Find research datasets worth reusing

Inter-Chemical Correlation results for the study: HHEARx2018-2120 (The impact of tobacco smoke exposure and environmental exposures on the pulmonary microbiome and outcomes of critically ill children)

Title: The impact of tobacco smoke exposure and environmental exposures on the pulmonary microbiome and outcomes of critically ill children Species: Homo sapiens Number of samples: 1090 Number of named analytes: 12 Datasource url: https://hheardatacenter.mssm.edu/PublicFile/ViewPublicFile?projectid=42

Inter-Chemical Correlation results for the study: HHEARx2017-1598 (Evaluation of Environmental Exposures in TEDDY)

Title: Evaluation of Environmental Exposures in TEDDY Species: Homo sapiens Number of samples: 1025 Number of named analytes: 45 Datasource url: https://hheardatacenter.mssm.edu/PublicFile/ViewPublicFile?projectid=37

Inter-Chemical Correlation results for the study: HHEARx2016-1461 (ECHO ReCHARGE Study - Environmental Exposures)

Title: ECHO ReCHARGE Study - Environmental Exposures Species: Homo sapiens Number of samples: 1231 Number of named analytes: 75 Datasource url: https://hheardatacenter.mssm.edu/PublicFile/ViewPublicFile?projectid=17

opencc-zeroJun 2024View details →

Inter-Chemical Correlation results for the study: HHEARx2016-1432 (Micronutrient deficiencies, environmental exposures and severe malaria: Risk factors for adverse neurodevelopmental outcomes in Ugandan children)

Title: Micronutrient deficiencies, environmental exposures and severe malaria: Risk factors for adverse neurodevelopmental outcomes in Ugandan children Species: Homo sapiens Number of samples: 1256 Number of named analytes: 51 Datasource url: https://hheardatacenter.mssm.edu/PublicFile/ViewPublicFile?projectid=5

Inter-Chemical Correlation results for the study: HHEARx2017-1839 (Zika Virus Congenital Health Outcomes and the Impact of Maternal Environmental Exposures)

Title: Zika Virus Congenital Health Outcomes and the Impact of Maternal Environmental Exposures Species: Homo sapiens Number of samples: 2705 Number of named analytes: 10 Datasource url: https://hheardatacenter.mssm.edu/PublicFile/ViewPublicFile?projectid=61

opencc-zeroJun 2024View details →

Inter-Chemical Correlation results for the study: HHEARx2016-1407 (Pediatric Inner-City Environmental Exposures at School and Home and Asthma Study)

Title: Pediatric Inner-City Environmental Exposures at School and Home and Asthma Study Species: Homo sapiens Number of samples: 157 Number of named analytes: 28 Datasource url: https://hheardatacenter.mssm.edu/PublicFile/ViewPublicFile?projectid=2

zenodo44/100

Exposure to pesticides data for residents and bystanders, and for environmental risk assessment

In 2014, EFSA has commissioned a study to review and evaluate all published data related to the exposure to pesticides for residents and bystanders and for environmental risk assessment. The aim was to conduct a literature review and to produce a database containing all published data (predominately peer-reviewed publications supplemented by grey-literature) for the last 25-years, which will support the non-dietary exposure assessment to pesticides for bystanders and residents, as well as daily air concentration (vapours and aerosols) of pesticides, drift values from spray, seed and granular applications, and dislodgeable foliar residues. The data has been collated via a systematic and extensive literature review defined and managed according to a pre-defined 'review protocol'. The data was also exported in a format that meets the requirements of the EFSA Data Collection Framework (DCF). Based on quality and relevance criteria, articles and related studies have been selected. For dislodgeable foliar residues the assessment includes 27 articles (containing 49 discrete studies); for air concentrations, 26 articles (containing 84 discrete studies); for resident and bystander exposure, 5 articles (containing 8 discrete studies); and for drift values 55 articles (containing 275 discrete studies).   For dislodgeable foliar residues the data retained covered 17 crops (including grass, glasshouse crops, lucerne, and citrus) and 29 pesticides; for air concentrations the data retained covered 21 crops (including fruit, glasshouse crops, ornamentals, grass, vegetables and cereals) and 39 pesticides. For drift values, the data covers a range of crops and landscapes from cereals, grass and turf, orchards, vineyards and regenerated forestry. The vast majority of the data retrieved applies to field studies for liquid spray drift, measured either as ground deposits or collected at various heights and were conducted using fluorescent tracers rather than pesticides. No data was found for microbials (biopesticides). For resident and bystander exposure, many articles were rejected due to the applied inclusion/exclusion criteria.

opencc-by-4.0May 2017View details →

opencc-by-sa-4.0Jun 2023View details →

XIS: A daily spatiotemporal machine-learning model for environmental exposures in the contiguous United States

These Parquet files contain the outputs used for many analyses and plots in the linked papers. For temperature and humidity, the full sets of observations for cross-validation aren't included because we used restricted-use MADIS data.

opencc-by-4.0Dec 2021View details →

DNA methylation in clonal Duckweed lineages (Lemna minor L.) reflects current and historical environmental exposures.

The following depository contains raw phenotypic data and intermediate DNA methylation data presented in the article "DNA methylation in clonal Duckweed lineages (Lemna minor L.) reflects current and historical environmental exposures." : 1) Raw phenotypic data - Frond_area_Phase1_Phase2 -> Frond area measured at different time points (week 1, 6, 7 and 8) during the experiment. - Frond_number_Phase1_Phase2 -> Frond number measured at different time points (week 1, 6, 7 and 8) during the experiment. 2) Intermediate files obtained from running the epiGBS2 pipeline. The following files are available: - consensus_cluster.renamed.fa ->  epiGBS de novo loci. This file consists of the de novo epiGBS reference sequence file obtained during the de novo reference creation. - methylation.filtMETH -> The filtered DNA methylation data. This data was obtained after filtering the raw DNA methylation data. Cytosines which had a 10X coverage or higher and which were present in 80% of all samples were kept for further analysis. Demultiplexed and raw data were deposited at NCBI: BioProject: PRJNA883550

opencc-by-4.0Aug 2024View details →

An Assessment of the Ocular Toxicity of Two Major Sources of Environmental Exposure

These data contain information on chemicals released in to the air from burn pits in Iraq (waste disposal areas for US military bases) and the 2023 Ohio train derailment in East Palestine. The goals of the study were to 1) predict the effects of exposure to these chemicals on the ocular surface and 2) to call attention to the relationship between environmental events and long-term damage to the surface of the eye—in particular, dry eye disease, which is a known result of workplace chemical exposures. The study employed in silico methods through the ACD Labs Percepta platform, using data from the European Chemical Inventory and the Registry of Toxic Effects of Chemical Substances to model the chemicals’ probability of ocular irritation. Variables include the names of compounds identified from the burn pits and the train derailment, along with their chemical formulas, simplified molecular input line entry system (abbreviated to SMILES), and probability of causing eye irritation.

opencc-by-4.0Oct 2021View details →

Supplementary Material: Assessment of Environmental Pollution and Human Exposure to Pesticides by Wastewater Analysis in a Seven-Year Study in Athens, Greece

Supplementary Material

opencc-by-4.0Dec 2022View details →

Dataset for "Exposure and environmental engagement: A pilot integrating wearable sensors, air quality and citizen science"

The dataset contains anonymised readings of 7 citizens taking air quality measurements using PlumeLabs Flow 2 monitor. Data is for Falmouth/Penryn, and Bristol and it was collected between January 26, 2022 and March 9, 2022. CSV file: <ul> <li>latitude: unit degrees, positive values indicate North hemisphere.</li> <li>longitude, unit degrees, positive values indicate East.</li> <li>AQI: PlumeLabs' Air Quality Index.</li> <li>site: A refers to Falmouth/Penryn(UK), B refers to Bristol (UK).</li> <li>count: auxiliary variable that indicates that the record was comprised of a single reading.</li> </ul> Jupyter notebook: The air quality analysis was conducted with Python 3.9.16 alongside numpy 1.24.3, pandas 2.0.2, matplotlib 3.7.1, and cartopy 0.21.1 (background tiles by OpenStreetMaps).

zenodo36/100

Long-term changes in pituitary gene expression following developmental exposure to environmental contaminants (BPS, BDE-47, or TBBPA) in male mice.

Experimental DesignIn this study we evaluate the long-term gene expression changes in pituitary in male mice exposed developmentally to one of three known endocrine disrupting chemicals: bisphenol-S (BPS), 2,2',4,4'-tetrabromodiphenyl ether (BDE-47), and 3,3',5,5'-tetrabromobisphenol A (TBBPA).  Male mice were exposed to chemical treatment through their mothers' during pregnancy (umbilical blood flow) and nursing, from pregnancy day 8 through weaning at postnatal day 21 (PND21). Each chemical exposure was calculated to equal 0.2mg/kg bw/day. The details of exposure protocol are described elsewhere (Kim et al, 2015). The male pups were allowed to grow untreated until adulthood at PND140. At PND140, male mice were euthanized, then their pituitaries removed, snap frozen in liquid nitrogen, and then stored at -80°C. The data-files described below represent major steps of our analysis:1. FASTQ files for mouse pituitary RNA-seq data.Male mouse pituitary RNA was isolated using a Trizol protocol, checked for purity and concentration and then processed for mRNA sequencing using the Illumina TruSeq kit and protocol (TruSeq Stranded mRNA LP, Cat # 20020594 and TruSeq RNA Sg Idx SetB, Cat # 20020493, Illumina, San Diego, CA) following the manufacturer's recommended procedures. High throughput sequencing was conducted using the NextSeq500 sequencing system. cDNA libraries were single-end sequenced in 76 cycles using a NSQ 500/550 Hi Output KT v2.5 (Cat #20024906 Illumina, San-Diego, CA) in one multiplex run (N=3/exposure group).  Read filtering, trimming, and de-multiplexing were performed using the BaseSpace cloud service by Illumina (<a href="https://basespace.illumina.com/home/index">https://basespace.illumina.com/home/index</a>, RRID:SCR_011881). Processed reads were mapped to the mouse reference genome (MM10) using the RNA-Seq Alignment v. 1.1.1. software with Bowtie 2. Each FASTQ file is a compressed file representing data from one sequencing flow cell lane for each sample (4 files per sample). Sample identifiers are coded for treatment: X = Vehicle control, R = TBBPA, C = BDE-47, E = BPS. 2. Differential expression data.Aligned reads were used to assemble transcripts and analyze differential expression using Cufflinks Assembly & DE v. 2.1.0. package. Reads aligned to known annotated regions for both control and exposed groups were used to calculate log2 FPKM ratios.  Differentially expressed genes were identified as genes altered with false discovery rate significance ≤ 0.05 (FDR, q ≤ 0.05).  Data on all exposure groups are shown in different sheets of the same file - Differential_expression.xlsx.3. Enrichment of biological categories associated with DEGs induced by chemical exposures. All differentially expressed genes were uploaded to Metascape for the analysis of enriched biological categories using default settings. Results of Metascape analysis are shown in two MS Excel files per exposure group, one showing negatively enriched categories and one positively enriched categories. The title of each file consists of three parts connected via underscore sign: the name of the chemical, the direction of enrichment, and the name of analysis - metascape (e.g., BDE-47_negative_metascape.xlsx).4. Pathway analysis for chemical exposures.All differentially expressed genes were uploaded to Ingenuity Pathway Analysis and enriched canonical pathways were identified  using default settings . Altered molecular or disease pathways, their p-values, and associated differentially expressed genes are provided for each exposure. Data for all exposure groups are shown in different sheets of the same file - IPA_pathway_analysis.xlsx.References:Kim B, Colon E, Chawla S, Vandenberg LN, Suvorov A. Endocrine disruptors alter social behaviors and indirectly influence social hierarchies via changes in body weight. Environ Health. 2015 Aug 5;14:64. doi: 10.1186/s12940-015-0051-6. PMID: 26242739; PMCID: PMC4524022.

opencc-by-4.0Nov 2023View details →

zenodo36/100

A Modeling Framework for Near-Road Population Exposure to Traffic-Related PM2.5 and Environmental Equity Analysis: A Case Study in Atlanta, Georgia

This is the dataset for the NCST project "A Modeling Framework for Near-Road Population Exposure to Traffic-Related PM2.5 and Environmental Equity Analysis: A Case Study in Atlanta, Georgia" by the Georgia Tech research team.   Here is the abstract of the research:  In this study, a modeling framework for population exposure to traffic-related PM2.5 with high spatiotemporal resolution is proposed and applied to the I-575/I-75 Northwest Corridor (NWC) in Atlanta, GA, for environmental equity analysis.  The analyses retrieved trip data from the Atlanta Regional Commission’s (ARC) Activity-Based Model 2020 (ABM2020), after implementing path retention algorithms (Zhao, et al., 2019) to generate individual travel paths for more than 20 million predicted vehicle trips.  Emission rates for each link were retrieved from MOVES-Matrix given the ABM link speed and facility type, the ARC’s county-level fleet composition data, and regional fuel properties and I&M program parameters.  High-resolution downwind concentration profiles were predicted using EPA’s AERMOD microscale dispersion model with AERMET meteorology profiles for a huge array of receptors.  Trip-end locations were derived from the ABM trip data, and the on-road trajectories for each person-trip (vehicle trace data) were derived from the travel paths through network. ABM synthetic household and person data were used in demographic assessment, and linked to representative household latitude and longitude locations in the Epsilon 2019 household demographic dataset.  Individual exposure to traffic-related PM2.5 in time and space (average hourly concentration) was assessed by overlaying the second-by-second person location profiles (for 24 hours) against the hourly predicted PM2.5 concentration profiles.  The analyses summarize the results across 16 demographic groups and the aggregate population exposure are compared to assess potential impact differences across demographics.  High-income households in the corridor were exposed to less traffic-related air pollution as they tended to live further from the freeways.  The analyses did not reveal large disproportionate negative impacts on low income groups along this specific corridor, but lager disproportionate negative impacts are expected elsewhere in the metro area due to the spatial clustering of income groups along other corridors. Overall, the research demonstrates the applicability of the modeling framework and describes how the various elements (e.g., link screening, dispersion modeling, path tracing, etc.) are optimized on the supercomputing cluster.

opencc-by-4.0Oct 2024View details →

opencc-zeroOct 2022View details →

Magnitude-duration relationships of physiological sensitivity and environmental exposure improve climate change vulnerability assessments

Integrating thermal physiology with environmental temperature is essential to understanding distributions of species and vulnerability to climate change. Warming tolerance—the difference between an organism's maximum thermal tolerance (Tmax) and maximum habitat temperature (Thab)—is frequently used to integrate organismal sensitivity and environmental exposure. Traditionally, applications of warming tolerance define Tmax and Thab as invariable magnitudes, yet tolerance magnitude depends on exposure duration and diel temperature cycles expose organisms to a range of temperature magnitudes and durations. How traditional (i.e., acute) estimates of warming tolerance compare to estimates from prolonged exposures remains poorly understood. In this study, magnitude-duration curves for tolerances of one cold-water, two cool-water, and one warm-water species of freshwater fish were compiled from the literature and compared to magnitude-duration exposures from 66 streams across the eastern United States. Warming tolerances were estimated for exposure durations spanning 0.01 to 24 hours. Current acute (0.01 hours) warming tolerances ranged from median 6.30°C for the cold-water species to 9.68°C for the warm-water species. The lowest warming tolerances corresponded to prolonged exposures lasting median 3.85 to 5.30 hours among species and were 2.51 to 4.38°C lower than acute estimates. Although acute estimates remained positive in historically occupied and unoccupied streams (6.30°C versus 2.33°C), estimates based on prolonged exposure were positive at occupied streams of the cold-water species but transitioned to negative in unoccupied streams (2.19°C versus -1.12°C). Acute warming tolerances for the cold-water species also remained positive under future climate (6.29 to 4.23°C) but approached zero at prolonged durations (2.19 to 0.09°C) and transitioned to negative for 47.2% of streams. Results demonstrate that acute measures of Tmax and Thab overestimate warming tolerances and therefore underestimate climate change vulnerability. Integrating magnitude-duration relationships into warming tolerance estimates can elucidate physiological mechanisms underlying species distributions and can improve accuracy of climate change vulnerability assessments.

opencc-zeroDec 2022View details →

Can short-term data accurately model long-term environmental exposures? Investigating the multigenerational adaptation potential of Daphnia magna to environmental concentrations of organic ultraviolet filters

Organic ultraviolet filters (UVFs) are contaminants of concern, ubiquitously found in many aquatic environments due to their use in personal care products to protect against ultraviolet radiation. Research regarding the toxicity of UVFs such as avobenzone, octocrylene and oxybenzone indicates that these chemicals may pose a threat to invertebrate species; however, minimal long-term studies have been conducted to determine how these UVFs may affect continuously exposed populations. The present study modeled the effects of a 5-generation exposure of Daphnia magna to these UVFs at environmental concentrations. Avobenzone and octocrylene resulted in minor, transient decreases in reproduction and wet mass. Oxybenzone exposure resulted in > 40% mortality, 46% decreased reproduction and 4-fold greater reproductive failure over the F0 and F1 generations; however, normal function was largely regained by the F2 generation. These results indicate that Daphnia are able to acclimate over long-term exposures to concentrations of 6.59 μg/L avobenzone, ~0.6 μg/L octocrylene or 16.5 μg/L oxybenzone. This suggests that short-term studies indicating high toxicity may not accurately represent long-term outcomes in wild populations, adding additional complexity to risk assessment practices at a time when many regions are considering or implementing UVF bans in order to protect these most sensitive invertebrate species.

zenodo36/100

Internal exposure of Flemish teenagers to environmental pollutants: results of the Flemish Environment and Health Study

Supplementary Information of manuscript "Internal exposure of Flemish teenagers to environmental pollutants: results of the Flemish Environment and Health Study 2017-2018 (FLEHS IV) "

opencc-by-4.0Jan 2023View details →

opencc-zeroOct 2023View details →

Overcoming the congenitally disadvantageous mutation through adaptation to environmental UV exposure in land snails

Congenital fitness-disadvantageous mutations are not maintained in the population; they are purged from the population through processes such as purifying selection. However, these mutations could persist in the population as polymorphisms when it is advantageous for the individuals carrying them to adapt to a specific external environment. We tested this hypothesis using the dimorphic land snail Euhadra peliomphala simodae in Japan; these snails have dark or bright-coloured shells. The survival rate of dark snails at hatching was lower than that of the bright ones, as observed in the F1 progenies produced through crossing. Dark snails have a congenital fitness-disadvantageous mutation; however, they also have protection against ultraviolet radiation. They have a higher survival rate than the bright snails in a UV environment, as observed using the UV exposure experiments and UV transmittance measurements. This is a good example of a congenitally disadvantageous mutation that is advantageous for adapting to the external environment. These results explain the maintenance of polymorphism and highlight the genotypic and phenotypic diversity in the wild population.