AndreaBozzo/ceres-open-data-index huggingface dataset:
Illumina sequencing data for MEC study on high biofilm conductivity in a Geobacter-enriched biofilm

This study systematically assessed intracellular electron transfer (IET) and extracellular electron transfer (EET) kinetics with respect to anode potential (Eanode) in a mixed-culture biofilm anode enriched with Geobacter spp. High biofilm conductivity (0.96–1.24 mScm^-1) was maintained during Eanode changes from -0.2 to +0.2 V versus the standard hydrogen electrode (SHE), although the steady-state current density significantly decreased from 2.05 to 0.35 Am^-2 in a microbial electrochemical cell. Substantial increase of the Treponema population was observed in the biofilm anode at Eanode=+0.2 V, which reduced intracellular electron-transfer kinetics associated with the maximum specific substrate-utilization rate by a factor of ten. This result suggests that fast EET kinetics can be maintained under dynamic Eanode conditions in a highly conductive biofilm anode as a result of shift of main EET players in the biofilm anode, although Eanode changes can influence IET kinetics. 

This dataset is associated with the following publication:
Dhar, B., H. Ryu, H. Ren, J. Santodomingo, J. Chae, and H. Lee. High Biofilm Conductivity Maintained Despite Anode Potential Changes in a Geobacter-Enriched Biofilm.   ChemSusChem. Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim,  GERMANY, 9(24): 3485 –3491, (2016).

Tags: anode-potential, biofilm-conductivity, electron-transfer, microbial-electrochemical-cell
Organization: U.S. Environmental Protection Agency
Bacterial and archael 16S rRNA sequences and taxonomic summary tables for biofilm samples from the bio-reactors

A biofilm anode acclimated with acetate, acetate+methane, and methane growth media for over three years produced a steady current density of 1.6-2.3 mA/m^2 in a microbial electrochemical cell (MxC) fed with methane as the sole electron donor. Geobacter was the dominant genus for the bacterial domain (93%) in the biofilm anode, while methanogens (Methanocorpusculum labreanum and Methanosaeta concilii) accounted for 82% of the total archaeal clones in the biofilm. A fluorescence in situ hybridization (FISH) image clearly showed a biofilm of bacteria and archaea, supporting a syntrophic interaction between them for performing anaerobic oxidation of methane (AOM) in the biofilm anode. Measured cumulative coulombs correlated linearly to the methane-gas concentration in the range of 10% to 99.97% (R^2 ≥ 0.99) when the measurement was sustained for at least 50 min. Thus, cumulative coulombs over 50 min. could be used to quantify the methane concentration in gas samples. 

This dataset is associated with the following publication:
Gao, Y., H. Ryu, B. Rittmann, A. Hussain, and H. Lee. Quantification of the methane concentration using anaerobic oxidation of methane coupled to extracellular electron transfer.   Bioresource Technology. Elsevier Online, New York, NY, USA, 241: 979-984, (2017).

Tags: anaerobic-oxidation-of-methane, extracellular-electron-transfer, reverse-methanogenesis, sensors
Organization: U.S. Environmental Protection Agency
Scale Formation under Blended Phosphate Treatment for a Utility with Lead Pipes

Tap water lead profiles from the Del Toral et al (2013) study, grouped in disturbed and undisturbed Pb service line sites. 

This dataset is associated with the following publication:
Wasserstrom, L., S. Miller , S. Triantafyllidou, M. DeSantis, and M. Schock. Scale Formation under Blended Phosphate Treatment for a Utility with Lead Pipes.   Journal AWWA. American Water Works Association, Denver, CO, USA, 109(11): E464-E478, (2017).

Tags: blended-phosphate, corrosion-scale-mineralogy-morphology, disturbed-lead-service-line, galvanized-pipe, lead-corrosion, lead-profile, tap-water
Organization: U.S. Environmental Protection Agency
GoldenHeather_A-jhb9

No data are associated with this review/overview article. This dataset is not publicly accessible because: No data are associated with this review/overview paper. It can be accessed through the following means: N/D. Format: No data are associated with this review/overview paper. 

This dataset is associated with the following publication:
Golden, H., and N. Hoghooghi. Green infrastructure and its catchment-scale effects: an emerging science.   WIREs Water. John Wiley & Sons, Inc., Hoboken, NJ, USA, 5(1): e1254, (2018).

Tags: catchments, green-infrastructure, green-infrastrucutre, low-impact-development, watersheds
Organization: U.S. Environmental Protection Agency
NRSA enzyme decomposition model data

Microbial enzyme activities measured at more than 2000 US streams and rivers. These enzyme data were then used to predict organic matter decomposition and microbial respiration, and to predict carbon efflux from US streams and rivers. 

This dataset is associated with the following publication:
Hill, B., C. Elonen, A. Herlihy, T. Jicha, and R. Mitchell. A synoptic survey of microbial respiration, organic matter decomposition,  and carbon efflux in U.S. streams and rivers.   Limnology and Oceanography Bulletin. American Society of Limnology and Oceanography, Lawrence, KS, USA, 62(1): S147-S159, (2017).

Tags: co2-efflux, decomposition, ecoenzymes, mcirobial-respiration, river-continuum
Organization: U.S. Environmental Protection Agency
A field-based characterization of conductivity in areas of minimal alteration: a case example in the Cascades of northwestern United States

The data set contains 3 files from three sources (1) state (Washington and Oregon), (2) Combined EPA survey date  from Griffith, (3) data from USGS. 

This dataset is associated with the following publication:
Cormier, S., L. Zheng, G. Hayslip, and C. Flaherty. A field-based characterization of conductivity in areas of minimal alteration: a case example in the Cascades of northwestern United States.   SCIENCE OF THE TOTAL ENVIRONMENT. Elsevier BV, AMSTERDAM,  NETHERLANDS, 633: 1657-1666, (2018).

Tags: background-conductivity, benthic-macroinvertebrate, california, cascades, extirpation, oregon, specific-conductivity, washington
Organization: U.S. Environmental Protection Agency
Modeling Rabbit Responses to Single and Multiple Aerosol Exposures of Bacillus anthracis Spores Data Set

The two excel files contain all of the raw data that was modeled in the R code.  The 6 word documents contain all of the R code that can be used in R to model the raw rabbit data. 

This dataset is associated with the following publication:
Bartrand, T., H. Marks, M. Coleman, D. Donahue, S. Hines, J. Comer, and S. Taft. Modeling Rabbit Responses to Single and Multiple Aerosol Exposures of Bacillus anthracis Spores (HS 4.04.02 - 475).   RISK ANALYSIS. Blackwell Publishing, Malden, MA, USA, 37(5): 943-957, (2017).

Tags: anthrax, bacillus-anthracis, bacillus-antracis, biological, containment, dose-response, dose-respose, hazard-function, indoor-outdoor-decontamination, microbial-risk-assessment, mitigation, survival-analysis
Organization: U.S. Environmental Protection Agency
Buse_Francisella Medium

This dataset contains colony forming unit and qPCR data. 

This dataset is associated with the following publication:
Morris, B., H. Buse, N. Adcock, and E. Rice. A novel broth medium for enhanced growth of Francisella tularensis.   Letters in Applied Microbiology. Blackwell Publishing, Malden, MA, USA, 64(6): 393-468, (2017).

Tags: antibiotics, detection, enhanced-growth-medium, environmental, francisella, qpcr, rapid-methods, virulence
Organization: U.S. Environmental Protection Agency
Data for Brown et al MEA Developmental Neurotoxicity Screening Manuscript

These data are the individual parameter and well-level data that were support the conclusions in Brown et al. Note: the parameters CVtime and CVnetwork were not used. 

This dataset is associated with the following publication:
Brown, J., D. Hall, C. Frank, K. Wallace, W. Mundy, and T. Shafer. Editor's highlight: Evaluation of a Microelectrode Array-based Assay for Neural Network Ontogeny using Training Set Chemicals.   TOXICOLOGICAL SCIENCES. Society of Toxicology,    154(1): 126-139, (2016).

Tags: developmental-neurotoxicity, high-throughput-in-vitro-screening-assay, in-vitro-assay, microelectrode-array
Organization: U.S. Environmental Protection Agency
Simplified two and fifty-one region state-based EEIO model comparison

Supporting data for 2 region and 51 region models assessed in the manuscript "Exploring the relevance of spatial scale to life cycle inventory results using environmentally-extended input-output models of the United States". Includes results of the correlation and relative errors analysis, results in kg/$ intensities for the 17 commodities from the 2 region models and the 51 region model,  the 51-region model Make and Use tables, 10 NEI emissions and water withdrawal data aggregated by the 15 BEA sectors, interstate commodity flow data aggregated by BEA sectors between states, BEA national level Make and Use tables for 2012 at sector level, and state GDP data. 

This dataset is associated with the following publication:
Yang, Y., W. Ingwersen, and D. Meyer. Exploring the relevance of spatial scale to life cycle inventory results using environmentally-extended input-output models of the United States.   ENVIRONMENTAL MODELLING & SOFTWARE. Elsevier Science, New York, NY,   99: 52-57, (2018).

Tags: input-output-data, life-cycle-assessment, life-cycle-inventory-data, sustainability, us-state-life-cycle-inventory
Organization: U.S. Environmental Protection Agency
Metabolomic effects of CeO2, SiO2 and CuO metal oxide nanomaterials on HepG2 cells

The data set is a matrix of cellular biochemical (metabolites) in HepG2 cells treated with various metal oxide nanomaterials composed of CeO2, SiO2 and CuO. 

This dataset is associated with the following publication:
Kitchin, K., S. Stirdivant, B. Robinette, B. Castellon, and X. Liang. Metabolomic effects of CeO2, SiO2 and CuO metal oxide nanomaterials on HepG2 cells.   Particle and Fibre Toxicology. BioMed Central Ltd, London,  UK, 14(50): 1-16, (2017).

Tags: ceo2, cuo, fatty-acids, hepg2, metabolomics, nano-ceo2, nanomaterial, sio2
Organization: U.S. Environmental Protection Agency
Flow intermittence and ecosystem services in rivers of the Anthropocene_Figure 4_Journal of Applied Ecology

Counts of ecosystem service status (provided, altered, and lost/absent) during three hydrological phases (flowing, pool, dry) typically seen in intermittent rivers and ephemeral streams. The ecosystem services follow the Common International Classification of Ecosystem Services (CICES) version 4.3 across three broad categories of services (provisioning, regulating and cultural). Table 1 details these ecosystem services and how these may be altered when transitioned from flowing to pool or dry phases. 

This dataset is associated with the following publication:
Datry, T., A. Boulton, N. Bonada, K. Fritz, C. Leigh, E. Sauquet, K. Tockner, B. Hugueny, and C. Dahm. Flow intermittence and ecosystem services in rivers of the Anthropocene.   Journal of Applied Ecology. Blackwell Publishing, Malden, MA, USA, 55(1): 353-364, (2018).

Tags: anthropocene, biodiversity, climate-change, conservation, ecosystem-services, ephemeral-streams, flow-management, intermittent-rivers, management, rivers
Organization: U.S. Environmental Protection Agency
Association between Natural Resources for OutdoorActivities and Physical Inactivity

it includes available natural resources for outdoor activities, Physical inactivity and households income. 

This dataset is associated with the following publication:
Jiang , Y., Y. Yuan , A. Neale , L. Jackson , and M. Mehaffey. Association between Natural Resources for Outdoor Activities and Physical Inactivity: Results from the Contiguous United States.   International Journal of Environmental Research and Public Health. Molecular Diversity Preservation International, Basel,  SWITZERLAND, 13(8): 1-12, (2016).

Tags: community-health, diabetes, obsity, physical-inactivity, protected-areas, spatial-autocorrelation, spatial-lag-model
Organization: U.S. Environmental Protection Agency
A study of temporal effects of the model anti-androgen flutamide on components of the hypothalamic-pituitary-gonadal axis in adult fathead minnows

The aim of this study was to investigate temporal changes in the hypothalamic-pituitary-gonadal axis of fathead minnow treated with the model androgen receptor (AR) antagonist, flutamide. Reproductively-mature fish were exposed in a flow-through, measured test to either 50 or 500 µg flutamide/L for 8 d, followed by an 8-d recovery period in clean water. Samples were collected at 1, 2, 4 and 8 days during each phase of the experiment. Flutamide (500 µg/L) caused significant reductions in relative gonad size of the females on days 8 of the exposure and 1 of the recovery, and reduced expression of secondary sex characteristics in males during the exposure phase of the experiment. Ex vivo gonadal synthesis of testosterone in both sexes (and 17β-estradiol in females) was reduced in the 500 µg/L treatment within 2 d of exposure; however, steroid synthesis returned to levels comparable to controls by the end of the exposure portion of the test.  Steroid synthesis in males exposed to 50 µg flutamide/L was greater than in controls on days 4 and 8 of the exposure. Both the enhanced steroid production in the low treatment males, and return to control levels in the high treatment males and females during chemical exposure are indicative of a compensatory HPG response. One contributor to this response could be increased expression of genes responsible for enzymes involved in steroid synthesis; for example, transcripts for both cytochrome P450 side- chain cleavage and 11β-hydroxysteroid dehydrogenase were significantly elevated in flutamide-exposed males. Overall, responses of the HPG axis in adult male and female fathead minnows exposed to flutamide were both dynamic and comparatively rapid during exposure and recovery. This has ramifications both for the development of short-term fish assays to detect endocrine-active chemicals, and the derivation of robust adverse outcome pathways for AR antagonists in fish. 

This dataset is associated with the following publication:
Milsk, R., J. Cavalliin, E. Durhan, M. Kahl, E. Makynen, D. Martinovic-Weigelt, N.  Mueller, A. Schroeder, D. Villeneuve, and G. Ankley. A study of temporal effects of the model anti-androgen flutamide on components of the hypothalamic-pituitary-gonadal axis in adult fathead minnows.   AQUATIC TOXICOLOGY. Elsevier Science Ltd, New York, NY, USA, 180: 164-172, (2016).

Tags: adverse-outcome-pathway, androgen-receptor, antagonist, endocrine-disruption, fathead-minnow, fish, flutamide, mode-of-action-moa, reproduction
Organization: U.S. Environmental Protection Agency
Tetrabromobisphenol A In vitro Dermal Absopriton Data

In vitro dermal absorption data of tetrabromobisphenol A using human cadaver and rat skin. 

This dataset is associated with the following publication:
Knudsen, G., M. Hughes , K.L. McIntosh, J.M. Sanders, and L.S. Birnbaum. Estimation of Tetrabromobisphenol A (TBBPA)percutaneous uptake in humans using the parallelogram method..   TOXICOLOGY AND APPLIED PHARMACOLOGY. Academic Press Incorporated, Orlando, FL, USA, 289(2): 323-329, (2015).

Tags: absorption, brominated-flame-retardant, in-vitro, skin
Organization: U.S. Environmental Protection Agency
Toxicity Assessment for EPA's Hydraulic Fracturing Study

This dataset contains data used to develop multiple manuscripts on the toxicity of chemicals associated with the hydraulic fracturing industry. These manuscripts were developed as part of EPA's larger study on the potential for hydraulic fracturing to impact drinking water resources. For each manuscript, we have provided a separate Excel file containing all of the data used to develop that manuscript. The full list of chemicals and toxicity values used in the development of these manuscripts can also be found online in the draft database for EPA's hydraulic fracturing study (URL provided as part of the dataset). 

This dataset is associated with the following publications:
Yost , E., J. Stanek , R. Dewoskin , and L. Burgoon. Overview of Chronic Oral Toxicity Values for Chemicals Present in Hydraulic Fracturing Fluids, Flowback and Produced Waters.   ENVIRONMENTAL SCIENCE & TECHNOLOGY. American Chemical Society, Washington, DC, USA, 50: 4788-4797, (2016).
Yost , E., J. Stanek , R. Dewoskin , and L. Burgon. Estimating the Potential Toxicity of Chemicals Associated with Hydraulic Fracturing Operations Using Quantitative Structure Activity Relationship Modeling.   ENVIRONMENTAL SCIENCE & TECHNOLOGY. American Chemical Society, Washington, DC, USA, 50(14): 7732-7742, (2016).
Yost, E., J. Stanek, and L. Burgoon. A Decision Analysis Framework for Estimating the Potential Hazards for Drinking Water Resources of Chemicals Used in Hydraulic Fracturing Fluids.   SCIENCE OF THE TOTAL ENVIRONMENT. Elsevier BV, AMSTERDAM,  NETHERLANDS, 574: 1544-1558, (2016).

Tags: drinking-water, hazard-evaluation, hydraulic-fracturing, qsar, toxicity
Organization: U.S. Environmental Protection Agency
Citizen Science in the Ironbound Community

Time stamp data of non-identified locations within the Ironbound community.  A normalization data table is provided that defines established regression between sensors pod units 1-4 and State of New Jersey reference monitoring data performed during a collocation event.  In addition, a table is provided that defines the 90th percentile of air quality measures following data normalization. 

This dataset is associated with the following publication:
Kaufman, A., R. Williams, T. Barzyk, M. Greenberg, M. OShea, P. Sheridan, A. Hoang, C. Ash, A. Teitz, M. Mustafa, and S. Garvey. A Citizen Science and Government Collaboration: Developing Tools to Facilitate Community Air Monitoring.   ENVIRONMENTAL JUSTICE. Mary Ann Liebert, Inc., New Rochelle, NY, USA, 10(2): 1-11, (2017).

Tags: air-sensors-toolbox, citizen-science, citizen-science-air-monitor, fine-particulate-matter, low-cost-air-quality-sensors, nitrogen-dioxide
Organization: U.S. Environmental Protection Agency
Performance Evaluation of the United Nations Environment Programme Air Quality Unit

The Reference data represents reference monitoring data associated with EPA-operated air monitoring equipment located at its AIRS test site in the Research Triangle Park, NC campus.  The UN sensor pod data represents data collected simultaneously (collocated) as the Reference data and then subsequently used in a comparison of the agreement between sensor pod and reference monitors. Original time intervals of the various data collections are preserved in the two data sets. 

This dataset is associated with the following publication:
Williams, R., T. Conner, A. Clements, V. Foltescu, V. Nthusi, J. Jabbour, D. Nash, J. Rice, A. Kaufman, A. Rourk, and M. Srivastava. Performance Evaluation of the United Nations Environment Programme Air Quality Monitoring Unit. U.S. Environmental Protection Agency, Washington, DC, USA, 2017.

Tags: nitrogen-dioxide, particulate-matter, reference, sensor, sensor-pod, sulfur-dioxide, time-interval, united-nations
Organization: U.S. Environmental Protection Agency
Onset in-river conductivity sonde data

Onset HOBO Model U24-01 in-river sondes were deployed to measure water temperature and electrical conductivity at each of the ISCO sampling sites at 5 min intervals. 

This dataset is associated with the following publication:
Landis , M., A. Kamal, K. Kovalcik , C. Croghan , G. Norris , and A. Bergdale. The Impact of Commercially Treated Oil and Gas Produced Water Discharges on Bromide Concentrations and Modeled Brominated Trihalomethane Disinfection Byproducts at two Downstream Municipal Drinking Water Plants in the Upper Allegheny River, Pennsylvania, USA.   SCIENCE OF THE TOTAL ENVIRONMENT. Elsevier BV, AMSTERDAM,  NETHERLANDS, 542(2016): 505-520, (2016).

Tags: source-attribution, specific-conductivity
Organization: U.S. Environmental Protection Agency
ISCO Grab Sample Ion Chromatography Analytical Data

ISCO grab samples were collected from river, wastewater treatment plant discharge, and public drinking water intakes.  Samples were analyzed for major ions (ppb) using a dual Dionex Model ICS2000 Ion Chromatography System, and Specific Conductivity (μS/cm) using Mettler Toledo Model S47-K meter equipped with an InLab®731 probe. 

This dataset is associated with the following publication:
Landis , M., A. Kamal, K. Kovalcik , C. Croghan , G. Norris , and A. Bergdale. The Impact of Commercially Treated Oil and Gas Produced Water Discharges on Bromide Concentrations and Modeled Brominated Trihalomethane Disinfection Byproducts at two Downstream Municipal Drinking Water Plants in the Upper Allegheny River, Pennsylvania, USA.   SCIENCE OF THE TOTAL ENVIRONMENT. Elsevier BV, AMSTERDAM,  NETHERLANDS, 542(2016): 505-520, (2016).

Tags: major-ions, source-attribution, specific-conductivity
Organization: U.S. Environmental Protection Agency
Differential genomic effects on signaling pathways by two different CeO2 nanoparticles in HepG2 cells

Differential genomic effects on signaling pathways by two different CeO2 nanoparticles in HepG2 cells. 

This dataset is associated with the following publication:
Thai , S., K. Wallace , C. Jones , H. Ren , B. Castellon, J. Crooks , E.A. Grulke, and K. Kitchin. Differential genomic effects on signaling pathways by two different CeO2 nanoparticles in HepG2 cells.   Journal of Nanoscience and Nanotechnology. American Scientific Publishers, VALENCIA, CA, USA, 15(12): 9925-37, (2015).

Tags: mrna-profiling, nano-ceo2, nanomaterial, nanoparticle, signaling-pathways, warburg-effect
Organization: U.S. Environmental Protection Agency
YSI multimeter data

A YSI Model 556 multi-parameter instrument was utilized to collect traceable temperature compensated specific conductivity (SC) readings to scale each Onset in-river sonde using manufacturer provided HOBOware® Conductivity Assistant software. The YSI instrument was calibrated each morning using YSI-3161 1000 μS cm−1 standard solution, checked again each night, and checked weekly using YSI-3165 100,000 μS cm−1 standard solution.
Daily calibration check precision (n = 42) was 98 ± 2% (mean ± standard deviation), and the weekly high range linearity check precision (n = 9) was 95 ± 4%. 

This dataset is associated with the following publication:
Landis , M., A. Kamal, K. Kovalcik , C. Croghan , G. Norris , and A. Bergdale. The Impact of Commercially Treated Oil and Gas Produced Water Discharges on Bromide Concentrations and Modeled Brominated Trihalomethane Disinfection Byproducts at two Downstream Municipal Drinking Water Plants in the Upper Allegheny River, Pennsylvania, USA.   SCIENCE OF THE TOTAL ENVIRONMENT. Elsevier BV, AMSTERDAM,  NETHERLANDS, 542(2016): 505-520, (2016).

Tags: source-attribution, specific-conductivity
Organization: U.S. Environmental Protection Agency