cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15485/1609128
title: Dual-domain column experiment data for aquifer sediments from Riverton, WY, 2018, examining groundwater mobility and speciation of arsenic

description: This dataset is a compilation of the data that supported the publication of Kumar et al. (2020) in ES&T, http://dx.doi.org/10.1021/acs.est.9b06502. The data is from a dual domain column experiment examining the impact of redox interfaces on arsenic speciation and mobility in natural groundwater sediments that were collected at the Riverton, WY, US Department of Energy Office of Legacy Management field site. The abstract for the associated publication reads:Groundwater contamination by As from natural and anthropogenic sources is a world-wide concern. Redox heterogeneities over space and time are common and can influence the molecular-level speciation of As, and thus As release/retention, but are largely unexplored. Here we present results from a dual-domain column experiment, with natural organic-rich, fine-grained, and sulfidic sediments embedded as lenses (referred to as ‘reducing lenses’) within natural aquifer sand. We show that redox interfaces in sulfur-rich, alkaline aquifers may release concerning levels of As, even when sediment As concentration is low (&lt;2 mg/kg), due to the formation of mobile thioarsenates at aqueous sulfide:Fe molar ratios &lt;1. In our experiments, this behavior occurred in the aquifer sand between reducing lenses and was attributed to the spreading of sulfidic conditions and subsequent Fe reductive dissolution. In contrast, inside reducing lenses (and some locations in the aquifer) the aqueous sulfide:Fe molar ratios exceeded 1 and aqueous sulfide:As molar ratios exceeded 100, which partitioned As(III)-S to the solid phase (associated with organics or as realgar (As4S4)). These results highlight the importance of thioarsenates in natural sediments and indicate that redox interfaces and sediment heterogeneities could locally degrade groundwater quality, even in aquifers with unconcerning solid phase As concentrations.
DOI: 10.15485/1631972
title: Depth-resolved soil data from DOE-LM Riverton Wyoming site, April-September 2017

description: Averaged (from 3 to 5 replicates) and QA/QC:d data for soil cores taken roughly every month in the period April 5 to September 13 in 2017 at a location close to DOE Legacy Management well 855 at the Riverton, Wyoming floodplain site. The groundwater at this site exhibits persistent U, Mo, and sulfate plumes and is one of the field sites in focus for the SLAC Groundwater Quality SFA program. Cores were separated into 5-20 cm segments based on soil horizonation and each segment was subsampled for microbial analyses (data available at the NCBI Single Read Archive (SRA) Database, https://www.ncbi.nlm.nih.gov/sra/, BioProject ID# PRJNA626616) in addition to the soil analyses included in this dataset. The soil analyses dataset includes aerobic and anaerobic respiration rate estimates (MicroResp method), water content estimates (on collected samples, not in situ), total C, N, S, Ca, K, Mg, Na, Fe, As, Mo, U, and organic-C concentrations, water extractable concentrations of the same elements, and HCl-extractable Fe(II) concentrations.There are four files included in this data package: metadataFile.csv, avgDataFile.csv, methodFile.csv, and RVT2017soilData.xlsx. The excel file contains the same information as the individual csv-files (in separate tabs).
DOI: 10.15485/1804744
title: Stochastic simulations of temporally and spatially variable Fe cycling within a floodplain aquifer

description: This data package contains model input and output files for local and global sensitivity analysis (SA) of a reactive transport model simulating redox cycling within a floodplain aquifer. The reaction network is implemented in CrunchFlow and focuses on spatially and temporally heterogeneous Fe cycling, though it contains several other species and redox pathways (37 aqueous species and 7 minerals in total). The package contains data from 600 Monte Carlo simulations (for global SA) and 104 one-at-a-time simulations (for local SA). It includes all input files required to run the CrunchFlow model, as well as limited model output – .csv files containing time series of primary species concentrations at 21 grid cells within the domain. These time series files contain the following species: H+, CO32-, SO42-, Cl-, Ca2+, Mg2+, Na+, K+, Fe(II), Fe(III), HS-, CH3COO-, O2(aq), S(aq), and Br-.These data were used to demonstrate the application of a novel form of global SA, distance-based generalized sensitivity analysis (DGSA) to a reactive transport model. The 2D model simulates the export of reduced species from pockets of fine-grained, organic-rich sediments embedded in a coarse sand aquifer. Stochastic simulations jointly varied 17 key model input parameters across several orders of magnitude, including the spatial variability of each parameter. DGSA on the model results reveal that the amplitude and variability of exported Fe(II) are most sensitive to the interaction between sand permeability and individual reaction rates. By contrast, the propagation of reducing conditions downgradient from the fine-grained lenses depends most heavily on the rate of dissolved organic carbon and sulfate release from the fines.
DOI: 10.15485/1810547
title: Total metals & anion concentration data; Slate River floodplain, Crested Butte, CO; May 2020-September 2020

description: This data package includes processed and undiluted measurements for metal and anion concentrations from pore water (groundwater) samples from the Slate River floodplain of Crested Butte, CO, a focus field site for the SLAC Floodplain Hydro-Biogeochemistry SFA. The data was generated as part of the work targeting the overarching research question for the SLAC SFA: How do ubiquitous subsurface interfaces mediate molecular-scale biogeochemical processes and groundwater quality in floodplains and watersheds? Samples were collected between May and September of 2020. These measurements were all recorded at the Arizona Laboratory for Emerging Contaminants (ALEC) at the University of Arizona located in Tucson, AZ. Groundwater samples were extracted from a network of installed rhizon (Rhizosphere Research Products, part no. 19.60.21F, 0.6 micrometer mesh size) and piezometer wells within the river floodplain. All water samples were shaded from sun exposure during extraction from the subsurface and preserved at 4C until measured at ALEC.Analysis by ICP-MS:Measurements for total metals were made on the Agilent 7700x ICP-MS (for total metals) – Agilent Technologies, Santa Clara, CA.The analytical QA/QC protocol was adapted from US EPA Method 200.8 for analysis by ICP-MS. Calibration standards were prepared from multi-element stock solution (Sigma-Aldrich Multielement standard solution for ICP, St. Louis, MO) using matrix matched to sample solutions (either 2% HCl or HNO3 from AriStar Plus,grade acids from VWR Scientific). Calibration curves include at least 7 points with correlation coefficients &gt; 0.995. The QC protocol includes a continuing calibration blank (CCB), a continuing calibration verification (CCV) solution and at least one quality control sample (QCS) to be analyzed just after calibration and again after every 12 samples and at the completion of the run. The QCS solutions are from an independent source, such as NIST SRM 1643e - Trace Elements in Water, or QCS solutions from High Purity Standards (Charleston, SC). Acceptable QC responses must be between 90 and 110% of the certified value. An internal standard (Rh) is added via on-line addition into the sample line using a mixing tee.Analysis by Ion Chromatography (Anions):The protocol follows Method 4110 in Standard Methods for Examination of Water and Wastewater.The instrument used is the Thermo Scientific Dionex ICS-6000 using AS+AG22 column set for anion analysis with isocratic method using sodium carbonate eluent. Detection is by chemical suppression of eluent conductivity. Quality control solutions and mixed analyte standards purchased from Inorganic Ventures, Christiansburg, VA.All files are in csv format.
DOI: 10.15485/1829500
title: Specific conductivity, pH, dissolved oxygen, water temperature and alkalinity in-situ data; Slate River floodplain, Crested Butte, CO; March 2021-October 2021

description: This data package includes a time-series of field measurements from March to October 2021 in groundwater and surface water from the Slate River floodplain in Crested Butte, CO, a focus field site for the SLAC Floodplain Hydro-Biogeochemistry SFA. The data was generated as part of the work targeting the overarching research question for the SLAC SFA: How do ubiquitous subsurface interfaces mediate molecular-scale biogeochemical processes and groundwater quality in floodplains and watersheds? The data package includes 5 data files, one for each measured variable: specific conductivity, pH, dissolved oxygen, water temperature and alkalinity. All measurements were recorded in the field immediately after water sampling. Groundwater samples were extracted from a network of installed rhizons (Rhizosphere Research Products, part no. 19.60.21F, 0.6 micrometer mesh size) and piezometer wells within the floodplain. In addition to the data files, there is a terminology file explaining the terms used, a file level metadata file, and a sensor file with metadata about the sensors used.All files are in csv format.
DOI: 10.15485/1834207
title: Time Series Surface Temperature of Variably Inundated Sediment across 30 North American Rivers

description: This dataset supports a broader study examining drivers of organic matter chemistry in variably inundated hyporheic zone sediments and further linking that chemistry to biogeochemical rates. The dataset provides surficial temperature time series that can be used to infer the dynamics of inundation prior to the collection of sediments. Those inferred inundation histories can then be used to help interpret variation in the organic matter chemistry. There are related data that will be published, such as FTICR-MS data on organic matter chemistry and sediment moisture. A data package with those data is forthcoming.This dataset is comprised of two folders: (1) ECA1_iButtonData and (2) ECA1_SitePhotos. The ECA1_iButtonData folder contains: (1) file-level metadata, (2) data dictionary, (3) field metadata, (4) installation methods, (5) iButton deployment protocol, (6) readme, and (7) folder of individual time series temperature csv files for each iButton sensor deployed. The ECA1_SitePhotos folder contains site photographs taken in the field. All files are .csv, .txt, .pdf, or .jpg.
DOI: 10.15485/1834208
title: FTICR, NPOC, TN, and Moisture of Variably Inundated Sediment across 48 North American Rivers

description: This dataset supports a broader study examining drivers of organic matter chemistry in variably inundated hyporheic zone sediments and further linking that chemistry to biogeochemical rates. The dataset provides physical and chemical sediment data collected from 48 rivers across North America. There are related data that will be published, including surficial sediment temperature time series that can be used to infer the dynamics of inundation prior to the collection of sediments. This dataset is comprised of two folders: (1) ECA2_Sediment and (2) ECA2_SitePhotos. The ECA2_Sediment folder contains: (1) file-level metadata; (2) data dictionary; (3) field metadata; (4) non-purgeable organic carbon (NPOC), total nitrogen (TN), and sediment moisture; (5) sediment sampling protocol, (6) readme, and (7) folder of high resolution characterization of organic matter from sediment extracts via 12 Tesla Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) through the Environmental Molecular Sciences Laboratory (EMSL; https://www.pnnl.gov/environmental-molecular-sciences-laboratory). The FTICR-MS files are .xml, and the data package includes instructions for using Formularity (https://omics.pnl.gov/software/formularity) and an R script to process the data based on the user's specific needs. All other files are .csv, .txt, or .pdf. The ECA2_SitePhotos folder contains a readme and site photographs taken in the field. All files are .txt or .jpg.
DOI: 10.15485/1875296
title: Total metals, sulfur and organic carbon data; Slate River floodplain, Crested Butte, CO; March 2021-October 2021

description: This data package includes processed and undiluted measurements for metal, sulfur and organic carbon concentrations from pore water (groundwater) samples from the Slate River floodplain of Crested Butte, CO, a focus field site for the SLAC Floodplain Hydro-Biogeochemistry SFA. The data was generated as part of the work targeting the overarching research question for the SLAC SFA: How do ubiquitous subsurface interfaces mediate molecular-scale biogeochemical processes and groundwater quality in floodplains and watersheds? Samples were collected between March and October of 2021. These measurements were all recorded at the Environmental Measurements Facility (EM-1) at Stanford University in Stanford, CA. Groundwater samples were extracted from a network of installed rhizon (Rhizosphere Research Products, part no. 19.60.21F, 0.6 micrometer mesh size) and piezometer wells within the river floodplain. All water samples were shaded from sun exposure during extraction from the subsurface and preserved at 2C until measured at EM-1.Analysis by ICP-MS:Measurements for total metals were performed on an inductively coupled plasma optical emission spectrometer (ICP-OES; iCAP 6300, Thermo Scientific, Cambridge, U.K.). Calibration standards were prepared from the mulit element stock solution (Sigma-Aldrich Multielement standard for ICP, St. Louis, MO) using matrix matched to sample solutions (2% HNO3). Calibration curves included 5 points with correlation coefficients of &gt;0.99. The QC protocol includes a continuing calibration blank and quality control samples that are analyzed just after calibration and again every 20 samples and at the completion of the run. Acceptable QC responses must be between 90-110% of the certified value. Analysis by Total Organic Carbon:Dissolved organic carbon concentrations were quantified on a total organic carbon (TOC) analyzer (TOC-L, Shimadzu, Kyoto, Japan) running the NPOC method. Standard curves were developed using an Organic Carbon Standard from RICCA Chemical Company (Arlington,TX). A series of 4 to 6 standards were automatically diluted by the instrument in a concentration range that spans that of the samples. A blank sample was run just after the calibration curve and at the end of the run. A QC sample was run every 25 samples. Acceptable QC responses must be between 90-110% of the certified value.All files are in csv format.
DOI: 10.15485/1896309
title: In-situ electrochemical and water quality data; Slate River and East River floodplains, Crested Butte, CO; May 2022-September 2022

description: This data package includes a time-series of field measurements from May to September 2022 in groundwater and surface water from the Slate River and East River floodplains in Crested Butte, CO, a focus field site for the SLAC Floodplain Hydro-Biogeochemistry SFA. The data was generated as part of the work targeting the overarching research question for the SLAC SFA: How do ubiquitous subsurface interfaces mediate molecular-scale biogeochemical processes and groundwater quality in floodplains and watersheds? The data package includes 5 data files, one for each measured variable: specific conductivity, pH, dissolved oxygen, water temperature and alkalinity. All measurements were recorded in the field immediately after water sampling. Groundwater samples were extracted from a network of installed rhizons (Rhizosphere Research Products, part no. 19.60.21F, 0.6 micrometer mesh size) and piezometer wells within the floodplain. In addition to the data files, there is a terminology file explaining the terms used, a file level metadata file, and a sensor file with metadata about the sensors used.All files are in csv format.
DOI: 10.18112/openneuro.ds005226.v1.0.4
title: An fMRI Datasets for Image Interpretation Tasks Under Different Occluded Conditions
DOI: 10.57770/sheqs2
title: Flagellar assembly factor FliW2 de-represses Helicobacter pylori FlaA-mediated motility by allosteric obstruction of global regulator CsrA

description: Helicobacter pylori colonizes the human stomach as a dominant member of the gastric microbiota and is a causative agent of gastric infections that may lead to the development of gastroduodenal diseases and gastric cancer. Unlike Gammaproteobacteria, which are mostly found in intestinal niches, H. pylori’s gastric milieu constitutes a uniquely hostile ecological niche. Enabling it to survive in the stomach, H. pylori constitutively expresses flagellar biosynthesis, chemotaxis, and motility as essential housekeeping functions in vivo. Previous studies have reported that the inactivation of csrA, the gene encoding for carbon storage regulator A, affects the flagellar motility, biofilm formation, and in vivo colonization of H. pylori virulence. CsrA regulates the expression of downstream genes via mechanisms that operate posttranscriptionally and translationally. Although CsrA is a critical determinant of gene regulation and flagellar biosynthesis in H. pylori, the modulation of CsrA is uncertain. In this study, we attempted to understand whether H. pylori CsrA activity is regulated by protein antagonism and how this mechanism affects H. pylori motility. We employed a comparative genomic analysis to identify two fliW homologs (jhp1081-encoded FliW1 and jhp1291-encoded FliW2) from the H. pylori J99 genome. Characterization of the isogenic fliW2 mutant strain by phenotypic and biochemical analyses demonstrated the crucial role of FliW2 in flagellar motility through a direct interaction between FliW2 and CsrA. Using a machine learning approach to predict FliW2-CsrA binding domains and an in vivo bacterial two-hybrid system, our investigation showed that the C-terminal region of CsrA is critical for the CsrA-FliW2 interaction that may indirectly occlude CsrA’s RNA binding. Our data points to novel regulatory roles that the H. pylori flagellar assembly factor FliW2 has in obstructing CsrA activity and antagonizing CsrA’s blocking of flaA mRNA processing and translation. Our findings reveal a new regulatory mechanism of flagellar motility in H. pylori.
DOI: 10.57770/gne2dh
title: Identity-Driven News Authentication Strategy in Echo Chambers Echo Chambers

description: 本論文感謝臺灣傳播調查資料庫提供分析資料(2019年面訪資料，原始資料參見https://crctaiwan.dcat.nycu.edu.tw/AnnualSurvey.asp) 另，提供內文專家評估計算媒體偏見的原始資料、本研究分析結果 This study acknowledges the Taiwan Communication Survey Database for providing the analytical data (2019 face-to-face interview data, original data available at https://crctaiwan.dcat.nycu.edu.tw/AnnualSurvey.asp Additionally, the original data used for expert evaluation in calculating media bias, as well as the analytical results of this study, are provided.
DOI: 10.25582/data.2024-02.3028639/2513991
title: Data for EMSL Project 51287 from February 2024
DOI: 10.25582/data.2024-02.3028642/2513992
title: Data for EMSL Project 51287 from February 2024
DOI: 10.25582/data.2024-02.3028647/2513993
title: Data for EMSL Project 51287 from February 2024
DOI: 10.25582/data.2024-02.3028653/2513994
title: Data for EMSL Project 51287 from February 2024
DOI: 10.25582/data.2024-02.3028661/2513995
title: Data for EMSL Project 51287 from February 2024
DOI: 10.25582/data.2024-02.3028663/2513996
title: Data for EMSL Project 51287 from February 2024
DOI: 10.25582/data.2024-02.3028673/2513997
title: Data for EMSL Project 51287 from February 2024
DOI: 10.25582/data.2024-02.3028676/2513998
title: Data for EMSL Project 51287 from February 2024
DOI: 10.25582/data.2024-02.3028679/2513999
title: Data for EMSL Project 51287 from February 2024
DOI: 10.25582/data.2024-02.3028691/2514000
title: Data for EMSL Project 51287 from February 2024
DOI: 10.25582/data.2024-02.3028705/2514001
title: Data for EMSL Project 51287 from February 2024
DOI: 10.25582/data.2024-02.3028710/2514002
title: Data for EMSL Project 51287 from February 2024
DOI: 10.25582/data.2024-02.3028713/2514003
title: Data for EMSL Project 51287 from February 2024
DOI: 10.25582/data.2024-02.3028714/2514004
title: Data for EMSL Project 51287 from February 2024
DOI: 10.25582/data.2024-02.3028715/2514005
title: Data for EMSL Project 51287 from February 2024
DOI: 10.25582/data.2024-02.3028718/2514006
title: Data for EMSL Project 51287 from February 2024
DOI: 10.25582/data.2024-02.3028735/2514007
title: Data for EMSL Project 51287 from February 2024
DOI: 10.20350/digitalcsic/17074
title: Coordinates of sampling sites in aquatic environments of Madrid County (2017-2022) [in Spanish]

description: This dataset encompasses data on freshwater sites sampled for environmental data and algae in Madrid County in the 2017-2022 period.
description: Madrid Sampling Sites (2017-2022).txt
DOI: 10.25582/data.2024-02.3028741/2514008
title: Data for EMSL Project 51287 from February 2024
DOI: 10.25582/data.2024-02.3028743/2514009
title: Data for EMSL Project 51287 from February 2024
DOI: 10.25582/data.2024-02.3028744/2514010
title: Data for EMSL Project 51287 from February 2024
DOI: 10.25582/data.2024-02.3028745/2514011
title: Data for EMSL Project 51287 from February 2024
DOI: 10.20350/digitalcsic/17070
title: Field data on aquatic environments of Madrid County (2017-2022) [in Spanish]

description: Álvarez Cobelas, Miguel. Methodology of Las Madres lake study. https://doi.org/10.20350/digitalCSIC/16357 . http://hdl.handle.net/10261/360220
description: This dataset encompasses field data on freshwater sites sampled for environmental data and algae in Madrid County in the 2017-2022 period.
description: Madrid Field Data (2017-2022).txt
DOI: 10.25582/data.2024-02.3028746/2514012
title: Data for EMSL Project 51287 from February 2024
DOI: 10.20350/digitalcsic/17071
title: Field data on aquatic environments of Madrid County (May 2019) [in Spanish]

description: Álvarez Cobelas, Miguel. Methodology of Las Madres lake study. https://doi.org/10.20350/digitalCSIC/16357 . http://hdl.handle.net/10261/360220
description: This dataset encompasses field data on freshwater sites sampled for environmental data and algae in Madrid County in 2019, May.
description: Madrid Field Data (2019, May).txt
DOI: 10.25582/data.2024-02.3028759/2514013
title: Data for EMSL Project 51287 from February 2024
DOI: 10.20350/digitalcsic/17072
title: Nutrient data on aquatic environments of Madrid County (2018-2022) [in Spanish]

description: Álvarez Cobelas, Miguel. Methodology of Las Madres lake study. https://doi.org/10.20350/digitalCSIC/16357 . http://hdl.handle.net/10261/360220
description: This dataset encompasses nutrient data on freshwater sites sampled for environmental data and algae in Madrid County gathered in 2018-2022.
description: Madrid Nutrient Data (2018-2022).txt
DOI: 10.25582/data.2024-02.3028768/2514014
title: Data for EMSL Project 51287 from February 2024
DOI: 10.20350/digitalcsic/17073
title: Nutrient data on aquatic environments of Madrid County (May 2019) [in Spanish]

description: Álvarez Cobelas, Miguel. Methodology of Las Madres lake study. https://doi.org/10.20350/digitalCSIC/16357 . http://hdl.handle.net/10261/360220
description: This dataset encompasses nutrient data on freshwater sites sampled for environmental data and algae in Madrid County gathered in May, 2019.
description: Madrid Nutrient Data (2019, May).txt
DOI: 10.25582/data.2024-02.3028793/2514015
title: Data for EMSL Project 51287 from February 2024
DOI: 10.20350/digitalcsic/17076
title: Coordinates of sampling sites in aquatic environments of Madrid County (May 2019) [in Spanish]

description: This dataset encompasses data on freshwater sites sampled for environmental data and algae in Madrid County in 2019, May.
description: Madrid Sampling Sites (2019, May).txt
DOI: 10.25582/data.2024-02.3028797/2514016
title: Data for EMSL Project 51287 from February 2024
DOI: 10.25582/data.2024-02.3028799/2514017
title: Data for EMSL Project 51287 from February 2024