cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.23719/1520861
title: The Residential Population Generator (RPGen): A tool to parameterize residential, demographic, and physiological data to model intraindividual exposure, dose, and risk

description: This repository contains scripts, input files, and some example output files for the Residential Population Generator, an R-based tool to generate synthetic human residental populations to use in making estimates of near-field chemical exposures. This tool is most readily adapted for using in the workflow for CHEM, the Combined Human Exposure Model, avaialable in two other GitHub repositories in the HumanExposure project, including ProductUseScheduler and source2dose. CHEM is currently best suited to estimating exposure to product use. Outputs from RPGen are translated into ProductUseScheduler, which with subsequent outputs used in source2dose.
DOI: 10.23719/1520773
title: Water temperature trends

description: Water temperature trends
DOI: 10.23719/1519408
title: Dataset for Ebullition dominates methane fluxes from the water surface across different ecohydrological patches in a temperate freshwater marsh

description: Dataset for Ebullition dominates methane fluxes from the water surface across different ecohydrological patches in a temperate freshwater marsh
DOI: 10.23719/1504436
title: Respirometric Screening and Characterization of Mitochondrial Toxicants Within the ToxCast Phase I and II Chemical Libraries

description: These are the raw data files for TOXSCI manuscript 19-0578 entitled, “Respirometric Screening and Characterization of Mitochondrial Toxicants Within the ToxCast Phase I and II Chemical Libraries”:
Description from readme.txt file:

1) sc_seahorse.lvl0.merged.data.csv- contains all mapped raw OCR data from tier 1 single-concentration RSA screening of 1,042 Toxcast Phase I and II chemicals

2) mc_seahorse.lvl0.merged.data.csv- contains all mapped raw OCR data from tier 2 multi-concentration RSA screening of 249 actives from tier 1

3) EFA.lvl0.merged.data.csv- contains all mapped raw OCR data from tier 3 EFA screening of 149 putative electron transport chain inhibitors

4) mc5_mc6_ncct_mito_nov2019.csv- level 5 and 6 outputs from ToxCast pipeline (tcpl) analysis

5) RawMC3_ToxCast_by_aeid.csv- level 3 tcpl outputs for all mitochondrial ToxCast assays

6) RawMC5_ToxCast_by_aeid.csv- level 5 tcpl outputs for all mitochondrial ToxCast assays

7) ref.set.chems.csv- sixty reference chemicals used to compared assay performance

8) study_code.R- R script used to analyze data and generate figures and tables
DOI: 10.23719/1518723
title: Impact of wildfire on particulate matter in the southeastern United States in November 2016

description: a study about wild fire in the US in 2016
DOI: 10.23719/1520515
title: Laboratory Data From Ghana Water Testing for E-coli

description: There is no dataset uploaded. Data is from a non-EPA source.
DOI: 10.23719/1505444
title: Questionnaire data and results of serum tests, SAFE/NIEHS study

description: The dataset includes personally identifying data from questionnaires (demographic, socioeconomic, behavioral and health data) as well as results of laboratory tests of serum samples for biomarkers of health and antibody responses to pathogens.
DOI: 10.23719/1519343
title: sea fog study data

description: The data includes the input for the WRF-CMAQ coupled model and the model output.
DOI: 10.6084/m9.figshare.23559582.v1
title: Supplementary Material for: Acacetin alleviates cardiac fibrosis via TGF-β1/Smad and AKT/mTOR signal pathways in spontaneous hypertensive rats

description: Introduction: Attenuation of the activation of cardiac fibroblasts contributes to reduce the excessive extracellular matrix deposition and cardiac structural remodeling in hypertensive hearts. Acacetin has shown to play a protective role in doxorubicin-induced cardiomyopathy. The aim of this study was to investigate the potential molecular mechanisms underlying the protective role of acacetin on hypertension-induced fibrosis in the heart. Methods: Echocardiography, pathological morphological and western-blotting techniques were used to evaluate the anti-fibrosis effects in spontaneous hypertensive rat (SHR) which were daily intragastric administrated with acacetin (10mg/kg and 20mg/kg) for 6 weeks. Angiotensin II (Ang II) was used to induce cellular fibrosis in human cardiac fibroblasts in the absence and presence of acacetin treatment for 48 hours. Results: Acacetin alleviated hypertension-induced left ventricular posterior wall thickness and relieved cardiac remodeling in SHR. The expressions of collagen-1, collagen-III and alpha-SMA were remarkedly decreased after treatment with acacetin (n=6, P&lt;0.05). The wound closure rate and the number of migratory cells per field were decreased by 3 and 10 µmol/L acacetin in Ang II-treated fibroblasts (n=6, P &lt; 0.05). Acacetin (10µmol/L) inhibited Ang II-induced upregulation of collagen-1 and collagen-III (n=6, P &lt; 0.05), and downregulation of the expression of alpha-SMA reversed the differentiation of fibroblasts to myofibroblasts. Acacetin also decreased the expression of TGF-β1, the fraction of p-Smad3/Smad3, and p-AKT and p-mTOR, but increased the expression of Smad7 (n=6, P &lt; 0.05). Furthermore, acacetin inhibited TGF-β1 agonist SRI and AKT agonist SC79 caused fibrotic effect. Conclusion: In summary, acacetin inhibits the hypertension-associated cardiac fibrotic processes through regulating TGF-β/Smad3, AKT/mTOR signal transduction pathways.
DOI: 10.23719/1520772
title: CATHGEN Traffic-related air pollution, vascular disease, and epigenetic aging

description: The data contains location information, DNA methylation (transformed into epigenetic aging biomakers), dates of examination, demographics, disease diagnoses, and traffic-related air pollution exposures. It is stored as a series of data frames suitable for use in the R programming language.
DOI: 10.23719/1503856
title: Final Transcripts for River Metrics

description: Plain text of focus group transcripts
DOI: 10.23719/1504530
title: Selecting a Minimal set of Androgen Receptor Assays for Screening Chemicals

description: Screening certain environmental chemicals for their ability to interact with endocrine targets, including the androgen receptor (AR), is an important global concern. We previously developed a model using a battery of eleven in vitro AR assays to predict in vivo AR activity. Here we describe a revised mathematical modelling approach that also incorporates data from newly available assays and demonstrate that subsets of assays can provide close to the same level of predictivity. These subset models are evaluated against the full model using 1820 chemicals, as well as in vitro and in vivo reference chemicals from the literature.
DOI: 10.23719/1518896
title: National Birth Defect Prevention Study Protocol for Public Access and Data Sharing

description: Protocol for requesting public access to these data via CDC.
DOI: 10.23719/1419835
title: Toxoplasma gondii, greenspaces and biomarkers of allostatic load

description: Residential greenness, biomarkers of chronic stress and allostatic load, demographic and health characteristics, and Toxoplasma gondii serostatus data on 300 individuals
DOI: 10.23719/1520934
title: Link to supplemental material including all the data needed to replicate the analysis.

description: This is a link to the supplemental material from the manuscript that includes all of the data and R code needed to replicate the analysis.
DOI: 10.23719/1518682
title: Cormier, S.M., 2017. Dataset for: A Field-based Model of the Relationship Between Extirpation of Salt-intolerant Benthic Invertebrates and Background Conductivity. USEPA Environmental Dataset Gateway.  https://doi.org/10.23719/1371707

description: Data sets and individual XCD results used to develop the field-based benchmarks are available at the U.S. EPA Environmental Dataset Gateway (https://doi.org/10.23719/1371707) (Cormier, 2017). Data are contained in three zip files. The folder “Biological.zip” contains occurrences of benthic invertebrate genera in 24 state data sets.  This paper uses only the data from West Virginia ecoregions 69 and 70. The folder “Environmental.zip” contains environmental data sorted into 24 data sets. The folder “model.zip” contains the calculated XC95 values, probability of observation plots as generalized additive models, and the cumulative frequency distribution for benthic invertebrate genera from WV69 and 70 plus data sets used to develop other models not discussed in this paper. 

A spreadsheet for calculating XC95 values and XCD05 is described in Cormier et al. (2018c). The tools, data sets, example calculations, and example outputs are available online at https://wiley.figshare.com/ieam and https://github.com/smcormier/Biological-Extirpation-Analysis-Tools-BEAT/releases/tag/v.1.0.2. Alternatively, calculation of XC95, GAM plots, XCD05 can be calculated using batch R-code. Similarly, the R-code and data sets are available on GitHub (https://github.com/leppott/XC95).
DOI: 10.23719/1520777
title: Genome Sequence Data Set02

description: The Whole Genome Shotgun project has been deposited in DDBJ/ENA/GenBank under the BioProject PRJNA487286 with the following accession numbers CP061840 (chromosome) and CP061841 (plasmid). The raw sequence reads have been submitted to the NCBI SRA under the accession numbers SRR13076822 and SRR13076823.
DOI: 10.23719/1519287
title: Burrow Geometry and Hazards: Case Histories of GPR for Mapping Animal Burrows

description: The data are GPR records
DOI: 10.23719/1520967
title: Fractured Rock Geophysics Method Selection Tool Software

description: This software was developed in collaboration with the USGS
DOI: 10.23719/1520554
title: Case Histories of GPR for Animal Burrows Mapping and Geometry

description: Geophysical ground penetrating radar data.
DOI: 10.23719/1518912
title: Geophysical and hydrological data for Fredericktown, MO proposed landfill site characterization

description: Geophysical and hydrological data
DOI: 10.23719/1520963
title: Patient records of  pulmonary isolation of Nontuberculous Mycobacteria (NTM) 

description: Dataset includes patient records of pulmonary isolation of Nontuberculous Mycobacteria (NTM) from North Carolina State Laboratory of Public Health for the years 2006-2010
DOI: 10.23719/1520964
title: patient records of  pulmonary isolation of Nontuberculous Mycobacteria (NTM) at the block level

description: This dataset contains patient records of  pulmonary isolation of Nontuberculous Mycobacteria (NTM) from North Carolina State Laboratory of Public Health, local soil data from the Soil Survey Geographic Database (SSURGO, Natural Resources Conservation Service, United States Department of Agriculture), land use data from the 2011 National Land Cover Database (NLCD), paved and dirt road data from the 2010 Navteq street dataset, and census-block level characteristics from the U.S. Census. The data is aggregated at the census-block level.
DOI: 10.23719/1517581
title: Predicted Background Conductivity Data 

description: This "Predicted Background Conductivity" view consists of a shapefile derived from National Hydrography Dataset Plus Version 2.0 which displays modeled natural background conductivity for the continental United States.
The displayed information is based on specific conductivity predictions for stream segments in the contiguous United States from the Natural Background Specific Conductivity (NBSC) model. The NBSC model was developed using a random forest modeling approach and enables comparison with measured in-stream conductivity. Geology, soil, vegetation, climate and other empirically measured data were used as inputs. The NBSC model was designed for streams with natural background SC < 2000 µS/cm.  Above this level (typical for freshwater), NBSC model estimates may be less reliable.  Data for some parameters that affect background SC were not readily available and were therefore not included in the model. These include freshwater and marine interfaces, natural mineral springs, salt deposits which may affect groundwater and streams, and other natural sources of salts.  In such areas, the model is likely to underestimate SC. Local knowledge is often necessary to assess differences between predicted and measured background SC. More information about the model and datasets can be found at Freshwater Explorer Story Metadata.
The calculated predicted background conductivity for individual stream segments in the contiguous U.S.A. and metadata are accessible from the ArcGIS platform on Predicted Background Conductivity Data.  Data is available as table (from Data) or in by pointing and clicking on a stream segment (from Visualization) (https://arcg.is/9vnrv).  This data set is used in the Freshwater Explorer Beta 0.1 which on Jan. 2020 is password protected but can be obtained by requesting access from cormier.susan@epa.gov and then using the link: https://arcg.is/KHb9S.
DOI: 10.23719/1518712
title: Challenges and Opportunities for Translational Research on Congenital Anomalies of External Genitalia: Summary of an NIDDK/AUA Workshop

description: This was a summary article from a workshop and did not produce new data.
DOI: 10.23719/1506013
title:  ghioandrew_fulvicacid_fig5A.xlsx 

description: Excel files for "A fulvic acid-like substance participates in the pro-inflammatory effects of cigarette smoke and wood smoke particles"
DOI: 10.23719/1520484
title: Spatiotemporal variability of ammonia across the contiguous United States

description: These data are monthly mean annual CMAQ simulations as described in the manuscript.
DOI: 10.26179/jn6j-pn08
title: Cardiovascular Research in Antartica
DOI: 10.23719/1520454
title: Bioactivity screening of environmental chemicals using imaging-based high-throughput phenotypic profiling

description: In the present study, we adapted an existing phenotypic profiling assay (“Cell Painting”, (Bray et al., 2016)) to be compatible with in-house microfluidics capabilities for 384-well culture format, chemical exposures and fluorescent cytochemistry in order to facilitate concentration-response screening of several hundred environmental chemicals. In this assay, human-derived cells were labeled with multiple fluorescent probes to visualize various subcellular organelles and structural features. High content image analysis workflows were used to measure hundreds of morphological features at the level of the individual cell (i.e. shape of the cells, intensity, texture and distribution of fluorescent labels, etc.). The resultant data were then used to calculate well-level summary values, perform high-throughput concentration-response modeling and generate phenotypic response profiles. First, we identified and screened a set of candidate phenotypic reference chemicals for use as plate-based controls for evaluating HTPP assay performance during large-scale screening studies and identified an optimal exposure duration for HTPP screening. Second, we screened a set of 462 environmental chemicals in the U-2 OS cell model and derived in vitro potency estimates for bioactivity of all active chemicals. In addition, we demonstrated the technical reproducibility of the HTPP assay in concentration-response screening mode using the previously identified phenotypic reference chemicals. Next, we used reverse dosimetry to calculate administered equivalent doses (AEDs) corresponding to the thresholds for chemical bioactivity and compared those values to in vivo effect values from mammalian toxicity studies.
DOI: 10.23719/1519060
title: Total column NO2 from ground based pandora spectrometers at nine locations across the New York City metropolitan. 

description: Airborne and ground-based Pandora spectrometer NO2 column measurements were collected during the 2018 Long Island Sound Tropospheric Ozone Study (LISTOS) in the New York City/Long Island Sound region, which coincided with early observations from the Sentinel-5P TROPOspheric Monitoring Instrument (TROPOMI) instrument. Both airborne- and ground-based measurements are used to evaluate the TROPOMI NO2 Tropospheric Vertical Column (TrVC) product v1.2 in this region, which has high spatial and temporal heterogeneity in NO2. First, airborne and Pandora TrVCs are compared to evaluate the uncertainty of the airborne TrVC and establish the spatial representativeness of the Pandora observations. The 171 coincidences between Pandora and airborne TrVCs are found to be highly correlated (r2= 0.92 and slope of 1.03), with the largest individual differences being associated with high temporal and/or spatial variability. These reference measurements (Pandora and airborne) are complementary with respect to temporal coverage and spatial representativity. Pandora spectrometers can provide continuous long-term measurements but may lack areal representativity when operated in direct-sun mode. Airborne spectrometers are typically only deployed for short periods of time, but their observations are more spatially representative of the satellite measurements with the added capability of retrieving at subpixel resolutions of 250 m × 250 m over the entire TROPOMI pixels they overfly. Thus, airborne data are more correlated with TROPOMI measurements (r2=0.96) than Pandora measurements are with TROPOMI (r2=0.84). The largest outliers between TROPOMI and the reference measurements appear to stem from too spatially coarse a priori surface reflectivity (0.5∘) over bright urban scenes. In this work, this results during cloud-free scenes that, at times, are affected by errors in the TROPOMI cloud pressure retrieval impacting the calculation of tropospheric air mass factors. This factor causes a high bias in TROPOMI TrVCs of 4 %–11 %. Excluding these cloud-impacted points, TROPOMI has an overall low bias of 19 %–33 % during the LISTOS timeframe of June–September 2018. Part of this low bias is caused by coarse a priori profile input from the TM5-MP model; replacing these profiles with those from a 12 km North American Model–Community Multiscale Air Quality (NAMCMAQ) analysis results in a 12 %–14 % increase in the TrVCs. Even with this improvement, the TROPOMI-NAMCMAQ TrVCs have a 7 %–19 % low bias, indicating needed improvement in a priori assumptions in the air mass factor calculation. Future work should explore additional impacts of a priori inputs to further assess the remaining low biases in TROPOMI using these datasets.
DOI: 10.23719/1518646
title: Pend Oreille River temperature and FLIR

description: Water temperature data from the Pend Oreille River, Washington and Idaho, 2016-2018
The data were collected summer, 2016, 2017, and 2018. Continuous temperature loggers were deployed along the Pend Oreille River between Albeni Falls Dam and the Box Canyon Dam. Loggers were checked every 1-2 weeks throughout the summer.
DOI: 10.23719/1517805
title: Raster outputs in support of Sea Level Affecting Marshes Model (SLAMM) projections for salt marshes of the Lower Delaware Bay

description: These raster files are associated with the SLAMM projections presented in the EPA report, "Application of the Sea-Level Affecting Marshes Model (SLAMM) to the Lower Delaware Bay, with a Focus on Salt Marsh Habitat" (https://cfpub.epa.gov/si/si_public_record_report.cfm?Lab=NCEA&dirEntryId=344746). A subset of these projections are in turn presented in the journal article associated with the ScienceHub entry, "Framework for assessing salt marsh vulnerability to sea level rise to support management decision making: Delaware Bay case study".
DOI: 10.23719/1520919
title: Phenotypic Profiling of Reference Chemicals across Biologically Diverse Cell Types Using the Cell Painting Assay

description: Cell Painting is a high-throughput, phenotypic profiling assay that uses fluorescent cytochemistry o visualize a variety of organelles and high-content imaging to derive a large number of morphological features at the single cell level. Here, we used the Cell Painting assay to characterize the phenotypic effects of sixteen phenotypic reference chemicals in concentration- response screening mode across six biologically diverse human-derived cell lines (U-2 OS, MCF7, HepG2, A549, HTB-9, ARPE-19). All cell lines were labeled using the same cytochemistry protocol and the same set of phenotypic features were calculated. We found it necessary to optimize image acquisition settings and cell segmentation parameters for each cell type but did not adjust the cytochemistry protocol. For some reference chemicals, similar subsets of phenotypic features corresponding to a particular organelle were associated with the highest effect magnitudes in each affected cell type. Overall, for certain chemicals the Cell Painting assay yielded qualitatively similar biological activity profiles across a group of diverse, morphologically distinct human-derived cell lines without the requirement for cell-type specific optimization of cytochemistry protocols.
DOI: 10.23719/1518728
title: Migration corridor simulation - for second paper

description: The model scenario and associated outputs of the case study used to illustrate the migration corridor simulation model demonstrating fish fitness outcomes.
DOI: 10.23719/1519040
title: Fish bio-energetics model metadata

description: The Oregon stream temperatures used in Fig. 1 were sourced from 58 sites monitored by the Oregon Department of Environmental Quality and 17 sites monitored by The United States Geological Survey. These data are publicly available at https://www.oregon.gov/deq/wq/Pages/WQdata.aspx and https://waterdata.usgs.gov/nwis/sw, respectively. The water temperature data used in Figs. 2–4 are posted on GitHub at https://github.com/chris3jordan/Growth-Potential.
The code for processing water temperature and growth potential data for Figs. 2–4 is posted on GitHub at https://github.com/chris3jordan/Growth-Potential. The code for the numerical simulation is posted on GitHub at https://github.com/aimeefullerton/growth_regime_IBM.
DOI: 10.23719/1504465
title: Application of a multiplex salivary immunoassay to detect sporadic incident norovirus infections 

description: Epidemiology data from beachgoers including demographic details. Results from saliva tests for markers of  infection with waterborne pathogens
DOI: 10.23719/1520946
title: Assessment of Mercury Cycling in the St Louis River, MN using Mercury and Food Web (Carbon and Nitrogen) Stable Isotopes: U.S. Geological Survey Data Release

description: Mercury concentration, mercury stable isotope ratio, and carbon and nitrogen stable isotope ratio data as applicable for sediment, water, invertebrates, and fish collected from the St. Louis River Area of Concern (MN-WI) and the associated reference site, the lower Bad River (WI).
DOI: 10.5281/zenodo.7949946
title: Dataset for the publication 'Enset landrace diversity in major enset growing regions of Southern Ethiopia'

description: Enset (<em>Ensete ventricosum</em> (Welw.) Cheesman) is a major food security crop of the Southern Ethiopian highlands, where it is cultivated on small-holder subsistence farms. Data of survey results through interviews with 375 households is presented, covering 20 communities (kebeles) and eight ethnic groups, along an altitudinal range of 1,500 to 3,000 masl across the main enset-producing belt in Southern Ethiopia. A total of 296 locally named enset landraces were recorded. For each landrace, a number of descriptive traits (as reported by farmers) are available, as is the enset landrace composition of each farm. This data accompanies the publication ‘Blomme G, Kearsley E, Buta S, Chala A, Kebede R, Addis T, Yemataw Z. (2023). Enset landrace diversity in major enset growing regions of Southern Ethiopia. African Crop Science Journal, 31, 279-299’.