AndreaBozzo/ceres-open-data-index huggingface dataset:
Supplementary field, morphometric and genetic data for Mesocyclops pehpeiensis cyclopoid copepods reported from the western basin of Lake Erie (2016-2018).

Field collection data and stage, sex, specimen count, length and COI barcode BIN ID number (which links to genetic information in BOLD Systems V4) for the Asian cyclopoid copepod Mesocyclops pehpeiensis, a non-native zooplankton species recently reported in Lake Erie. Citation information for this dataset can be found in the EDG's Metadata Reference Information section and Data.gov's References section.

Tags: cyclopoid-copepods, mesocyclops-pehpeiensis
Organization: U.S. Environmental Protection Agency
(Data Set) Integrating Study Reporting Templates into the Manuscript Submission Process: A Pilot Data Extraction Exercise Feasibility Study (Authors share their opinions and provide user feedback on their data extraction user experience).

This file contains participant response data to Likert scale, open-ended responses and self-reported time taken to complete various tasks related to the extraction exercise.  This Excel file also contains:

1)	Examples of the Interactive HAWC Visuals that can be created after extracting data into the template.
2)	The Initial Post-Extraction Survey Tool ("Survey 1")
3)	The Final Post-Pilot Survey Tool ("Survey 2")
4)	Survey 2 Results: Willingness to Consider Structured Data During Publication Process (Table 2)
5)	Survey 1 Results: Participant Self-Reported Time Spent Performing Various Pilot Tasks (Table 3)
6)	Survey 1 Results:  Summary of Technical Assistance Provided by Team Members (Table 4)
7)	Survey 2 Results: Participant Responses Describing Pilot's Impact on Future Research Activities (Table 5)
8)	Survey 1 Results:  Initial Survey Likert Scale Results (Table 6)
9)	Repeat Extraction: Comparison of the First and Second Data Extraction Experience (Among the Same Participant)
10)	Survey 1 Results: Problematic & Easy Fields to Extract. 

This dataset is associated with the following publication:
Wilkins, A., P. Whaley, A. Persad, I. Druwe, J. Lee, M. Taylor, A. Shapiro, N. Blanton, C. Lemeris, and K. Thayer. Assessing author willingness to enter study information into structured data templates as part of the manuscript submission process: A pilot study.   Heliyon. Elsevier B.V., Amsterdam,  NETHERLANDS, 8(3): 1-9, (2022).

Tags: author-feedback, author-opinion, author-submission-requirements, automated-data-extraction, data-extraction, data-extraction-software, data-extraction-tool, data-sharing, data-summary, data-template, electronic-data-extraction-manuscript-submission, evidence-synthesis, knowledge-translation, machine-readable, meta-data, metadata, metadata-tagging, natural-language-processing, nlp, risk-of-bias-reporting, science-translation, semantic-authoring, structured-data, study-evaluation, study-quality, study-quality-reporting, systematic-review
Organization: U.S. Environmental Protection Agency
An integrated ecological modeling system for assessing impacts of multiple stressors on stream and riverine ecosystem services within river basins

We demonstrate a novel, spatially explicit assessment of the current condition of aquatic ecosystem services, with limited sensitivity analysis for the atmospheric contaminant mercury. The Integrated Ecological Modeling System (IEMS) forecasts water quality and quantity, habitat suitability for aquatic biota, fish biomasses, population densities, productivities, and contamination by methylmercury across headwater watersheds. We applied this IEMS to the Coal River Basin (CRB), West Virginia (USA), an 8-digit hydrologic unit watershed, by simulating a network of 97 stream segments using the SWAT watershed model, a watershed mercury loading model, the WASP water quality model, the PiSCES fish community estimation model, a fish habitat suitability model, the BASS fish community and bioaccumulation model, and an ecoservices post-processer. Model application was facilitated by automated data retrieval and model setup and updated model wrappers and interfaces for data transfers between these models from a prior study. This companion study evaluates baseline predictions of ecoservices provided for 1990–2010 for the population of streams in the CRB and serves as a foundation for future model development. 

This dataset is associated with the following publication:
Johnston , J., C. Barber , K. Wolfe , M. Galvin , M. Cyterski , and R. Parmar. An integrated ecological modeling system for assessing impacts of multiple stressors on stream and riverine ecosystem services within river basins.   ECOLOGICAL MODELLING. Elsevier Science BV, Amsterdam,  NETHERLANDS, 354: 104-114, (2017).

Tags: aquatic-ecosystem-services, forecasting, freshwater-provisioning, integrated-ecological-modeling, landuse-change, multiple-stressors, spatially-explicit-exposure
Organization: U.S. Environmental Protection Agency
Summary of Evaluation of Commercially Available Air Sensor Performance in Biomass Burning Plumes (Revised Version)

Reference and sensor data from grassland prescribed burn experiments in 2017 and chamber burn experiments in 2018 used in the paper "Summary of Evaluation of Commercially Available Air Sensor Performance in Biomass Burning Plumes" by Whitehill et al.

Tags: carbon-dioxide, carbon-monoxide, sensors, wildland-fire
Organization: U.S. Environmental Protection Agency
Enhanced Susceptibility of Methylmercury Bioaccumulation into Seston of the Laurentian Great Lakes

Data were created in order to examine mercury concentrations, cycling, and biotic transfer in the Great Lakes and is in response to mercury concentrations in fish that are above consumption advisory levels. 

This dataset is associated with the following publication:
Ogorek, J., R. Lepak, J. Hoffman, J. DeWild, T. Rosera, M. Tate, J. Hurley, and D. Krabbenhoft. Enhanced sensitivity of methylmercury bioaccumulation into seston of the Laurentian Great Lakes.   ENVIRONMENTAL SCIENCE & TECHNOLOGY. American Chemical Society, Washington, DC, USA, 55(18): 12714-12723, (2021).

Tags: animal-derived-food, bioaccumulation, dissolved-organic-matter, food, mercury
Organization: U.S. Environmental Protection Agency
Impact of Waterfall Formation on River Long Profiles, CA 2021

This lidar dataset was collected as part of an NCALM Seed grant for Sophie Rothman at the University of Nevada, Reno. This study used airborne lidar to assess how self-generation and retreat of bedrock steps and waterfalls can alter river profiles. The study area is along selected rivers within the Sierra Nevada mountains in California and covers approximately 73 km2.

Organization: OpenTopography
Survey of 1920 Haiyuan Earthquake Rupture, China 2013-2017

This dataset covers the 170 km-long western and middle sections of the 1920 Haiyuan Earthquake surface rupture across Gansu and Ningxia, China. The data is photogrammetrically derived from 0.5 m-resolution tri-stereo Pleiades optical imagery acquired by Airbus Defence and Space using the ERDAS IMAGINE software

Organization: OpenTopography
Using Carbon, Nitrogen, and Mercury Isotope Values to Distinguish Mercury Sources to Alaskan Lake Trout

This data release includes results of raw water, soil, seston, and fish tissue samples collected from lakes in southwestern Alaska between 2011 and 2016. Specifically, these data include total mercury and methylmercury concentrations in water, size-sieved seston, and particulate matter of 13 remote lakes. Additionally, these data include soil and volcanic ash measurements from the surrounding watersheds. Finally, these data include energetic profiling of seston, lake trout, and sockeye salmon as well as mercury isotope measurements of the fishes. These data are important when interpreting mercury mass balance flows and bioavailability to the food web and are a part of an associated journal article published in Environmental Science and Technology Letters (https://doi.org/10.1021/acs.estlett.2c00096). 

This dataset is associated with the following publication:
Lepak, R., J. Ogorek, K. Bartz, S. Janssen, M. Tate, Y. Runsheng, J. Hurley, D. Young, C. Eagles-Smith, and D. Krabbenhoft. Using Carbon, Nitrogen, and Mercury Isotope Values to Distinguish Mercury Sources to Alaskan Lake Trout.   Environmental Science & Technology Letters. American Chemical Society, Washington, DC, USA, 9(4): 312-319, (2022).

Tags: alaska, climate-change, isotope, lake-trout, mercury, volcano
Organization: U.S. Environmental Protection Agency
H12088: NOS Hydrographic Survey , Southern Portion of Cook Inlet, Alaska, 2009-09-05

The National Oceanic and Atmospheric Administration (NOAA) has the statutory mandate to collect hydrographic data in support of nautical chart compilation for safe navigation and to provide background data for engineers, scientific, and other commercial and industrial activities. Hydrographic survey data primarily consist of water depths, but may also include features (e.g. rocks, wrecks), navigation aids, shoreline identification, and bottom type information.
							NOAA is responsible for archiving and distributing the source data as described in this metadata record.

Tags: acoustic sounders, alaska, bathymetry, bathymetry/seafloor topography, continent, doc/noaa/nesdis/ncei, doc/noaa/nesdis/ngdc, earth remote sensing instruments, earth science, global positioning system/inertial measurement unit, gps, gps receivers, gps/imu, hydrographic surveys for selected locations within the united states (hydro_bathy_2006), in situ ocean-based platforms, in situ/laboratory instruments, marine sediments, mbes, msbs, multibeam mapping system, multibeam swath bathymetry system, national centers for environmental information, national geophysical data center, nesdis, noaa, north america, ocean, oceans, passive remote sensing, positioning/navigation, profilers/sounders, seafloor topography, sediment composition, seldovia bay, ships, sonar, sound navigation and ranging, southern portion of cook inlet, u.s. department of commerce, united states of america, water depth
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Distribution of data in ECOTOX across species, chemicals, and effects (June 2021 update)

The ECOTOXicology Knowledgebase (ECOTOX) has been in development since the early 1980s and is maintained by the  U.S. EPA Great Lakes Toxicology and Ecology Division. ECOTOX includes curated data from toxicity tests from aquatic and terrestrial species, with results available on the web-based application: www.epa.gov/ecotox. This paper includes overview summaries of the entirety of the data currently included in ECOTOX (as of September 2020 update), with the source data for these summaries included in this Excel file. 

This dataset is associated with the following publication:
Olker, J., C. Elonen, A. Pilli, A. Anderson, B. Kinzinger, S. Erickson, M. Skopinski, A. Pomplun, C. LaLone, C. Russom, and D. Hoff. The ECOTOXicology Knowledgebase: A Curated Database of Ecologically Relevant Toxicity Tests to Support Environmental Research and Risk Assessment.   ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY. Society of Environmental Toxicology and Chemistry, Pensacola, FL, USA, 41(6): 1520-1539, (2022).

Tags: aquatic-toxicity, data-curation, database, ecotox-knowledgebase, ecotoxicology, toxicity-data
Organization: U.S. Environmental Protection Agency
PFAS 150 Evidence Map

This research effort describes a systematic evidence map of relevant health literature for ~150 Per and Polyfluoroalkyl Substances (PFAS). The literature search results, screening and tagging results, and data extractions are all available via download from the provided URLS from HERO, HAWC, and Tableau respectively.  In addition, supplemental data files that capture the literature search synonyms, strings, and results are available in the excel file.  The word file includes additional information about the results from searching gray literature and other resources consulted, as well as appendixes of human and animal design considerations. The full manuscript contains additional URLs and data with interactive visualizations. 

This dataset is associated with the following publication:
Carlson, L., M. Angrish, A. Shirke, E. Radke-Farabaugh, B. Schulz, A. Kraft, R. Judson, G. Patlewicz, R. Blain, C. Lin, N. Vetter, C. Lemeris, P. Hartman, H. Hubbard, X. Arzuaga, A. Davis, L. Dishaw, I. Druwe, H. Hollinger, R. Jones, J. Kaiser, L. Lizarraga, P. Noyes, M. Taylor, A. Shapiro, A. Williams, and K. Thayer. Systematic Evidence Map for Over One Hundred and Fifty Per- and Polyfluoroalkyl Substances (PFAS).   ENVIRONMENTAL HEALTH PERSPECTIVES. National Institute of Environmental Health Sciences (NIEHS), Research Triangle Park, NC, USA, 130(5): 1-20, (2022).

Tags: per-and-polyfluoroalkyl-substances-pfas, systematic-evidence-map, systematic-review
Organization: U.S. Environmental Protection Agency
Data for children's soil and dust ingestion estimates using SHEDS-S/D model

These data are the inputs and variables needed to populate the SHEDS-S/D model to generate children's soil and dust ingestion estimates. 

This dataset is associated with the following publication:
Tulve, N., H. Ozkaynak, G. Glen, J. Cohen, H. Hubbard, K. Thomas, and L. Phillips. Model based prediction of age-specific soil and dust ingestion rates for children.   Journal of Exposure Science and Environmental Epidemiology. Nature Publishing Group, London,  UK, 32(578): 472-480, (2022).

Tags: children, dust-ingestion, model, sheds-s-d, soil-ingestion
Organization: U.S. Environmental Protection Agency
Investigating the potential for microbially induced carbonate precipitation to treat mine waste

In this study, the feasibility of promoting microbially induced carbonate precipitation (MICP) in mine waste piles by using an environmental bacterial enrichment is explored, with goals to mitigate erosion and infiltration and reduce metals leaching. MICP has been widely studied as a biotechnology for use in strengthening soils, impacting permeability of porous media and fractures, and mitigating fugitive dust emissions, among other applications.  This technology has also been explored for remediation applications, including co-precipitation of radionuclides in contaminated groundwater as well as stabilization of mine waste and fly ash.  In this study, we utilize a native bacterial enrichment to promote MICP on seven mine waste samples with variability in acid production and extent of toxic metal leaching.  Over the course of fifteen applications of MICP solutions and bacteria on the surface of waste rock in bench-scale columns, calcium carbonate mineral formed on grain surfaces within the waste samples and the effluent from acid-producing wastes increased in pH during MICP treatment. The performance of MICP was evaluated with humidity cell and synthetic precipitation leaching procedure (SPLP) tests. Humidity cell and SPLP leaching tests revealed reductions in Cd, Pb and Zn in leachate of almost all samples, mixed results for Cu, and As increasing in most leachate samples after treatment. While reduction in metals leaching varied between different waste rock samples, MICP-driven formation of calcium carbonate was observed in all mine waste samples by the end of treatment. While the distribution of CaCO3 coating was uneven in microscopic images, the technology has potential for coating solid mine waste and reducing release of acid and some metals. This study provides a laboratory assessment of the feasibility of MICP to stabilize mine waste piles in situ and mitigate release of toxic metals into the environment. 

This dataset is associated with the following publication:
Proudfoot, D., L. Brooks, C.H. Gammons, E. Barth, D. Bless, R.M. Nagisetty, and E.G.  Lauchnor. Investigating the potential for microbially induced carbonate precipitation to treat mine waste.   JOURNAL OF HAZARDOUS MATERIALS. Elsevier Science Ltd, New York, NY, USA, 424 part C: 127490, (2022).

Tags: bacterial-ureolysis, calcium-carbonate, leaching-tests, waste-rock
Organization: U.S. Environmental Protection Agency
A Generic Pharmacokinetic Model for Quantifying Mother-to-Offspring Transfer of Lipophilic Persistent Environmental Chemicals

This data set includes source code files and associated data files that implement a pharmacokinetic (PK) model for lipophilic persistent environmental chemicals (LPECs) that can be used to simulate various exposure scenarios involving pregnant and nursing maternal animals and offspring. The model is described in a manuscript entitled "A Generic Pharmacokinetic Model for Mother-to-Offspring Transfer of Lipophilic Persistent Environmental Chemicals" by Kapraun et al.

Tags: childrens-environmental-health, lactational-transfer, lipophilic-persistent-environmental-chemical, pharmacokinetic-model, pregnancy
Organization: U.S. Environmental Protection Agency
Private Domestic Well Estimates (2010)

This data provides improved estimates of the dependence and spatial distribution of housing units reliant on private domestic wells by census block group and block. Nationally, based on an understanding of well use from state well logs and the housing unit density, an estimated 23 million housing units are being served by this water resource, 17 per cent of the population. In 1990, 15.1 million households were reliant on wells. In the ensuing 30 years there has been over a 50 percent increase in the number of households relying on these wells. This dataset will assist in a better understanding of the reliance on private domestic wells in the US, better positioning local, state, and federal groups in protecting this water resource from contaminant sources. 

This dataset is associated with the following publication:
Murray, A., A. Hall, J. Weaver, and F. Kremer. Methods for Estimating Locations of Housing Units Served by Private Domestic Wells in the United States Applied to 2010.   JOURNAL OF THE AMERICAN WATER RESOURCES ASSOCIATION. American Water Resources Association, Middleburg, VA, USA, 57(5): 828-843, (2021).

Tags: domestic-well, drinking-water, gis, groundwater
Organization: U.S. Environmental Protection Agency
Posted and R-Posted Bridges in New York State

This data set features a hyperlink to the New York State Department of Transportation’s Posted Bridges web page, which includes a link to the Posted Bridges interactive map.  The interface provides up-to-date information for locating Load-Posted, R-Posted and Other-Posted bridges throughout New York. This site has been developed as a reference tool for operators of Commercial Vehicles to identify and locate structures in New York State where access and use is limited based on the vehicle's weight. Legal weights are established in Section 385 of the Vehicle and Traffic Law.  All trucks operating over legal weight pursuant to a Divisible Load Overweight Permit are prohibited from crossing all R-Posted Bridges.

Organization: State of New York
Effects of deiodinase inhibition on amphibian metamorphosis

This dataset contains in vitro and in vivo biochemical and apical (i.e., growth/development) data pertaining to iodotyrosine deiodinase inhibition in the African clawed frog (Xenopus laevis). 

This dataset is associated with the following publication:
Haselman, J., J. Olker, P. Kosian, J. Korte, J. Denny, J. Tietge, M. Hornung, and S. Degitz. Characterization of the Mechanistic Linkages Between Iodothyronine Deiodinase Inhibition and Impaired Thyroid-Mediated Growth and Development in Xenopus Laevis Using Iopanoic Acid.   TOXICOLOGICAL SCIENCES. Society of Toxicology, RESTON, VA,  187(1): 139-149, (2022).

Tags: adverse-outcome-pathway, ecotoxicology, endocrine-disruption, thyroid
Organization: U.S. Environmental Protection Agency
Metadata: Wet nitrogen (N) deposition to urban Latin America: filling in the gaps with GEOS-Chem

The data include model outputs from the GEOS-Chem model and observational datasets. This dataset is not publicly accessible because: The data were not generated by EPA. It can be accessed through the following means: Data can be obtained from the Alexandra Ponette-Gonzalez, the lead author (alexandra.ponette@unt.edu). Format: Since EPA does not own the data, the format is unknown. 

This dataset is associated with the following publication:
Ponette-Gonzalez, A., H. Lewis, B. Henderson, D. Carnelos, G. Pineiro, K. Weathers, and D. Schwede. Wet nitrogen (N) deposition to urban Latin America: filling in the gaps with GEOS-Chem.   ATMOSPHERIC ENVIRONMENT. Elsevier Science Ltd, New York, NY, USA, 278: 119095, (2022).

Tags: atmospheric-deposition, geos-chem, nitrogen, south-america
Organization: U.S. Environmental Protection Agency
Biological, watershed land use & physiochemical data from streams sampled in the Georgia Coastal Plain

Benthic macroinvertebrates sampled from 76 small streams in the Georgia Coastal Plain.  Additional data includes in-situ physiochemcial water quality data, physical stream habitat data and land use data in the watershed draining to the sample stream reach, as well as in the immediate riparian zone adjacent to all stream reaches upstream of the sample reach.  These data were used to develop a biological condition index for evaluating stream restoration projects in this region. Citation information for this dataset can be found in the EDG's Metadata Reference Information section and Data.gov's References section.

Tags: coastal-plain, headwater-streams, macroinvertebrate-index, stream-mitigation, success-criteria
Organization: U.S. Environmental Protection Agency
useeior v1.0.0 supporting data

Supporting data associated with useeior v1.0.0 software.  https://github.com/USEPA/useeior/tree/v1.0.0. 
The supporting data include model specification files, sector correspondence files, data and metadata files for all economic data used in model building, as described in the associated publication. 

This dataset is associated with the following publication:
Li, M., W.W. Ingwersen, B. Young, J. Vendries, and C. Birney. useeior: An Open-Source R Package for Building and Using US Environmentally-Extended Input–Output Models.   Applied Sciences. MDPI AG, Basel,  SWITZERLAND, 12(4): 4469, (2022).

Tags: bea, environmental-input-output, input-output, model-builder, r-language, software-package, useeio
Organization: U.S. Environmental Protection Agency
Probabilistic modelling of developmental neurotoxicity based on a simplified adverse outcome pathway network

Table of contents																	
Table S1	DNT inventory	List of sources and associated data collected for the development of the Bayesian hierarchical model. 															
Table S2	Data collection	It contains the compiled raw data.															
Table S3	Final dataset	It contains data after curation agreed to be included in the Bayesian hierarchical model.															
Table S4	List of encoders	Machine readable format used to encode the data.															
Table S5	Machine readable	The final dataset translated into a machine readable file using the encoders listed above.															
Table S6	Results for DNT	Based on the cut-offs derived from the results themselves, three classes of DNT are proposed (low, medium and high predicted probability). Results are summarised accordingly. 

This dataset is associated with the following publication:
Spinu, N., M. Cronin, J. Lao, A. Bal-Price, I. Campia, S. Enoch, J. Madden, L. Lagares, M. Novic, D. Pamies, S. Scholz, D. Villeneuve, and A. Worth. Probabilistic modelling of developmental neurotoxicity based on a simplified adverse outcome pathway network.   Computational Toxicology. Elsevier B.V., Amsterdam,  NETHERLANDS, 21: 100206, (2022).

Tags: adverse-outcome-pathways-aops, computational-toxicology, developmental-neurotoxicity, new-approach-methods-alternatives-to-animal-testi, screening-and-prioritization
Organization: U.S. Environmental Protection Agency