AndreaBozzo/ceres-open-data-index huggingface dataset:
Nontarget Screening of Per- and Polyfluoroalkyl Substances Binding to Human Liver Fatty Acid Binding Protein

Current studies on nontarget analysis and toxicities of PFASs are disconnected, due to the challenges posed by the large numbers (>1,000) and diverse structures of PFASs. The SECC method provides a high-throughput experimental way to tackle the challenge of prioritizing PFASs according to key proteins, especially when their authentic standards are not available. While this study is focused on hL-FABP due to its critical role in regulating the toxicokinetics of PFASs, the protein-centric method could also be adapted to screen PFASs binding to other key proteins, such as PPARs. Computational toxicology is the predominant strategy for high-throughput predictions of toxicities of chemical contaminants. This dataset is not publicly accessible because: Data generated and owned by external academic lab with chemicals provided by the EPA under an MTA. EPA's contribution was assisting in manuscript writing. It can be accessed through the following means: Contact the Corresponding author: Hui Peng, e-mail: hui.peng@utoronto.ca, Department of Chemistry, University of Toronto, Toronto, Ontario, M5S3H6, Canada. Format: Not available. 

This dataset is associated with the following publication:
Yang, D., J. Han, D. Ross Hall, J. Sun, J. Fu, S. Kutarna, K. Houck, C. LaLone, J. Doering, C. Ng, and H. Peng. Nontarget Screening of Per- and Polyfluoroalkyl Substances Binding to Human Liver Fatty Acid Binding Protein.   ENVIRONMENTAL SCIENCE & TECHNOLOGY. American Chemical Society, Washington, DC, USA, 54(9): 5676-5686, (2020).

Tags: aqueous-film-forming-foams, hydrophobicity, nontargeted-analysis, size-exclusion-chromatography
Organization: U.S. Environmental Protection Agency
Tox21BodyMap: A webtool to map chemical effects on the human body

This manuscript describes development of a novel tool called Tox21BodyMap. This tool is designed to map biological assay data onto organs of the human body, facilitating predictions between chemical exposure and apical effects. Tox21BodyMap maps chemical effects to biological target tissues uses tissue-specific gene expression and high throughput screening data. High throughput screening sources includes ToxCast and Tox21. Tox21BodyMap is a freely available, online tool. 

This dataset is associated with the following publication:
Borrel, A., S. Auerbach, K. Houck, and N. Kleinstreuer. Tox21BodyMap: A webtool to map chemical effects on the human body.   NUCLEIC ACIDS RESEARCH. Oxford University Press, Cary, NC, USA, 48(W1): W472-W476, (2020).

Tags: data-visualization, high-throughput-screening-assay, tox21, tox21bodymap, toxcast
Organization: U.S. Environmental Protection Agency
Field Analyzer Raw Data from 2 Proceedings

Information on data sources for field analyzer manuscript calculations. This dataset is not publicly accessible because: This data was not generated by EPA, but rather used by EPA researchers to calculate basic statistics (R square and slope), as part of this literature review. It can be accessed through the following means: These two old conference proceedings are available in book volumes that can be found in libraries, with page numbers as specified below:
- Argent, V.A., Southall, J.M. and D'Costa, E. (1994) Analysis of water for lead and copper using disposable sensor technology. American Water Works Association – Annual Conference, pp. 43-54, New York, New York.
- Wiese, P.M. (1989) Monitoring method for lead in first-draw drinking water samples. American Water Works Association - Annual Conference and Exposition, pp. 1309-1313, Los Angeles, California. Format: Data from three tables in two old conference proceedings were used to calculate basic statistics (R square and slope):
- Table 2 and 4 in Proceeding "Argent, V.A., Southall, J.M. and D'Costa, E. (1994) Analysis of water for lead and copper using disposable sensor technology. American Water Works Association – Annual Conference, pp. 43-54, New York, New York."
- Table 2 in Proceeding "Wiese, P.M. (1989) Monitoring method for lead in first-draw drinking water samples. American Water Works Association - Annual Conference and Exposition, pp. 1309-1313, Los Angeles, California.". 

This dataset is associated with the following publication:
Dore, E., D. Lytle, L. Wasserstrom, J. Swertfeger, and S. Triantafyllidou. Field Analyzers for Lead Quantification in Drinking Water Samples.   CRITICAL REVIEWS IN ENVIRONMENTAL SCIENCE AND TECHNOLOGY. CRC Press LLC, Boca Raton, FL, USA, 50(20): 999-999, (2020).

Tags: anodic-stripping-voltammetry, colorimetry, drinking-water, field-analyzer, fluorescence, laboratory-methods, lead
Organization: U.S. Environmental Protection Agency
2016 RNA sequencesfor cyanobacterial bloom

The data contained in this worksheets provide sequences submitted for public access, analysis for RNA sequences generated in this study. The data and analysis are for a manuscript "The trait repertoire enabling cyanobacterial blooms assessed through comparative genomic complexity ". 

This dataset is associated with the following publication:
Cao, H., Y. Shimura, M.M. Steffen, Z. Yang, J. Lu, A. Joel, L. Jenkins, M. Kawachi, Y. Yin, and F. Garcia-Pichel. The Trait Repertoire Enabling Cyanobacteria to Bloom Assessed through Comparative Genomic Complexity and Metatranscriptomics.   mBio. American Society for Microbiology, Washington, DC, USA, 11(3): e01155-20, (2020).

Tags: comparative-genomics, cyanobacterial-bloom, ecophysiology, metatranscriptome, microcystis-aeruginosa, pathway
Organization: U.S. Environmental Protection Agency
MHV metadata

Recovery efficiencies of murine hepatitis virus spiked into untreated wastewater and concentrated using seven different methods. This dataset is not publicly accessible because: Data us property of CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia. It can be accessed through the following means: Contact Warish Ahmed (Warish.Ahmed@csiro.au). Format: No public link for the data is available. Data will be in an excel format. 

This dataset is associated with the following publication:
Ahmed, W., P. Bertsch, A. Bivins, K. Bibby, K. Farkas, A. Gathercole, E. Haramoto, P. Gyawali, A. Korajkic, B. McMinn, J. Mueller, S. Simpson, W.J.M. Smith, E.M. Symonds, K.V. Thomas, R. Verhagen, and M. Kitajima. Comparison of virus concentration methods for the RT-qPCR-based recovery of murine hepatitis virus, a surrogate for SARS-CoV-2 from untreated wastewater.   SCIENCE OF THE TOTAL ENVIRONMENT. Elsevier BV, AMSTERDAM,  NETHERLANDS, 739: 139960, (2020).

Tags: concentration-method, coronavirus-surrogate, murine-hepatitis-virus, wastewater
Organization: U.S. Environmental Protection Agency
PFAS levels in blood serum in Wilmington, NC

PFAS concentrations in blood serum. This dataset is not publicly accessible because: Data is the property of the research leads (NC State University). It can be accessed through the following means: Contact Jane Hoppin of NC State University (jahoppin@ncsu.edu). Format: Data is quantitative measurements of blood serum levels for PFAS levels in human serum formated as MS Raw files and instrument vendor quantification files. 

This dataset is associated with the following publication:
Kotlarz, N., J. McCord, D. Collier, C.S. Lea, M. Strynar, A. Lindstrom, A.A. Wilkie, J.Y. Islam, K. Matney, P. Tarte, M. Polera, K. Burdette, J. DeWitt, K. May, R.C. Smart, D.R.U. Knappe, and J.A. Hoppin. Measurement of Novel, Drinking Water-Associated PFAS in Blood from Adults and Children in Wilmington, North Carolina.   ENVIRONMENTAL HEALTH PERSPECTIVES. National Institute of Environmental Health Sciences (NIEHS), Research Triangle Park, NC, USA, 128(7): 77005, (2020).

Tags: cape-fear-river, genx, mass-spectrometry, pfas, serum
Organization: U.S. Environmental Protection Agency
Contiguous Low Oxygen Waters Between the Continental Shelf Hypoxia Zone and Nearshore Coastal Waters of Louisiana, USA: Interpreting 30 Years of Profiling Data and Three-Dimensional Ecosystem Modeling

These data include field observations from Northern Gulf of Mexico research surveys from numerous research organizations between 1985 through 2015. Data also include hydrodynamic and water quality model data generated by the Coastal Generalized Ecosystem Model (CGEM) between 2003-2007. 

Tags: gulf-of-mexico, hypoxia, nutrients, water-quality-simulation-modeling
Organization: U.S. Environmental Protection Agency
IMPACT OF E-CIGARETTE FLAVORING AGENTS ON ACTIVITY OF MICROSOMAL RECOMBINANT CYP2A6, THE PRIMARY NICOTINE-METABOLIZING-ENZYME

Most of the data illustrates the effects that some e-cigarette flavoring agents, as well as some of the chemical components of those flavoring agents, directly have on the cytochrome P450 2A6 enzyme activity. 

This dataset is associated with the following publication:
Winters, B., T. Kochar, P. Clapp, I. Jaspers, and M. Madden. Impact of E-Cigarette Flavoring Agents on Activity of Microsomal Recombinant CYP2A6, The Primary Nicotine-Metabolizing-Enzyme.   CHEMICAL RESEARCH IN TOXICOLOGY. American Chemical Society, Washington, DC, USA, 33(7): 1689-1697, (2020).

Tags: cellular-volatiles, cytochromep450, high-throughput-in-vitro-screening-assay
Organization: U.S. Environmental Protection Agency
US EPA EnviroAtlas Meter-Scale Urban Land Cover (MULC) Data Characteristics

Meter-scale Urban Land Cover (MULC), a unique, high resolution (one meter2 per pixel) land cover dataset, has been developed for 30 US communities for the United States Environmental Protection Agency (US EPA) EnviroAtlas. MULC data categorize the landscape into these land cover classes: impervious surface, tree, grass-herbaceous, shrub, soil-barren, water, wetland and agriculture. MULC data are used to calculate approximately 100 EnviroAtlas metrics that serve as indicators of nature’s benefits (ecosystem goods and services). MULC, a dataset for which development is ongoing, is produced by multiple classification methods using aerial photo and LiDAR datasets. The mean overall fuzzy accuracy across the EnviroAtlas communities is 88% and mean Kappa coefficient is 0.84. MULC is available in EnviroAtlas via web browser, web map service (WMS) in the user’s geographic information system (GIS), and as downloadable data at EPA Environmental Data Gateway. Fact Sheets and metadata for each MULC Community are available through EnviroAtlas. Some MULC applications include mapping green and grey infrastructure, connecting land cover with socioeconomic/demographic variables, street tree planting, urban heat island analysis, mosquito habitat risk mapping and bikeway planning. This article provides practical guidance for using MULC effectively and developing similar high resolution (HR) land cover data. 

This dataset is associated with the following publication:
Pilant, D., K. Endres, D. Rosenbaum, and G. Gundersen. US EPA EnviroAtlas Meter-Scale Urban Land Cover (MULC): 1-m Pixel Land Cover Class Definitions and Guidance.   Remote Sensing. MDPI AG, Basel,  SWITZERLAND, 12(12): 1909, (2020).

Tags: 1-meter-pixel, decision-support, ecosystem-services, enviroatlas, gis, high-spatial-resolution-land-cover-data, image-classification, machine-learning, object-based-image-classification, pixel-based-image-classification, remote-sensing
Organization: U.S. Environmental Protection Agency
MagnusonMatthew_A-f1w2_dataset_20200228.xlsx

Data corresponding to the figures in the paper. 

This dataset is associated with the following publication:
Xing, Y., J. Szabo, M. Magnuson, and W. Harper. Clustering, Morphology, and Treatment Resistance of Bacillus Globigii Spores Recovered from a Pilot-Scale Activated Sludge System.   CHEMOSPHERE. Elsevier Science Ltd, New York, NY, USA, 260( 127591): 6, (2020).

Tags: atomic-force-microscopy, bacillus-globigii, imaging, pilot-plant-study, spore-resistance
Organization: U.S. Environmental Protection Agency
BuseHelen_A-d51w_SciHub dataset

This dataset contains all the raw data as described in the accompanying published manuscript.  The data is organized by type (water quality, culture data, statistical data, and qPCR data) by sampling time point (Fall, Winter, Spring, or Summer followed by the year 2016, 2017, 2018, or 2019). 

This dataset is associated with the following publication:
Buse, H.Y., B. Morris, V. Gomez-Alvarez, J. Szabo, and J. Hall. Legionella Diversity and Spatiotemporal Variation in the Occurrence of Opportunistic Pathogens within a Large Building Water System.   PATHOGENS. MDPI AG, Basel,  SWITZERLAND, 9(567): 28, (2020).

Tags: biofilm, colony-forming-units, environmental-monitoring, first-draw, free-chlorine, heterotrophic-plate-count, monochloramine, most-probably-number, opportunistic-pathogen, ph, potable-water, premise-plumbing-systems, quantitative-polymerase-chain-reaction, second-draw, temperature, total-chlorine, turbidity, whole-genome-sequencing
Organization: U.S. Environmental Protection Agency
Data used in Figures and Tables in this Research Effort

The data will explain the information that went into the figures. 

This dataset is associated with the following publication:
Lytle, D., M. Tang, A. Francis, A. O'Donnell, and J. Newton. The Effect of Chloride, Sulfate, and Dissolved Inorganic Carbon on Iron Release from Cast Iron.   WATER RESEARCH. Elsevier Science Ltd, New York, NY, USA, 183: 116037, (2020).

Tags: bicarbonate, chloride, iron-corrosion, molecular-diffusion-model, sulfate, water-discoloration
Organization: U.S. Environmental Protection Agency
Performance and Characterization Data of a Degassed Anaerobic Membrane Biofilm Reactor Version 1

The goal of this study was to develop and evaluate an anerobic treatment system designed to overcome limitations associated with mass transfer resistances caused by fouling of dissolved methane recovery membranes in anaerobic membrane bioreactors. To this end, a novel attached growth anaerobic treatment system designed to emphasize the growth of the attached biofilm, rather than its removal, to optimize reactor performance. To accomplish this, a methane producing biofilm was developed on the shell side surface of submerged hollow fiber membranes, which allowed for immediate recovery of methane as it was produced, negating the liquid boundary layer and mass transfer fouling resistances.  Impacts of membrane surface treatment on biofilm development were investigated as well. Details of the performance and characterization of the anaerobic treatment system can be found in DAMBR_Performance_and_Characterization_Data.xlsx. 

This dataset is associated with the following publication:
Crone, B., G. Sorial, J. Pressman, H. Ryu, S. Keely, N. Brinkman, C. Bennett-Stamper, and J. Garland. Design and Evaluation of Degassed Anaerobic Membrane Biofilm Reactors for Improved Methane Recovery.   Bioresource Technology Reports. Elsevier B.V., Amsterdam,  NETHERLANDS, 10: 100407, (2020).

Tags: anaerobic-bioreactors, net-zero, wastewater
Organization: U.S. Environmental Protection Agency
Contribution of Offshore Wind to the Power Grid: U.S. Air Quality Implications

Offshore wind (OSW) is an established technology in Europe, but it has not yet gained market share in the United States (U.S.). There is, however, increasing interest in and action supporting OSW development from many coastal states, predominantly along the Atlantic coast. As OSW grows in the U.S., as seems likely, it will displace existing and future generation assets. Depending on the energy resources used by those generators, emissions from the electric power sector will change. This research explores combinations of two energy sector drivers, OSW costs and carbon dioxide (CO2) mitigation stringency, to measure the changes in the energy mix and quantify OSW’s impact on the resulting emissions. This dataset is not publicly accessible because: This is a very large access file in a format specifically for the times model. It can be accessed through the following means: Contact Carol Lenox at lenox.carol@epa.gov. Format: The data resides in a number of excel files and in the corresponding TIMES model. 

This dataset is associated with the following publication:
Browning, M., and C. Lenox. Contribution of Offshore Wind to the Power Grid: U.S. Air Quality Implications.   Applied Energy. Elsevier B.V., Amsterdam,  NETHERLANDS, 276: 115474, (2020).

Tags: air-quality, energy, greenhouse-gas, markal, modeling, systems-analyses
Organization: U.S. Environmental Protection Agency
Chemical composition and disinfection by-product (DBP) formation of biofilms from reactors

There are two parts of data; 1) fluorescence excitation-emission matrices (EEMs) and 2) disinfection by-products (DBP) such as THM and HAA. 

This dataset is associated with the following publication:
Li, L., Y. Jeon, H. Ryu, J. Santo Domingo, and Y. Seo. Assessing the chemical compositions and disinfection byproduct formation of biofilms: Application of fluorescence excitation-emission spectroscopy coupled with parallel factor analysis.   CHEMOSPHERE. Elsevier Science Ltd, New York, NY, USA, 246: 125745, (2019).

Tags: biofilms, correlation, disinfection-by-products, engineered-water-systems, fluorescence-excitation-emission-matrix
Organization: U.S. Environmental Protection Agency
Buse cbFtPCR_raw data compiled

This is a compiled data set for the qPCR analyses, bacterial enumeration analyses, and water quality parameters collected for this study. 

This dataset is associated with the following publication:
Buse, H., B. Morris, and E. Rice. Early detection of viable Francisella tularensis in environmental matrices byculture-based PCR.   BMC Microbiology. BioMed Central Ltd, London,  UK, 20(66): 15, (2020).

Tags: human-pathogen, molecular-detection, potable-water, remediation, select-agent, viability
Organization: U.S. Environmental Protection Agency
Omaha Property Values and GI

In Omaha, NE, more than 25 GI projects have been completed to date, with several featuring GI practices in public parks. Using a repeat sales model , we examined the effect of GI on the value of nearby single-family homes, based on housing sales and characteristic data from 2000 to 2018. We evaluated the sales price for homes using a buffer zone of 0-0.5km, and three additional models: homes within 0-0.25km, 0.25-0.5km, and greater than 0.5km from parks where GI was installed for 25,472 sale pairs. In addition to the repeat sales model, we performed a hot spot analysis on several demographic characteristics to capture systematic differences at a smaller spatial scale and over a longer time period than the repeat sales model could capture. We used US Census data on race and household income to examine changing patterns over time and space, and a spatial lag Maximum Likelihood Estimation model to determine if the location of GI correlated with either of these demographics. 

This dataset is associated with the following publication:
Hoover, F., J. Price, and M. Hopton. Examining the Effects of Green Infrastructure on Residential Sales Prices in Omaha, NE.   Urban Forestry & Urban Greening. Elsevier B.V., Amsterdam,  NETHERLANDS, 54: 126778, (2020).

Tags: ecosystem-services, green-infrastructure, hedonic-analysis, repeat-sales, residential-property-sales, scenario-planning, stormwater-management
Organization: U.S. Environmental Protection Agency
MagnusonMatthew_A-893d_dataset_20180816.xlsx

The dataset contains the raw data for the graphs in the paper. 

This dataset is associated with the following publication:
Haupert, L., and M. Magnuson. Numerical Model for Decontamination of Organic Contaminants in Polyethylene Drinking Water Pipes in Premise Plumbing by Flushing.   JOURNAL OF ENVIRONMENTAL ENGINEERING. American Society of Civil Engineers  (ASCE), Reston, VA, USA, 145(7): 1-22, (2019).

Tags: decontamiation, flushing, pex, polyethylene, toluene, water-infrastructure-decontamination, water-security
Organization: U.S. Environmental Protection Agency
MagnusonMatthew_A-5hqn_dataset_20180604

Data corresponding to the figures in the paper. 

This dataset is associated with the following publication:
Jolin, W., M. Magnuson, and M. Kaminski. High Pressure Decontamination of Building Materials During Radiological Incident Recovery.   JOURNAL OF ENVIRONMENTAL RADIOACTIVITY. Elsevier Science Ltd, New York, NY, USA, 208-209: 105858, (2019).

Tags: americium, cesium, decontamination, europium, nuclear-power-plant, pressure-washing, radiological, strontium, urban
Organization: U.S. Environmental Protection Agency
Regional design guide values based on Atlas-14

This dataset contains processed and modeling data on design storm (precipitation and wind) in the past and for projections.  The original data for modeling analysis were derived from the publicly available sources by other federal agencies as noted in the metadata and individual datasheets. 

This dataset is associated with the following publication:
Liang, M., S. Julius, Z. Dong, J. Neal, and Y. Yang. Assessing and Managing Design Storm Variability and Projection Uncertainty in a Changing Coastal Environment.   JOURNAL OF ENVIRONMENTAL MANAGEMENT. Elsevier Science Ltd, New York, NY, USA, 264: 110494, (2020).

Tags: climate-adaptation, climate-projection, coastal-flooding, design-storm, system-vulnerability, urban-infrastructure, water-infrastructure
Organization: U.S. Environmental Protection Agency
IML Critical Zone Observatory, Clear Creek Aug 2014 Lidar Survey (532 nm)

This dataset was collected using the Optech Aquarius ALTM, a hybrid laser mapping system which collects simultaneous land and shallow water-depth measurements using a beam wavelength of 532 nm. This dataset was collected by NCALM for PI Dr. Praveen Kumar, University of Illinois. Clear Creek is part of the Intensively Managed Landscapes (ILM) Critical Zone Observatory (CZO).   The requested survey area consisted of two rectangles - called East and West - enclosing approximately 204 square kilometers along with their associated watercourse corridors. The West rectangle is located 35 km NW of Iowa City, Iowa and the East rectangle is located 10 km NW of the same city. This survey was performed with 2 different LiDAR systems: 1) Optech Gemini Airborne Laser Terrain Mapper (ALTM) (available here) which is an infrared laser mapping sensor and 2) Optech Aquarius ALTM (this dataset) which is a hybrid laser mapping system as it collects simultaneous land and shallow water-depth measurements. It operates in the green spectrum, thus enabling it to penetrate water. These LiDAR mapping systems along with an Optech 12-bit full waveform digitizer were mounted consecutively in a twin-engine Piper PA- 31-350 Navajo Chieftain (Tail Number N154WW).   Full waveform files are available via this link.

Organization: OpenTopography
High Resolution Topography of the Kashihe Fault, northern Tian Shan

This dataset comprises six high-resolution structure-from-motion (SfM) models (<0.5 m/pixel) surveyed by a small four-rotor unmanned drones along the Kashihe Fault which is a Holocene active right-lateral strike-slip fault and bounds the northern margin of the Ili Basin in the northern Tian Shan.  The flight height of unmanned drones was set from 140 to 200 m based on the different target areas. The images were processed with Agisoft Photoscan Pro software. After manual identification of the GCP targets with a horizontal error of 2 cm and a vertical error of 4 cm, high-precision digital elevation models (DEMs) (<0.5 m/pixel) were obtained using Photoscan to transpose from a relative to an absolute coordinate system. The DEMs display the fault kinematics and offsets on the late Quaternary geomorphic surfaces for six local areas.

Organization: OpenTopography