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At least 1,045 records · Page 58

Data from: "A guide to using GitHub for developing and versioning data standards and reporting formats"

These data are the results of a systematic review that investigated how data standards and reporting formats are documented on the version control platform GitHub. Our systematic review identified 32 data standards in earth science, environmental science, and ecology that use GitHub for version control of data standard documents. In our analysis, we characterized the documents and content within each of the 32 GitHub repositories to identify common practices for groups that version control their documents on GitHub.In this data package, there are 8 CSV files that contain data that we characterized from each repository, according to the location within the repository. For example, in 'readme_pages.csv' we characterize the content that appears across the 32 GitHub repositories included in our systematic review. Each of the 8 CSV files has an associated data dictionary file (names appended with '_dd.csv' and here we describe each content category within CSV files.There is one file-level metadata file (flmd.csv) that provides a description of each file within the data package.

54 ENVIRONMENTAL SCIENCES↗

CLM simulated data at three FLUXNET sites and three SNOTEL sites in the Colorado River Basin

This data package includes 6 csv files that include Community Land Model (CLM) simulations for three Fluxnet sites (i.e., US-NR1, US-GLE and US-VCM) and three SNOTEL sites (i.e., ER-BT, ER-SP and ER-PK) in the Upper Colorado River Basin area. Data inputs include meteorological forcing data (obtained from Fluxnet and SNOTEL databases) and CLM-simulated evapotranspiration (ET) data from 2005 to 2016. These datasets support the development of subseasonal regime approach based on statistics driven Hidden Markov Model to assess intra- and inter-annual variability of ET, which improves our understanding of climate change's impacts on water resources and ecosystem dynamics in the Colorado River Basin.

54 ENVIRONMENTAL SCIENCES↗

Data used in Wainwright, H.M. et al. 2021, “Watershed zonation through hillslope clustering for tractably quantifying above- and belowground watershed heterogeneity and functions”

This data package contains spatial data layers and processing scripts used in Wainwright, H.M. et al. 2021, “Watershed zonation approach for tractably quantifying above-and- belowground watershed heterogeneity and functions”. The purpose of the data and paper is to develop a watershed zonation approach for characterizing watershed organization and function in a tractable manner by applying clustering methods to multiple spatial data layers. The data package contains the geotiff files of spatial data layers, and the processed data values corresponding to the figures in the paper. The Data_description file describe each file in details. The spatial data sets (geotiff) are included in the zip files.

54 ENVIRONMENTAL SCIENCES↗

Data from: “Enabling FAIR data in Earth and environmental science with community-centric (meta)data reporting formats”

This dataset contains supplementary information for a manuscript describing the ESS-DIVE (Environmental Systems Science Data Infrastructure for a Virtual Ecosystem) data repository's community data and metadata reporting formats. The purpose of creating the ESS-DIVE reporting formats was to provide guidelines for formatting some of the diverse data types that can be found in the ESS-DIVE repository. The 6 teams of community partners who developed the reporting formats included scientists and engineers from across the Department of Energy National Lab network. Additionally, during the development process, 247 individuals representing 128 institutions provided input on the formats. The primary files in this dataset are 10 data and metadata crosswalk for ESS-DIVE’s reporting formats (all files ending in _crosswalk.csv). The crosswalks compare elements used in each of the reporting formats to other related standards and data resources (e.g., repositories, datasets, data systems). This dataset also contains additional files recommended by ESS-DIVE’s file-level metadata reporting format. Each data file has an associated dictionary (files ending in _dd.csv) which provide a brief description of each standard or data resource consulted in the data reporting format development process. The flmd.csv file describes each file contained within the dataset.

54 ENVIRONMENTAL SCIENCES↗

FTICR-MS, Sensor, and Environmental Data from 5 Streams Impacted by the 2020 Holiday Farm Fire Associated with: "Spatiotemporal controls on the delivery of dissolved organic matter to streams following a wildfire"

This data package is associated with the publication "Spatiotemporal Controls on the Delivery of Dissolved Organic Matter to Streams Following a Wildfire" submitted to Geophysical Research Letters (Roebuck et al., 2022). The study aims to understand storm induced transport of pyrogenic materials to streams impacted by varying degrees of burn severity. Time series samples (24 samples in 1-hour intervals) were collected at 5 sites within the McKenzie River Watershed (Oregon, USA) whose catchment were each completely engulfed by the 2020 Holiday Farm Fire. The samples were collected in November 2020 during the first major storm pulse following the conclusion of the wildfire. Samples were characterized for dissolved organic carbon, total dissolved nitrogen, and by ultra-high resolution mass spectrometry. In situ turbidity data also collected.This data package contains 4 primary folders that include the following: 1) Metadata, 2) EnvData (Environmental Data), 3) SensorData, and 4) FTICR_SupportingData. The package contains a single file-level metadata (flmd) file. Each primary folder also contains individual data dictionaries (dd) to define and provide descriptors of column/row headers and data flags. The FTICR_SupportingData, folder 4, contains raw, unprocessed FTICR-MS Data files in addition to a csv containing processed FTICR-MS data. This package contains the following file types: csv, xml, pdf.

54 ENVIRONMENTAL SCIENCES↗

Subsurface electrical conductivity across the BEO site inferred using a capacitively coupled resistivity survey in May 2013, Utqiagvik, Alaska

Multiple transects across and around the Barrow Environmental Observatory (BEO) site were surveyed using a capacitively coupled resistivity tool to infer the subsurface electrical conductivity in the top ~6 m in order to improve the understanding of heterogeneity in ice and salinity content. This work was led by the environmental geophysics team from Lawrence Berkeley National Laboratory as part of the Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic). The acquisition was performed in May 2013 using a capacitively coupled resistivity tool (OhmMapper from Geometrics, Inc) mounted behind a sled hooked to a snowmobile. Twenty-eight ~750 m long transects cover the NGEE intensive site (polygon areas A, B, C, D) in the BEO with a measurement (apparent resistivity for 5 different geometries) taken every 1.5 to 2 m. The survey also includes other transects that have been acquired along Electrical Resistivity Tomography (ERT) transects previously acquired at the site (Site 0, AB, and BD), and several long transects (up to 7 km each) around the BEO site crossing several Drained Thawed Lake Basins (DTLB). The various transects acquired during this survey cover a distance of about 100 km. All the datasets are provided with the acquisition geometry and the associated subsurface apparent electrical conductivity. In addition, the 28 transects at the BEO intensive site were inverted to infer the subsurface electrical conductivity. Unprocessed and processed data products are included in this package. This metadata document contains a description of the survey and processing steps and the inferred products.The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic) was a 15-year research effort (2012-2027) to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy’s Office of Biological and Environmental Research. The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska, and 2) multiple areas in the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska. Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy’s Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗

Organic Matter Concentration and Composition in November 2021 and April 2022 from 12 Streams Impacted by the 2020 Holiday Farm Fire (v2)

This dataset represents results from a field study aiming to understand storm induced transport of pyrogenic materials to streams impacted by varying degrees of burn severity. Time series samples were collected at 5 sites within the McKenzie River Watershed (Oregon, USA) whose catchment were each completely engulfed by the 2020 Holiday Farm Fire. An additional 7 sites were sampled once during the storm. The samples were collected during storm events in November 2020, January 2021, November 2021, and April 2022. Samples were characterized for benezenepolycarboxylic acids (BPCA), ultra-high resolution mass spectrometry, dissolved organic carbon and optics (absorbance and fluorescence). Fourier-transform ion cyclotron resonance mass spectrometry (FTICR) and dissolved organic carbon data from the November 2020 (referred to as “EWEB_2020”) sampling can be found in a separate data package (doi: 10.15485/1869708). NOTE: The 2020 samples were run on FTICR-MS in two unique instances. The first run can be found in the previous data package (EWEB_2020). The second run is included in this data package. These samples were run for a second time so that the data were more directly interoperable with the other samples in this data package. We have not done any investigation into the differences/similarities between these datasets and the previously ran/published data in the other data package. This data package was originally published in November 2024. It was updated in April 2025 (v2; new and modified files). See the change history section below for more details. For details on how to navigate data packages generated by this project, see https://data.ess-dive.lbl.gov/portals/PNNLRiverCorridorSFA/About. This dataset contains (1) file-level metadata; (2) data dictionary; (3) data package readme; (4) metadata; (5) methods information; (6) dissolved organic carbon (DOC, measured as non-purgeable organic carbon, NPOC) data; (7) excitation emission matrix (EEM) methods; and (8) a sub-folder with processed EEM data (9) benzene polycarboxylic acid (BPCA) concentration data; (10) Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) methods; and (11) folder of high-resolution characterization of organic matter via 12 Tesla FTICR-MS generated through the Environmental Molecular Sciences Laboratory (EMSL; https://www.pnnl.gov/environmental-molecular-sciences-laboratory). The EEMs sub-folder contains two additional folders; the Absorbance and Fluorescence folders which contain the processed EEMs absorbance and fluorescence data respectively. This package contains the following file types: csv, xml, pdf.

54 ENVIRONMENTAL SCIENCES↗

Hyporheic zone, river, and groundwater metagenome resolved genomes and rpS3 genes in East River Watershed, Colorado USA Summer 2020, 2021

Here we present metagenome assembled genomes (MAGs) for the bacterial and archaeal communities from water filter collected across 8 locations along the East River Watershed, CO, and 1 nearby groundwater well. The purpose was to look for connectivity and similarities across the network and to see the impact of the groundwater. As a part of Lawrence Berkeley National Laboratory (LBNL) Watershed Science Focus Area (SFA), we assessed community composition and strain similarities between the sites and we also compared it to previous metagenomic studies within the watershed looking at floodplain (Matheus Carnevali et al. 2021) and hillslope (Lavy et al. 2019) microbiomes. Here we present metagenome assembled genomes (MAGs) for the bacterial and archaeal communities from filters across 8 locations during August 2020 and July 2021. This resulted in 32 samples. The groundwater sample was sequenced at UC Berkley's QB3. The other 31 samples were sequenced at University of Maryland. Metagenomes were assembled using four autobinners and the best bins were selected using dasTool. The genomes were dereplicated at 95% with dRep and the subset of winning genomes were manually curated based on visual inspection of taxonomic profile, GC content, coverage, and a set of 51 bacterial single copy genes (BSCG), and 38 archaeal signal copy genes (ASCG). The dataset includes a zip file of 311 genomes (HZ_River_SW_MAGS_Dereplicated_95.zip). The dataset additionally includes a zipped file of ribosomal protein small subunit 3 (rpS3) proteins from the hyporheic zone and river data (rpS3_Proteins_HZ_River.zip), a metadata file used to register associated samples with IGSNs (International Generic Sample Numbers) (samples.csv), a location metadata file (locations.csv). This work was supported by the Watershed Function Science Focus Area at Lawrence Berkeley National Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-05CH11231.

DNA↗

Functional trait data for 11 canopy tree species in the control and drought treatments at AU-DRO (2018-2019)

This data package contains foliar abscisic acid levels, xylem anatomy, foliar d13C, leaf mass per area, leaf water potentials, non-structural carbohydrates, and pressure volume curve traits for 11 canopy tree species in the control and drought treatments at the Daintree Rainforest Observatory in Queensland, Australia (AU-DRO). Data were collected at the end of the dry season (Nov 2018) and end of the wet season (May 2019). The species included in the dataset are: Castanospermum australe, Cleistanthus myrianthus, Cryptocarya mackinnoniana, Dysoxylum papuanum, Elaeocarpus angustifolius (Elaeocarpus grandis), Endiandra microneura, Mallotus paniculatus, Myristica globosa, Rockinghamia angustifolia, Synima cordierorum, Syzygium spp. These data correspond to the previously archived dataset “Leaf gas exchange data, Nov 2018 and May 2019, Daintree Rainforest, Australia. NGEE-Tropics Data Archive” (DOI: 10.15486/ngt/1773854).

54 ENVIRONMENTAL SCIENCES↗

A new era of ferroelectric thin films for nonvolatile memories

Ferroelectric films have potential applications in nonvolatile memory devices. In addition to the well-established perovskite-structure oxide ferroelectrics, hafnia- and wurtzite-based ferroelectrics have recently attracted considerable attention because of the improved scalability of the ferroelectric response (down to nanometer thicknesses), their compatibility with silicon fabrication processes, and the availability of deposition methods that realize three-dimensional structures. Furthermore, due to their high compatibility with silicon processes, these are also expected to be used in emerging energy-efficient applications, such as neuromorphic computing and reservoir computing. In this article, we review the fundamentals of hafnia- and wurtzite-based ferroelectrics and their advantages and issues for developing in nonvolatile memory devices. Then, possible emerging applications are discussed.

36 MATERIALS SCIENCE↗

Deposition and dielectric characterization of highly oriented V 2 O 5 thin films

The possibility of ferroelectricity in orthorhombic V 2 O 5 thin flms was investigated. Films were deposited via either a chemical solution deposition (CSD) route or by RF magnetron sputtering. Highly (001) oriented V 2 O 5 flms were achieved with both deposition routes at temperatures as low as 300°C. No evidence for ferroelectricity was observed, even in flms which had been doped to provide local nuclei for polarization reversal. Loss originated from mid-gap trap states stemming from oxygen vacancies that were observed with photoluminescence, supplemented by piezoresponse force microscopy measurements. Furthermore, these trap states may have helped mimic ferroelectricity in previous reports on V 2 O 5 .

36 MATERIALS SCIENCE↗

A Novel Platform for Evaluating Dose Rate Effects on Oxidative Damage to Peptides: Toward a High-Throughput Method to Characterize the Mechanisms Underlying the FLASH Effect

High dose rate radiation has gained considerable interest recently as a possible avenue for increasing the therapeutic window in cancer radiation treatment. The sparing of healthy tissue at high dose rates relative to conventional dose rates, while maintaining tumor control, has been termed the FLASH effect. Although the effect has been validated in animal models using multiple radiation sources, it is not yet well understood. Here, in this work, we demonstrate a new experimental platform for quantifying oxidative damage to protein sidechains in solution as a function of radiation dose rate and oxygen availability using liquid chromatography mass spectrometry. Using this reductionist approach, we show that for both X-ray and electron sources, isolated peptides in solution are oxidatively modified to different extents as a function of both dose rate and oxygen availability. Our method provides an experimental platform for exploring the parameter space of the dose rate effect on oxidative changes to proteins in solution.

61 RADIATION PROTECTION AND DOSIMETRY↗

AmeriFlux US-YK1 Yukon-Kuskokwim Delta, Izaviknek-Kingaglia uplands, Burned 2015

This is the AmeriFlux version of the carbon flux data for the site US-YK1 Yukon-Kuskokwim Delta, Izaviknek-Kingaglia uplands, Burned 2015. Site Description - Tower installed in the Yukon-Kuskokwim Delta in July 2019, in an area that was burned in year 2015. Discontinuous permafrost zone in a wetland tundra ecosystem characterized by peat plateaus and wetlands

Natali, Susan↗

AmeriFlux CA-CF3 Churchill Fen Site 3

This is the AmeriFlux version of the carbon flux data for the site CA-CF3 Churchill Fen Site 3. Site Description - Fen site dominated by sedges. Flat, high water table. Frozen for long periods each year. Close to Arctic Ocean coast so affected by land/sea breezes and coastal weather.

Arndt, Kyle↗

AmeriFlux CA-Mtk Mittimatalik (Pond Inlet) Tundra

This is the AmeriFlux version of the carbon flux data for the site CA-Mtk Mittimatalik (Pond Inlet) Tundra. Site Description - Mesic to dry tundra with dwarf shrubs, grasses, forbs, and moss vegitation. Thin organic soil layer of 10 cm with sandy soils.

Arndt, Kyle [Woodwell Climate Research Center]↗

AmeriFlux CA-RSB Resolute Bay Polar Desert

This is the AmeriFlux version of the carbon flux data for the site CA-RSB Resolute Bay Polar Desert. Site Description - Polar desert on a gentle slope. Sparse grases and forbs in lower lying areas between microtopography in ice wedge polygon formations.

Arndt, Kyle [Woodwell Climate Research Center]↗

AmeriFlux US-CAK Council Alaska Tundra

This is the AmeriFlux version of the carbon flux data for the site US-CAK Council Alaska Tundra. Site Description - Subarctic tussock tundra, discontinuous permafrost

Arndt, Kyle [Woodwell Climate Research Center]↗

AmeriFlux FLUXNET-1F CA-Mtk Mittimatalik (Pond Inlet) Tundra

This is the AmeriFlux Management Project (AMP) created FLUXNET-1F version of the carbon flux data for the site CA-Mtk Mittimatalik (Pond Inlet) Tundra. This is the FLUXNET version of the carbon flux data for the site CA-Mtk Mittimatalik (Pond Inlet) Tundra produced by applying the standard ONEFlux (1F) software. Site Description - Mesic to dry tundra with dwarf shrubs, grasses, forbs, and moss vegitation. Thin organic soil layer of 10 cm with sandy soils.

Arndt, Kyle [Woodwell Climate Research Center]↗