cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.23719/1528701
title: In vitro transcriptomic analyses reveal pathway perturbations, estrogenic activities, and potencies of data-poor BPA alternative chemicals 

description: GEOSite dataset for article 'In vitro transcriptomic analyses reveal pathway perturbations, estrogenic activities, and potencies of data-poor BPA alternative chemicals '
DOI: 10.23719/1528702
title: Evaluation of Per- and Polyfluoroalkyl Substances (PFAS) In Vitro Toxicity Testing for Developmental Neurotoxicity

description: R-language data files from "Carstens KE, Freudenrich T, Wallace K, Choo S, Carpenter A, Smeltz M, Clifton MS, Henderson WM, Richard AM, Patlewicz G, Wetmore BA, Paul Friedman K, Shafer T. Evaluation of Per- and Polyfluoroalkyl Substances (PFAS) In Vitro Toxicity Testing for Developmental Neurotoxicity. Chem Res Toxicol. 2023 Mar 20;36(3):402-419. doi: 10.1021/acs.chemrestox.2c00344. Epub 2023 Feb 23. PMID: 36821828."
DOI: 10.23719/1527908
title: Datasets for manuscript "Predicting chemical end-of-life scenarios using structure-based classification models"

description: As described in the README.md file, the GitHub repository github.com/USEPA/PRTR-QSTR-models/tree/data-driven are Python scripts written to run Quantitative Structure–Transfer Relationship (QSTR) models based on chemical structure-based machine learning (ML) models for supporting environmental regulatory decision-making. Using features associated with annual chemical transfer amounts, chemical generator industry sectors, environmental policy stringency, gross value added by industry sectors, chemical descriptors, and chemical unit prices, as in the GitHub repository PRTR_transfers, the QSTR models developed here can predict potential EoL activities for chemicals transferred to off-site locations for EoL management. Also, this contribution shows that QSTR models aid in estimating the mass fraction allocation of chemicals of concern transferred off-site for EoL activities.
Also, it describes the Python libraries required for running the code, how to use it, the obtained outputs files after running the Python script, and how to obtain all manuscript figures and results.
DOI: 10.23719/1528688
title: Occurrence of aetokthonotoxin producer in natural samples – a PCR protocol for easy detection

description: No EPA data was generated for the current manuscript.  LC/MS and LC/MS-MS data were generated by collaborators in Germany.  Sequencing data from this study is available at the NCBI under accession numbers OQ325307, OQ325311–OQ325313 and
OQ338813–OQ338815.  Additional data will be made available on request by the corresponding author.
DOI: 10.23719/1523157
title: DriLube VOC Concentrations, Pressure & Vacuum Readings and Metadata

description: There are 3 main databases. #1 is the VOC concentrations of soil gas and indoor air samples collected over the site. #2 is the pressure readings used to monitor the pressure differential between subslab and indoor air. #3 is the vacuum reading used to monitor effectiveness, strength, and reach of vacuum created during the SVE operation.
DOI: 10.23719/1523478
title: SH for Improving PM2.5 forecasts

description: -Aerosol Optical Depth (AOD) data sets are used from satellite instruments MODIS Terra and Aqua and VIIRS which included a combination of the Dark Tark and Deep Blue algorithms and AOD from the NASA AERONET Network.

-Surface PM2.5 data sets are from the State and Local Monitoring Station and Interagency Monitoring of Protected Visual Environments Networks.

-PM2.5 model based data sets are from 3 separate chemical transport models; GEOS-Chem, WRF-Chem, and WRF-CMAQ. The EPA WRF-CMAQ data set is publicly available via the U.S. EPA Remote Sensing Information Gateway application.  For CMAQ data access, users must first download and install the RSIG application at: https://www.epa.gov/hesc/remote-sensing-information-gateway.
DOI: 10.23719/1524717
title: Evaluation of 147 Perfluoroalkyl Substances for Immunosuppressive and other Activities Through Phenotypic Screening of Human Primary Cells

description: Dataset for journal article 'Evaluation of 147 Perfluoroalkyl Substances for Immunosuppressive and other Activities Through Phenotypic Screening of Human Primary Cells'. 
Per- and polyfluoroalkyl substances (PFAS) are a large class of chemicals in widespread use for diverse applications in commerce resulting in significant presence in the environment. Extensive studies of several of the highly produced members of the class have demonstrated potential for adverse health consequences to humans and the environment as well as highly pervasive and persistent exposures. Here we report testing results of 147 PFAS substances in a phenotypic screening platform of primary human cell co-culture systems, the BioMAP® Diversity PLUS panel, used to model complex tissue and disease biology of organs (vasculature, immune system, skin, lung) and general tissue biology. PFAS were tested at four concentrations ranging from approximately 0.06 to 60 micromolar in order to minimize influence from confounding effects of polypharmacology resulting from qualitatively different activities at higher concentrations. We also compared response profiles for all PFAS with an existing database of responses for the BioMAP assays to identify other potential mechanisms of activity for this diverse chemical family.
DOI: 10.23719/1528482
title: Datasets associated with journal article 'Combining phenotypic profiling and targeted RNA-Seq reveals linkages between transcriptional perturbations and chemical effects on cell morphology: Retinoic acid as an example' by Nyffeler, J, et.al.

description: We evaluated the Templated Oligo with Sequencing Readout (TempO-Seq) assay for High-throughput transcriptomic screening of a small set of environmental chemicals. This assay yields sequencing reads of exactly 50 base pairs that can be rapidly aligned to generate gene counts, and is compatible with cell lysates prepared in multiwell format. The version of the TempO-Seq assay we evaluated provides nearly whole transcriptome coverage (>20,000 genes). This study encompasses 2 replicates of a 384-well plate design. The majority of wells contain U-2 OS cells exposed to 11 test chemicals at 7 different concentrations (two replicate per test chemical, concentration, and plate), and additional reference samples and controls. Controls include DMSO vehicle treatments (22 per plate). Reference samples include bulk lysate MCF7 samples (2 DMSO treated and 2 TSA treated samples per plate), reference chemical treatments (3 chemicals at single conc each, per plate), and vendor-provided reference RNA mixtures (UHRR and HBRR).
DOI: 10.23719/1528946
title: High-throughput AR dimerization assay identifies androgen disrupting chemicals and metabolites

description: Repository for supplemental files and code for paper titled "High-throughput AR Dimerization Assay Identifies Androgen Disrupting Chemicals and Metabolites", 2022.
DOI: 10.6084/m9.figshare.23161250
title: Mangosteen Transcriptome and Transdecoder Files

description: Mangosteen Illumina RNA sequences were obtained from the NCBI Sequence Read Archive (SRA) databases. Trimmomatic 0.39 was used to remove adaptor sequences and low-quality reads from Illumina data with default parameter (TruSeq3-PE-2.fa:2:30:10 SLIDINGWINDOW:4:5 LEADING:5 TRAILING:5 MINLEN:25). Next, the clean Illumina data was used for <i>de novo</i> transcriptome assembly using Trinity v.2.9.1 with default parameters (adding the following parameter: normalize_by_read_set; min_kmer_cov=2; no bowtie) to generate a single Trinity assembly. After assembly, non-redundant genes/ reference transcriptome were obtained using TGICL with default settings. Next, Transdecoder was used to generate a total of 93,923 predicted peptides.
DOI: 10.6084/m9.figshare.23161250.v1
title: Mangosteen Transcriptome and and Transdecoder Files

description: Mangosteen Illumina RNA sequences were obtained from the NCBI Sequence Read Archive (SRA) databases. Trimmomatic 0.39 was used to remove adaptor sequences and low-quality reads from Illumina data with default parameter (TruSeq3-PE-2.fa:2:30:10 SLIDINGWINDOW:4:5 LEADING:5 TRAILING:5 MINLEN:25). Next, the clean Illumina data was used for <i>de novo</i> transcriptome assembly using Trinity v.2.9.1 with default parameters (adding the following parameter: normalize_by_read_set; min_kmer_cov=2; no bowtie) to generate a single Trinity assembly. After assembly, non-redundant genes/ reference transcriptome were obtained using TGICL with default settings. Next, Transdecoder was used to generate a total of 93,923 predicted peptides.
DOI: 10.23719/1528692
title: ARGs in Kewaunee County Riverbed Sediment and Surface Water: Data from Beattie et al. 2018

description: The relative abundance of antibiotic resistance genes measured from spatially and temporally distributed sampling in Kewaunee County, Wisconsin.
DOI: 10.23719/1528962
title: Concentrations of human fecal indicators in wastewater in Kentucky sewersheds

description: This dataset reports concentrations of RNAse P, PMMoV, and CrAssphage, as measured by qPCR, in wastewater at 28 sites including water treatment plants as well as smaller sewersheds. All sites are in the Louisville, KY, USA metro area.
DOI: 10.23719/1503845
title: Data for a Spatial Causal Analysis of Wildland Fire-Contributed PM2.5 During Wildfire Seasons 2008 - 2012

description: Data during wildfire seasons (May 1 - October 31) over the years 2008 - 2012 in the contiguous U.S. used for spatial causal analysis of wildland fire-contributed PM2.5. The two sources of PM2.5 data are monitor data from the EPA’s Air Quality System (AQS) and simulated PM2.5 from the CMAQ model.
DOI: 10.23719/1526313
title: Chemical Screening in an Estrogen Receptor Transactivation Assay with Metabolic Competence

description: This is an original dataset generated at the U.S. EPA. Data was analyzed with the ToxCast Pipeline and deposited for release in invitroDB accessible via the U.S. EPA CompTox Chemicals Dashboard.
Dataset is a zip file containing two Excel spreadsheets titled   AIME-ERTA_384_Tables_All_Submission_v2    and   README_AIME-ERTA_384_Manuscript_Sup_Data_v2
DOI: 10.23719/1527757
title: Datasets for manuscript "Tracking end-of-life stage of chemicals: a scalable data-centric and chemical-centric approach"

description: As described in the README.md file, the GitHub repository PRTR_transfers are Python scripts written to run a data-centric and chemical-centric framework for tracking EoL chemical flow transfers, identifying potential EoL exposure scenarios, and performing Chemical Flow Analysis (CFA). Also, the created Extract, Transform, and Load (ETL) pipeline leverages publicly-accessible Pollutant Release and Transfer Register (PRTR) systems belonging to Organization for Economic Cooperation and Development (OECD) member countries. The Life Cycle Inventory (LCI) data obtained by the ETL is stored in a Structured Query Language (SQL) database called PRTR_transfers that could be connected to Machine Learning Operations (MLOps) in production environments, making the framework scalable for real-world applications. The data ingestion pipeline can supply data at an annual rate, ensuring labeled data can be ingested into data-driven models if retraining is needed, especially to face problems like data and concept drift that could drastically affect the performance of data-driven models.
Also, it describes the Python libraries required for running the code, how to use it, the obtained outputs files after running the Python script, and how to obtain all manuscript figures (file Manuscript Figures-EDA.ipynb) and results.
DOI: 10.23719/1527861
title: Assessing the relative importance of stressors to the benthic index, M-AMBI: an example from U.S. estuaries

description: These are these are the data used in the paper:
Assessing the relative importance of stressors to the benthic index, M-AMBI: an example from U.S. estuaries
DOI: 10.5285/8a09e8be-607d-470c-a8f9-fdbae536de8f
title: Corinth Rift, Greece Fault Location and Activity Rate data

description: The data are derived from interpretation of seismic reflection profiles within the offshore Corinth Rift, Greece (the Gulf of Corinth) integrated with IODP scientific ocean drilling borehole data from IODP Expedition 381 (McNeill et al., 2019a, 2019b).
The data include rift fault coordinate (location, geometry) information and slip rate and extension rate information for the major faults.
Seismic reflection data were published in Taylor et al. (2011) and in Nixon et al. (2016). Preliminary fault interpretations and rate data, prior to IODP drilling, were published in Nixon et al. (2016).
Details of datasets:
The data can be viewed in GIS software (ArcGIS, QGIS) or the Excel and .dbf files can be used for viewing of rate data and import of fault coordinates into other software.
The 4 folders are for different time periods with shape files for the N-Dipping and S-Dipping Faults in the offshore Corinth Rift and respective slip and extension (horizontal) rates.
The shapefiles are digitised fault traces for the basement offsetting faults, picked from the Multichannel Seismic Data collected by the R/V Maurice Ewing. 
Fault traces are segmented and each segment has an average throw (vertical) rate (Tavg) in mm/yr. The rates for the segments are averages based on measurements at the ends of each segment.
The major fault trace segments also have slip-rates (slip_rate) and extension-rates (ext_rate or extension_) in mm/yr. All rates as well as the names for major faults can be located in the attribute table of the shape files along with X- and Y-coordinates. The coordinate system is WGS84 UTM Zone 34N. 
The shape files can be loaded into a GIS (ArcGIS, QGIS etc.) allowing mapping and visualization of the fault traces and their activity rates. 
In addition, the attribute tables are .dbf files found within each folder. These have also been provided as .xlsx (Excel) files which include the fault coordinate information, and slip rates and extension rates along the major faults. 
References
McNeill, L.C., Shillington, D.J., Carter, G.D.O., and the Expedition 381 Participants, 2019a. Corinth Active Rift Development. Proceedings of the International Ocean Discovery Program, 381: College Station, TX (International Ocean Discovery Program).
McNeill, L.C., Shillington, D.J., et al., 2019b, High-resolution record reveals climate-driven environmental and sedimentary changes in an active rift, Scientific Reports, 9, 3116.
Nixon, C.W., McNeill, L.C., Bull, J.M., Bell, R.E., Gawthorpe, R.L., Henstock, T.J., Christodoulou, D., Ford, M., Taylor, B., Sakellariou, S. et al., 2016. Rapid spatiotemporal variations in rift structure during development of the Corinth Rift, central Greece. Tectonics, 35, 1225–1248.
Taylor, B., J. R. Weiss, A. M. Goodliffe, M. Sachpazi, M. Laigle, and A. Hirn (2011), The structures, stratigraphy and evolution of the Gulf of Corinth Rift, Greece, Geophys. J. Int., 185(3), 1189–1219.
DOI: 10.23719/1519210
title: MODELING BIOLOGICAL INDICATORS ACROSS SPACE AND TIME AT A NATIONAL SCALE

description: Represents spatial predictions of biological condition at unsampled streams and lakes across the counterminous US. Also includes spatial predictions channel dimensions of unsamples streams.
DOI: 10.23719/1529112
title: AMR in urban karst groundwater systems

description: The data set includes relative abundances of antimicrobial resistance genes in urban karst groundwater systems in western Kentucky
DOI: 10.23719/1528992
title: Non-EPA data for GoDeep Manuscript

description: GCAM-USA results in support of the manuscript.
DOI: 10.23719/1528636
title: Metadata for ‘Synoptic sketches’ of water quality along stream flowpaths: a watershed monitoring approach for heterogeneous landscapes

description: Water quality data collected from multiple streams in the Chesapeake Bay watershed
DOI: 10.23719/1529126
title: CMAQ CONUS (12US2) Input data for 2015-12-22 to 2016-01-31

description: Input files for running the Community Multiscale Air Quality (CMAQ) modeling system.  Input files include emissions, meteorology, boundary and initial conditions, and other ancillary data needed for running a simulation over the contiguous United States (12US2 domain) for December 22, 2015 - January 31, 2016.  These input data can be used with two online tutorials described in Efstathiou et al. to set up and run a CMAQ simulation on Amazon Web Services and Microsoft Azure cloud computing resources. 

Data are netcdf formatted files using I/O API data structures (https://www.cmascenter.org/ioapi/). Information on variables within the files (variable names and units) and the model projection and grid structure is contained in the header information of each netcdf file.
DOI: 10.23719/1529149
title: Dataset for 'From vision toward best practices: Evaluating in vitro transcriptomic points of departure for application in risk assessment using a uniform workflow'

description: Data for Reardon AJF, et al., From vision toward best practices: Evaluating in vitro transcriptomic points of departure for application in risk assessment using a uniform workflow. Front. Toxicol. 5:1194895. doi: 10.3389/ftox.2023.1194895. PMC10242042
DOI: 10.23719/1529094
title: Per- and Polyfluoroalkyl Substances (PFAS) in mixtures show additive effects on transcriptomic points of departure in human liver spheroids

description: Data for "Addicks GC, Rowan-Carroll A, Reardon A, Leingartner K, Williams A, Meier MJ, Moffat I, Carrier R, Lorusso L, Wetmore BA, Yauk C, Atlas E. Per- and Polyfluoroalkyl Substances (PFAS) in mixtures show additive effects on transcriptomic points of departure in human liver spheroids. Toxicol Sci. 2023 May 17:kfad044. doi: 10.1093/toxsci/kfad044. Epub ahead of print. PMID: 37195416."
DOI: 10.23719/1518719
title: MagnusonMatthew_A-rr5q_dataset_20200526.docx

description: All data is tabulated within the journal article.
DOI: 10.23719/1529159
title: Chesapeake Bay Nutrient Inventory (1985-2019)

description: Leverage existing nutrient input/output data from the Chesapeake Bay Program's CAST database to develop nitrogen and phosphorus inventories. These inventories will highlight spatiotemporal variability in point and non-point source pollution throughout the watershed, and can be used to monitor progress in decreasing pollution sources as well as retrospective water quality analyses looking to explain past water quality trends.
DOI: 10.23719/1528515
title: IEUBK evaluation dataset

description: All data are provided within report tables available on the website with appropriate header information.
DOI: 10.23719/1527714
title: Biosolids PFAS data

description: Data were generated at the University of Florida
DOI: 10.23719/1518526
title: Dataset used in ORD-035008 - A Set of Six Gene Expression Biomarkers and Their Thresholds Identify Rat Liver Tumorigens in Short-Term Assays

description: The links provided include the DrugMatrix-Affymetrix study, the TG-GATES study, and the TempO-Seq S1500+ study.
DOI: 10.5281/zenodo.7257831
title: 3D models of bead, pendant and softstone vessel fragments found during the 2021 excavations at Kalba (K4)

description: The 3D models of the three objects were created within the joint excavations project at Kalba (K4), United Arab Emirates, of the Sharjah Archaeology Authority (SAA), the Austrian Archaeological Institute (OeAI) of the Austrian Academy of Sciences (OeAW) and the Leibniz-Zentrum für Archäologie (LEIZA). For each object the following data are available: 3D model with colour values reflecting the curvature (MSII filter) in ply format, texture image for the 3D model in png format, metadata of the 3D acquisition and processing in ttl and json format. The 3D models were created with the Structure from Motion (SfM) technique using Agisoft Metashape software. The images were taken with a Nikon Z50 mirrorless camera and a 90 mm lens. The models obtained were post-processed using GigaMesh (https://gigamesh.eu) to calculate curvature with the MSII built-in filter and to create scaled 2D views. The export of the 3D metadata with information about the 3D model and the 3D acquisition and processing was done with pyhton scripts in agisoft metashape (https://doi.org/10.5281/zenodo.7468298).
DOI: 10.5281/zenodo.7257830
title: 3D models of bead, pendant and softstone vessel fragments found during the 2021 excavations at Kalba (K4)

description: The 3D models of the three objects were created within the joint excavations project at Kalba (K4), United Arab Emirates, of the Sharjah Archaeology Authority (SAA), the Austrian Archaeological Institute (OeAI) of the Austrian Academy of Sciences (OeAW) and the Leibniz-Zentrum für Archäologie (LEIZA). For each object the following data are available: 3D model with colour values reflecting the curvature (MSII filter) in ply format, texture image for the 3D model in png format, metadata of the 3D acquisition and processing in ttl and json format. The 3D models were created with the Structure from Motion (SfM) technique using Agisoft Metashape software. The images were taken with a Nikon Z50 mirrorless camera and a 90 mm lens. The models obtained were post-processed using GigaMesh (https://gigamesh.eu) to calculate curvature with the MSII built-in filter and to create scaled 2D views. The export of the 3D metadata with information about the 3D model and the 3D acquisition and processing was done with pyhton scripts in agisoft metashape (https://doi.org/10.5281/zenodo.7468298).
DOI: 10.23719/1529346
title: National Lakes Physical Habitat Data

description: National Lakes Assessment physical habitat data - 2007 and 2012 data
DOI: 10.7925/drs1.duchas_4688893
title: Seanfhocail

description: Story collected by Tadhg Ó Caomháin, a student at Naomh Breandán, Baile na nGall school (Ballynagall or Ballydavid, Co. Kerry) from informant Tomás Ó Pronsías.
description: Collected as part of the Schools' Folklore scheme, 1937-1938, under the supervision of teacher Tadhg Ó Caomháin.
description: Supported by funding from the Department of Arts, Heritage and the Gaeltacht (Ireland), University College Dublin, and the National Folklore Foundation (Fondúireacht Bhéaloideas Éireann), 2014-2016.
DOI: 10.7925/drs1.duchas_5075103
title: Béaloideas

description: Story collected by Áine Bhreathnach, a student at Moymore, Sráid na Cathrach school (Moymore South, Co. Clare) (no informant identified).
description: Collected as part of the Schools' Folklore scheme, 1937-1938, under the supervision of teacher Séamus Ó Frighil.
description: Supported by funding from the Department of Arts, Heritage and the Gaeltacht (Ireland), University College Dublin, and the National Folklore Foundation (Fondúireacht Bhéaloideas Éireann), 2014-2016.
DOI: 10.7925/drs1.duchas_4947285
title: Lore of Certain Days

description: Story collected by Donal Linehan, a student at Dromcollchoille (B.) school (Dromcolliher, Co. Limerick) from informant Edmond Linehan.
description: Collected as part of the Schools' Folklore scheme, 1937-1938, under the supervision of teacher Pádraig Ó Mathghamhna.
description: Supported by funding from the Department of Arts, Heritage and the Gaeltacht (Ireland), University College Dublin, and the National Folklore Foundation (Fondúireacht Bhéaloideas Éireann), 2014-2016.
DOI: 10.7925/drs1.duchas_4947286
title: Shrove

description: Story collected by Jerry Newman, a student at Dromcollchoille (B.) school (Dromcolliher, Co. Limerick) (no informant identified).
description: Collected as part of the Schools' Folklore scheme, 1937-1938, under the supervision of teacher Pádraig Ó Mathghamhna.
description: Supported by funding from the Department of Arts, Heritage and the Gaeltacht (Ireland), University College Dublin, and the National Folklore Foundation (Fondúireacht Bhéaloideas Éireann), 2014-2016.