AndreaBozzo/ceres-open-data-index huggingface dataset:
Trends in non-native aquatic species richness in the United States reveal shifting patterns of both species introductions and sampling effort

Analysis of spatio-temporal trends in non-native species distributions across the continental United States, based on publicly available distribution data. 

This dataset is associated with the following publication:
Mangiante, M., A. Davis, S. Panlasigui, M. Neilson, I. Pfingsten, P. Fuller, and J. Darling. Trends in nonindigenous aquatic species richness in the United States reveal shifting spatial and temporal patterns of species introductions.   Aquatic Invasions. Regional Euro-Asian Biological Invasions Centre, Helsinki,  FINLAND, 13(3): 323-338, (2018).

Tags: aquatic-invasive-species, biodiversity, enviroatlas, geospatial-analysis, non-indigenous-aquatic-species, non-native-species-richness, sampling-effort, temporal-trends, threatened-and-endangered-species
Organization: U.S. Environmental Protection Agency
Regional Similarities and NOx-related Increases in Biogenic Secondary Organic Aerosol in Summertime Southeastern U.S.

Data set contains CMAQ model output for Look Rock, Tennessee and Centreville, Alabama during summer 2013. 

This dataset is associated with the following publication:
Liu, J., L. Russell, G. Ruggeri, S. Takahama, M. Claflin, P. Ziemann, H. Pye, B. Murphy, L. Xu, N. Ng, K. McKinney, S. Hapsari Budisulistiorini, T. Bertram, A. Nenes, and J. Surratt. Regional Similarities and NOx‐Related Increases in Biogenic Secondary Organic Aerosol in Summertime Southeastern United States.   JOURNAL OF GEOPHYSICAL RESEARCH-ATMOSPHERES. American Geophysical Union, Washington, DC, USA, 123(18): 10,620-10,636, (2018).

Tags: aerosol, cmaq, ftir, nox, pm2-5-air-quality-modeling, soa, soas
Organization: U.S. Environmental Protection Agency
Human Health Impact of Cross-Connections in Non-potable Reuse Systems

Provides estimated event risks and target dilution fractions for cross-connections in non-potable reuse systems. 

This dataset is associated with the following publication:
Schoen, M., M. Jahne, and J. Garland. Human Health Impact of Cross-Connections in Non-Potable Reuse Systems.   WATER. MDPI AG, Basel,  SWITZERLAND, 10(10): 1352, (2018).

Tags: cross-connection, non-potable, onsite, qmra, reclaimed, wastewater
Organization: U.S. Environmental Protection Agency
Assessing threats of non-native species to native freshwater biodiversity: Conservation priorities for the United States

Non-native species pose one of the greatest threats to native biodiversity, and may have particularly severe negative impacts in freshwater ecosystems. Identifying regions of spatial overlap between high freshwater biodiversity value and elevated stress associated with non-native species can thus inform the determination of conservation priorities. Here we employ geospatial analysis of species distribution data at the watershed scale, extracted from publicly available databases, to investigate the potential threat of non-native species to vulnerable aquatic animal taxa across the continental United States. We mapped non-native aquatic plant and animal species richness and an index of cumulative invasion pressure, which weights non-native richness by time since introduction in order to estimate overall negative impact associated with species introductions. These distributions were compared to distributions of native aquatic animal taxa (fish, amphibians, mollusks, and decapods) derived from the International Union for the Conservation of Nature (IUCN) database. To identify hotspots of native biodiversity value we mapped overall species richness, proportion of species listed by IUCN as threatened and endangered, and a community index of species rarity calculated at the watershed scale. An overall priority index allowed identification of watersheds experiencing high pressure from non-native species and also exhibiting high native biodiversity conservation value. While these priority regions are roughly consistent with previously reported attempts to map biodiversity conservation needs across the US, we also recognize novel priority areas characterized by moderate-to-high native diversity but extremely high invasion pressure. We further explore the utility of this approach by comparing priority areas with existing conservation protections as well as projected future threats associated with land use change. Our findings suggest that many regions of elevated freshwater biodiversity value are compromised by high invasion pressure, and also may be poorly safeguarded by existing conservation mechanisms and likely to experience significant additional stresses in the future. 

This dataset is associated with the following publication:
Panlasigui, S., A. Davis, M. Mangiante, and J. Darling. Assessing threats of non-native species to native freshwater biodiversity: Conservation priorities for the United States.   BIOLOGICAL CONSERVATION. Elsevier Science Ltd, New York, NY, USA, 224: 199-208, (2018).

Tags: biodiversity, enviroatlas, freshwater-biodiversity, geospatial-analysis, invasive-species, non-indigenous-aquatic-species, priority-mapping, threatened-and-endangered-species
Organization: U.S. Environmental Protection Agency
CPDat 2017

This dataset represents quantitative data on product chemical composition for >75,000 chemicals contained in >15,000 consumer products. The dataset provided at the FigShare link is fully described in the associated Scientific Data publication (Dionisio et al.). The dataset is presented in the form of a MySQL relational database, which mimics CPDat data available under the 'Exposure' tab of the CompTox Chemistry Dashboard (https://comptox.epa.gov/dashboard). 

This dataset is associated with the following publication:
Dionisio, K., K. Phillips, P. Price, C. Grulke, A. Williams, D. Biryol, T. Hong, and K. Isaacs. The Chemical and Products Database, a resource for exposure-relevant data on chemicals in consumer products.   Scientific Data. Springer Nature Group, New York, NY,  5: 180125, (2018).

Tags: chemical-exposure, consumer-products, exposure-modeling, high-throughput, product-composition
Organization: U.S. Environmental Protection Agency
Influence of uncertainties in burned area estimates on modeled wildland fire PM2.5 and ozone pollution in the contiguous U.S.

Data files used in manuscript - "Influence of burned area uncertainties on modeled wildland fire PM2.5 and ozone pollution in the contiguous U.S.". 

This dataset is associated with the following publication:
Koplitz, S., C. Nolte, G. Pouliot, J. Vukovich, and J. Beidler. Influence of uncertainties in burned area estimates on modeled wildland fire PM2.5 and ozone pollution in the contiguous U.S..   ATMOSPHERIC ENVIRONMENT. Elsevier Science Ltd, New York, NY, USA, 191: 328-339, (2018).

Tags: burned-area, cmaq, ozone, pm2-5, wildland-fires
Organization: U.S. Environmental Protection Agency
Plume encounters that exhibited elevated levels of at least one of the three reactive bromine compounds (Br2, BrNO2, and BrCl).

Plume encounters that exhibited elevated levels of at least one of the three reactive bromine compounds (Br2, BrNO2, and BrCl). 

This dataset is associated with the following publication:
Lee, B., F. Lopez-Hilfiker, J. Schroder, P. Campuzano-Jost, J. Jimenez, E. McDuffie, D. Fibiger, P. Veres, S. Brown, T. Campos, A. Weinheimer, F. Flocke, G. Norris, K. O'Mara, J. Green, M. Fiddler, S. Bililign, V. Shah, L. Jaeglé, and J. Thornton. Airborne Observations of Reactive Inorganic Chlorine and Bromine Species in the Exhaust of Coal‐Fired Power Plants.   JOURNAL OF GEOPHYSICAL RESEARCH-ATMOSPHERES. American Geophysical Union, Washington, DC, USA, 123(19): 11,225-11,237, (2018).

Tags: aircraft, bromine, coal, plume
Organization: U.S. Environmental Protection Agency
The Impacts of Potassium Permanganate and Powdered Activated Carbon on Cyanobacterial Toxin Release and Degradation

Underlying data for figures in the published manuscript. 

This dataset is associated with the following publication:
Dugan, N., S. Smith, and T. Sanan. The Impacts of Potassium Permanganate and Powdered Activated Carbon on Cyanotoxin Release.   Journal AWWA. American Water Works Association, Denver, CO, USA, 110(11): E31-E42, (2018).

Tags: activated-carbon, cyanobacteria, drinking-water-treatment, microcystin, microcystis-aeruginosa, oxidation, potassium-permanganate, toxin
Organization: U.S. Environmental Protection Agency
temperature, relative humidity, and fumigant concentration during fumigation of computers with methyl bromide or methyl iodide and the effect of fumigant on humidity sensors

These files contain time-course data for temperature, relative humidity, and fumigant concentration during the fumigation of computers with methyl bromide or methyl iodide. There is a also a file that shows the effect of fumigation on the sensitivity of the HOBO-U10 RH sensor. 

This dataset is associated with the following publication:
Lee, S., S. Serre, A. Adrion, and R. Scheffrahn. Impact of Sporicidal Fumigation with Methyl Bromide or Methyl Iodide on Electronic Equipment.   JOURNAL OF ENVIRONMENTAL MANAGEMENT. Elsevier Science Ltd, New York, NY, USA, 231: 1021-1027, (2019).

Tags: material-compatibility, methyl-bromide, methyl-iodide, sporicidal-fumigation
Organization: U.S. Environmental Protection Agency
weights of metal coupons before and after fumigation with methyl bromide or methyl iodide

This file contains the masses of metal coupons before and after fumigation with methyl bromide or methyl iodide. 

This dataset is associated with the following publication:
Lee, S., S. Serre, A. Adrion, and R. Scheffrahn. Impact of Sporicidal Fumigation with Methyl Bromide or Methyl Iodide on Electronic Equipment.   JOURNAL OF ENVIRONMENTAL MANAGEMENT. Elsevier Science Ltd, New York, NY, USA, 231: 1021-1027, (2019).

Tags: material-compatibility, methyl-bromide, methyl-iodide, sporicidal-fumigation
Organization: U.S. Environmental Protection Agency
Figure. 2 Data . CUOG wastewater dilution as a function of specific conductivity.

Application of ICP-OES for evaluating energy extraction and production wastewater discharge impacts on surface waters in
Western Pennsylvania Figure 2 data (Pancras et al., Science of the Total Environment 529 (2015) 21–29). 

This dataset is associated with the following publication:
Pancras, J.P., G. Norris , M. Landis , K. Kovalcik , J.K. McGee , and A. Kamal. Application of ICP-OES for Evaluating Energy Extraction and Production Wastewater Discharge Impacts on Surface Waters in Western Pennsylvania.   SCIENCE OF THE TOTAL ENVIRONMENT. Elsevier BV, AMSTERDAM,  NETHERLANDS, 529: 21-29, (2015).

Tags: elemental-composition, flue-gas-desulfurization, hydraulic-fracturing, icp-oes, oil-and-gas-wastewater
Organization: U.S. Environmental Protection Agency
XRD Raw data

XRD Raw data collected. 

This dataset is associated with the following publication:
Nadagouda , M., C. Han , D. Dionysiou, and L. Wang. An innovative zinc oxide-coated zeolite adsorbent for removal of humic acid.   JOURNAL OF HAZARDOUS MATERIALS. Elsevier Science Ltd, New York, NY, USA, 313: 283-290, (2016).

Tags: electrostatic-interaction-humic-acid-water-treatment-zeolite-zinc-oxide-natural-organic-matter
Organization: U.S. Environmental Protection Agency
Sequencing Data for Hospital Metagenomes

FASTA files containing the sequence data and for Assembled contigs (FastA), Predicted genes (FastA), Predicted proteins (FastA), Gene prediction (GFF v2). This dataset is not publicly accessible because: These are sequences that have already been deposited in publicly available databases and therefore we can avoid replication. Also the data is quite large and there are numerous files associated with these entries, which are included in the links below. It can be accessed through the following means: Using the following web links

https://www.ncbi.nlm.nih.gov/bioproject/PRJNA299404	
https://trace.ncbi.nlm.nih.gov/Traces/sra/?study=SRP065069
http://enve-omics.ce.gatech.edu/data/showerheads. Format: The data represent genome sequencing and assembly of 180 different contigs. 

This dataset is associated with the following publication:
Soto-Giron, M.J., L. Rodriguez, C. Luo , M. Elk, H. Ryu, J. Santodomingo , and K. Konstantinidis. Biofilms on Hospital Shower Hoses: Characterization and Implications for Nosocomial Infections.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY. American Society for Microbiology, Washington, DC, USA, 82(9): 2872-2883, (2016).

Tags: drinking-water, hosppital, metagenomes, shower-hoses
Organization: U.S. Environmental Protection Agency
QCL data turf microcosms 09Aug2017

Four turfgrass systems in or near the Pinehurst Resort and Country Club, Sandhills region, North Carolina, USA was sampled. Twenty intact soil cores (5 cm diameter x 10 cm length) were collected from each turfgrass system in January and August 2016, respectively. For each turfgrass system, a total of 12 intact soil cores were used to measure N effluxes during three-week incubation, representing three replicates and four treatments: (1) no N input and 23 °C, (2) low N input (i.e., addition of 5.9 mg N as NH4NO3, equivalent to 30 kg N ha-1) and 23 °C, (3) high N input (i.e., addition of 11.8 mg N as NH4NO3, equivalent to 60 kg N ha-1) and 23 °C, and (4) high N input and 13 °C for winter samples (or 33 °C for summer samples). On day 0, water and NH4NO3 solution were added to the respective soil cores to bring soil moisture to 60% water filled pore space (WFPS). Here, we estimated soil bulk density and moisture content from the other eight intact soil cores and then calculated soil porosity assuming that soil particle density was 2.65 g cm-3. These soil cores were also used for soil pH measurement. 
Soil N2O and CO2 effluxes were measured almost daily via soil cores closed for 2 h and then 30-ml gas samples withdrawn from headspaces using gas-tight push button syringes with one-way luer stopcocks. On day 4, 11, and 18, roughly 80 ml leachate was collected from each soil core after 80 ml distilled water poured slowly to soil surface, drained up to 2 h, and then vacuum pumped out. Nitrous oxide was measured using a dual quantum cascade laser (QCL) N2O measurement system (Model CWQCL-200-D, Aerodyne, Billerica, MA, USA) (Chen et al., 2016). The efflux rate of N2O (µg m-2 h-1) was calculated as: ((Csample-Cair) × M × V) / (r × m × t), where Csample and Cair are the N2O concentrations in the headspace of intact soil core and ambient air (ppbv), respectively; V is the volume of intact soil core headspace (L); M is the molar mass of N2O (g mol-1); r is the molar volume at 1 atm (23.47 L mol-1 at 13 oC, 24.29 L mol-1 at 23 oC, and 25.11 L mol-1 at 33 oC), m is soil core surface area (m2), and t is the incubation time (h). 
The QCL system also provided the mixing ratio of natural abundance of 15N in the center and edge position of N2O, i.e., 15Nα and 15Nβ, respectively. After normalized to total N2O-N concentration, these ratios were used to calculate the natural abundance of 15Nα and 15Nβ of N2O. Then, 15N site preference was estimated by δ15Nα - δ15Nβ and used to help probe the biological source of N2O efflux. 

This dataset is associated with the following publication:
Chen, H., T. Yang, Q. Xia, D. Bowman, D. Williams, J. Walker, and W. Shi. The extent and pathways of nitrogen loss in turfgrass systems: Age impacts.   SCIENCE OF THE TOTAL ENVIRONMENT. Elsevier BV, AMSTERDAM,  NETHERLANDS, 637638: 746-757, (2018).

Tags: chronosequence, reactive-n, soluble-organic-n, temperature, turfgrass
Organization: U.S. Environmental Protection Agency
RNA-sequencing analysis of Douglas-fir transcriptome responses to diesel emissions generated with CeO2 nanoparticle additive

Transcriptome changes of Douglas-fir seedlings were analyzed to investigate molecular impacts of exposure to airborne emissions released from combustion of diesel fuel containing engineered cerium dioxide (CeO2) nanoparticle catalysts (DECe). We analyzed mRNA-sequencing data from exposed one-year-old needles. Our hypothesis is that 2-week chamber exposure to DECe would induce certain distinct transcriptome changes in the needles compared with responses to conventional diesel exhaust (DE) or filtered DECe Gas Phase. Blast2GO gene ontologies (GOs) enriched by significantly up-regulated DECe transcripts were nested within the GOs for DE, however, 93.5% of enriched GOs for significantly down-regulated DECe transcripts were unique. DECe attenuated expression of genes that affect functions of transferases, kinases, transmembrane transporters, transcription factors, diester hydrolases and RNA polymerase III; processes of protein phosphorylation, responses to stimuli, hormones and chemicals, carbohydrate transport, RNA polymerase III transcription, and cellular anion homeostasis; plus, components of the plasma membrane. MapMan analysis also identified RNA regulation of transcription, protein degradation, and lipid metabolism pathways that were enriched with DECe down-regulated transcripts. Divergent DECe treatment effects were associated with significantly elevated needle uptake of cerium. DE affected expression of more genes than DECe. Nevertheless, unique transcriptome profile changes suggest that chronic DECe exposure may adversely affect plant growth and development. 

This dataset is associated with the following publication:
Reichman, J.R., P.T. Rygiewicz, M.G. Johnson, M.A. Bollman, B.M. Smith, Q.T. Krantz, C.J. King, K. Kovalcik, and C.P. Andersen. Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) Transcriptome Profile Changes Induced by Diesel Emissions Generated with CeO2 Nanoparticle Fuel Borne Catalyst.   ENVIRONMENTAL SCIENCE & TECHNOLOGY. American Chemical Society, Washington, DC, USA, 52(17): 10067-10077, (2018).

Tags: ammonium-nitrate, cerium-dioxide, douglas-fir, engineered-nanomaterials-enms, fuel-borne-catalyst, intergenerational-effects, isotope, isotopic-discrimination, nitrogen, pseudotsuga-menziesii, rna-sequencing, transcriptome
Organization: U.S. Environmental Protection Agency
June 2018 version of dataset

These are the data associated with each of the figures in the publication. 

This dataset is associated with the following publication:
Thursby, G., K. Sappington, and M. Etterson. Coupling Toxicokinetic-Toxicodynamic and Population Models for Assessing Aquatic Ecological Risks to Time-Varying Pesticide Exposures.   ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY. Society of Environmental Toxicology and Chemistry, Pensacola, FL, USA, 37(10): 2633-2644, (2018).

Tags: americamysis-bahia, matrix-modeling, population-level-risk-assessment, time-varying-exposures
Organization: U.S. Environmental Protection Agency
Table formatted data for Figures 1, 2, 3, 4, 5, and 6 regarding point of zero charge

This study utilized the Pb- and As-contaminated soils to determine the combined effect of pH with respect to PZC and different rates of P-application on pyromorphite formation, and Pb and arsenic (As) bioaccessibility as impacted by speciation changes. Solution chemistry analysis along with synchrotron-based Pb- and As-speciation, and bioaccessibility treatment effect ratios (TERs) were conducted. 

This dataset is associated with the following publication:
Karna, R., M. Noerpel, T. Luxton, and K. Scheckel. Point of Zero Charge: Role in Pyromorphite Formation and Bioaccessibility of Lead and Arsenic in Phosphate-Amended Soils.   Soil Systems. MDPI AG, Basel,  SWITZERLAND, 2(2): 22, (2018).

Tags: arsenic, in-situ-amendments, lead, metal-bioavailability, synchrotron-speciation
Organization: U.S. Environmental Protection Agency
Ozone-Induced Vascular Contractility and Pulmonary Injury are Differentially Impacted by Diets Enriched with Coconut Oil, Fish Oil, and Olive Oil

This data set is broken up into 2 Excel files.  In one file are all the data pertaining to the vascular and pulmonary effects of ozone exposure in rats fed either a normal diet or diet enriched with coconut oil, fish oil, or olive oil.  The different tabs of the spreadsheet pertain to each figure or table found in the manuscript.  This file was updated on 12/7/17 to reflect changes to Figure 3 in response to reviewers comments following submission to Toxicological Sciences.  In the second file is all the data for Figure 8 pertaining to the global microRNA assessment. 

This dataset is associated with the following publication:
Snow, S., W. Cheng, A. Henriquez, M. Hodge, V. Bass, G. Nelson, G. Carswell, J. Richards, M. Schladweiler, A. Ledbetter, B. Chorley, K. Gowdy, H. Tong, and U. Kodavanti. Ozone-Induced Vascular Contractility and Pulmonary Injury are Differentially Impacted by Diets Enriched with Coconut Oil, Fish Oil, and Olive Oil.   TOXICOLOGICAL SCIENCES. Society of Toxicology, RESTON, VA,  163(1): 57-69, (2018).

Tags: dietary-supplements, fish-oil, ozone, pulmonary-injury, vascular-contractility
Organization: U.S. Environmental Protection Agency
Zinc speciation results

The dataset contains two figures showing the synchrotron X-ray absorption near edge structure data (figure 4) and corresponding linear combination fitting data deciphering the distribution of zinc species (figure 5). 

This dataset is associated with the following publication:
Doolette, C., T. Lund, C. Li, K. Scheckel, E. Donner, P. Kopittke, E. Lombi, and J. Schjoerring. Foliar application of zinc sulphate and zinc EDTA to wheat leaves: differences in mobility, distribution, and speciation.   JOURNAL OF EXPERIMENTAL BOTANY. Oxford University Press, Cary, NC, USA, 69(18): 4469-4481, (2018).

Tags: contaminant-transport, nutrient-enrichment, plant-uptake, synchrotron-speciation, zinc
Organization: U.S. Environmental Protection Agency
Quantitative constraints on autoxidation and dimer formation from direct probing of monoterpene-derived peroxy radical chemistry

Laboratory data supporting "Quantitative constraints on autoxidation and dimer formation from direct probing of monoterpene-derived peroxy radical chemistry" by Zhao, Thornton, and Pye.  

Abstract: Organic peroxy radicals (RO2) are key intermediates in the atmospheric degradation of organic matter and fuel combustion, but to date, few direct studies of specific RO2 in complex reaction systems exist, leading to large gaps in our understanding of their fate. We show, using direct, speciated measurements of a suite of RO2 and gas-phase dimers from O3-initiated oxidation of α-pinene that ~150 gaseous dimers (C16-20H24-34O4-13) are primarily formed through RO2 cross-reactions, with a typical rate constant of 0.75-2×10-12 cm3 molecule-1 s-1 and a lower-limit dimer formation branching ratio of 4%. These findings imply a gaseous dimer yield that varies strongly with nitric oxide (NO) concentrations, of at least 0.2-2.5% by mole (0.5-6.6% by mass) for conditions typical of forested regions with low to moderate anthropogenic influence (i.e., ≤ 50 ppt NO). Given their very low volatility, the gaseous C16-20 dimers provide a potentially important organic medium for initial particle formation, and alone can explain 5-60% of α-pinene secondary organic aerosol mass yields measured at atmospherically relevant particle mass loadings. The responses of RO2, dimers, and highly-oxygenated multifunctional compounds (HOM) to reacted α-pinene concentration and NO imply that an average ~20% of primary α-pinene RO2 from OH reaction and 10% from ozonolysis autoxidize at 3-10 s-1 and ≥ 1 s-1, respectively, confirming both oxidation pathways produce HOM efficiently, even at higher NO concentrations typical of urban areas. Thus, gas-phase dimer formation and RO2 autoxdiation are ubiquitous sources of low-volatility organic compounds capable of contributing significantly to atmospheric new particle formation and growth. 

This dataset is associated with the following publication:
Zhao, Y., J. Thornton, and H. Pye. Quantitative constraints on autoxidation and dimer formation from direct probing of monoterpene-derived peroxy radical chemistry.   PNAS  (PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES). National Academy of Sciences, WASHINGTON, DC, USA, 115(48): 12142-12147, (2018).

Tags: autoxidation, biogenic-voc, dimer, hom, monoterpene, pinene, pm2-5, pm2-5-air-quality-modeling, semivolatile-organic-compounds-svocs, soa
Organization: U.S. Environmental Protection Agency