1,5-H shifts for four different isoprene peroxy radicals.  The rate constants are computed using the M062x density functional and an average of 4 different DFT methods given in tab 3 for comparison.  The average values are reported as the final rate constants determined by computational methods. 

This dataset is associated with the following publication:
Piletic, I., R. Howell, L. Bartolotti, T. Kleindienst, S. Kaushik, and E. Edney. Multigenerational Theoretical Study of Isoprene Peroxy Radical 1–5-Hydrogen Shift Reactions that Regenerate HOx Radicals and Produce Highly Oxidized Molecules.   JOURNAL OF PHYSICAL CHEMISTRY A. American Chemical Society, Washington, DC, USA, 123(4): 906-919, (2019).

Tags: air-quality, atmospheric-chemistry, cmaq, computational-chemistry, nox, ozone-concentrations, pm2-5
Organization: U.S. Environmental Protection Agency
In vitro and in vivo estrogen receptor data sets

In vitro and in vivo data for the estrogen receptor. The in vivo data is for binding, agonism, and antagonism. The in vivo data is from mouse uterotropic assay data.  The following columns are provided in each data set:  molecular id, SMILES structure, class (1=active, 0 =  inactive), and set (T=training, P=prediction set). 

This dataset is associated with the following publication:
Martin , T. Prediction of in vitro and in vivo oestrogen receptor activity using hierarchical clustering.   SAR AND QSAR IN ENVIRONMENTAL RESEARCH. Taylor & Francis, Inc., Philadelphia, PA, USA, 27(1): 17-30, (2016).

Tags: estrogenic-activity-in-vitro-and-in-vivo, qsar
Organization: U.S. Environmental Protection Agency