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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 991 records · Page 55
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

Complex ancestries of lager-brewing hybrids were shaped by standing variation in the wild yeast Saccharomyces eubayanus

Lager-style beers constitute the vast majority of the beer market, and yet, the genetic origin of the yeast strains that brew them has been shrouded in mystery and controversy. Unlike alestyle beers, which are generally brewed with Saccharomyces cerevisiae , lagers are brewed at colder temperatures with allopolyploid hybrids of Saccharomyces eubayanus x S. cerevisiae . Since the discovery of S. eubayanus in 2011, additional strains have been isolated from South America, North America, Australasia, and Asia, but only interspecies hybrids have been isolated in Europe. Here, using genome sequence data, we examine the relationships of these wild S. eubayanus strains to each other and to domesticated lager strains. Our results support the existence of a relatively low-diversity (π = 0.00197) lineage of S. eubayanus whose distribution stretches across the Holarctic ecozone and includes wild isolates from Tibet, new wild isolates from North America, and the S. eubayanus parents of lager yeasts. This Holarctic lineage is closely related to a population with higher diversity (π = 0.00275) that has been found primarily in South America but includes some widely distributed isolates. A second diverse South American population (π = 0.00354) and two early-diverging Asian subspecies are more distantly related. We further show that no single wild strain from the Holarctic lineage is the sole closest relative of lager yeasts. Instead, different parts of the genome portray different phylogenetic signals and ancestry, likely due to outcrossing and incomplete lineage sorting. Indeed, standing genetic variation within this wild Holarctic lineage of S. eubayanus is responsible for genetic variation still segregating among modern lager-brewing hybrids. Furthermore, we conclude that the relationships among wild strains of S. eubayanus and their domesticated hybrids reflect complex biogeographical and genetic processes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

LABEL: Fast and Accurate Lineage Assignment with Assessment of H5N1 and H9N2 Influenza A Hemagglutinins

The evolutionary classification of influenza genes into lineages is a first step in understanding their molecular epidemiology and can inform the subsequent implementation of control measures. We introduce a novel approach called Lineage Assignment By Extended Learning (LABEL) to rapidly determine cladistic information for any number of genes without the need for time-consuming sequence alignment, phylogenetic tree construction, or manual annotation. Instead, LABEL relies on hidden Markov model profiles and support vector machine training to hierarchically classify gene sequences by their similarity to pre-defined lineages. We assessed LABEL by analyzing the annotated hemagglutinin genes of highly pathogenic (H5N1) and low pathogenicity (H9N2) avian influenza A viruses. Using the WHO/FAO/OIE H5N1 evolution working group nomenclature, the LABEL pipeline quickly and accurately identified the H5 lineages of uncharacterized sequences. Moreover, we developed an updated clade nomenclature for the H9 hemagglutinin gene and show a similarly fast and reliable phylogenetic assessment with LABEL. While this study was focused on hemagglutinin sequences, LABEL could be applied to the analysis of any gene and shows great potential to guide molecular epidemiology activities, accelerate database annotation, and provide a data sorting tool for other large-scale bioinformatic studies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Cost-Effective Mapping of Benthic Habitats in Inland Reservoirs through Split-Beam Sonar, Indicator Kriging, and Historical Geologic Data

Because bottom substrate composition is an important control on the temporal and spatial location of the aquatic community, accurate maps of benthic habitats of inland lakes and reservoirs provide valuable information to managers, recreational users, and scientists. Therefore, we collected vertical, split-beam sonar data (roughness [E1], hardness [E2], and bathymetry) and sediment samples to make such maps. Statistical calibration between sonar parameters and sediment classes was problematic because the E1:E2 ratios for soft (muck and clay) sediments overlapped a lower and narrower range for hard (gravel) substrates. Thus, we used indicator kriging (IK) to map the probability that unsampled locations did not contain coarse sediments. To overcome the calibration issue we tested proxies for the natural processes and anthropogenic history of the reservoir as potential predictive variables. Of these, a geologic map proved to be the most useful. The central alluvial valley and mudflats contained mainly muck and organic-rich clays. The surrounding glacial till and shale bedrock uplands contained mainly poorly sorted gravels. Anomalies in the sonar data suggested that the organic-rich sediments also contained trapped gases, presenting additional interpretive issues for the mapping. We extended the capability of inexpensive split-beam sonar units through the incorporation of historic geologic maps and other records as well as validation with dredge samples. Through the integration of information from multiple data sets, were able to objectively identify bottom substrate and provide reservoir users with an accurate map of available benthic habitat.

bottom sediment, fisheries, geostatistics, GIS, ha↗
DOE OSTI2014

Genetic and Epigenetic Changes in Chromosomally Stable and Unstable Progeny of Irradiated Cells

Radiation induced genomic instability is a well-studied phenomenon, the underlying mechanisms of which are poorly understood. Persistent oxidative stress, mitochondrial dysfunction, elevated cytokine levels and epigenetic changes are among the mechanisms invoked in the perpetuation of the phenotype. To determine whether epigenetic aberrations affect genomic instability we measured DNA methylation, mRNA and microRNA (miR) levels in well characterized chromosomally stable and unstable clonally expanded single cell survivors of irradiation. While no changes in DNA methylation were observed for the gene promoters evaluated, increased LINE-1 methylation was observed for two unstable clones (LS12, CS9) and decreased Alu element methylation was observed for the other two unstable clones (115, Fe5.0-8). These relationships also manifested for mRNA and miR expression. mRNA identified for the LS12 and CS9 clones were most similar to each other (261 mRNA), while the 115 and Fe5.0-8 clones were more similar to each other, and surprisingly also similar to the two stable clones, 114 and 118 (286 mRNA among these four clones). Pathway analysis showed enrichment for pathways involved in mitochondrial function and cellular redox, themes routinely invoked in genomic instability. The commonalities between the two subgroups of clones were also observed for miR. The number of miR for which anti-correlated mRNA were identified suggests that these miR exert functional effects in each clone. The results of this study demonstrate significant genetic and epigenetic changes in unstable cells, but similar changes almost equally common in chromosomally stable cells. Possible conclusions might be that the chromosomally stable clones have some other form of instability, or that some of the observed changes represent a sort of radiation signature for and that other changes are related to genomic instability. Irrespective, these findings again suggest that a spectrum of changes both drive genomic instability and permit unstable cells to persist and proliferate.

Baulch, Janet E.↗
DOE OSTI2014

Enhancement of Synthetic Trichoderma -Based Enzyme Mixtures for Biomass Conversion with an Alternative Family 5 Glycosyl Hydrolase from Sporotrichum thermophile

Enzymatic conversion of lignocellulosic materials to fermentable sugars is a limiting step in the production of biofuels from biomass. We show here that combining enzymes from different microbial sources is one way to identify superior enzymes. Extracts of the thermophilic fungus Sporotrichum thermophile (synonym Myceliophthora thermophila) gave synergistic release of glucose (Glc) and xylose (Xyl) from pretreated corn stover when combined with an 8-component synthetic cocktail of enzymes from Trichoderma reesei. The S. thermophile extracts were fractionated and an enhancing factor identified as endo-β1,4- glucanase (StCel5A or EG2) of subfamily 5 of Glycosyl Hydrolase family 5 (GH5_5). In multi-component optimization experiments using a standard set of enzymes and either StCel5A or the ortholog from T. reesei (TrCel5A), reactions containing StCel5A yielded more Glc and Xyl. In a five-component optimization experiment (i.e., varying four core enzymes and the source of Cel5A), the optimal proportions for TrCel5A vs. StCel5A were similar for Glc yields, but markedly different for Xyl yields. Both enzymes were active on lichenan, glucomannan, and oat β-glucan; however, StCel5A but not TrCel5A was also active on β1,4-mannan, two types of galactomannan, and β1,4-xylan. Phylogenetically, fungal enzymes in GH5_5 sorted into two clades, with StCel5A and TrCel5A belonging to different clades. Structural differences with the potential to account for the differences in performance were deduced based on the known structure of TrCel5A and a homology-based model of StCel5A, including a loop near the active site of TrCel5A and the presence of four additional Trp residues in the active cleft of StCel5A. The results indicate that superior biomass-degrading enzymes can be identified by exploring taxonomic diversity combined with assays in the context of realistic enzyme combinations and realistic substrates. Substrate range may be a key factor contributing to superior performance within GH5_5.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Environmental control on the distribution of metabolic strategies of benthic microbial mats in Lake Fryxell, Antarctica

Ecological theories posit that heterogeneity in environmental conditions greatly affects community structure and function. However, the degree to which ecological theory developed using plant- and animal-dominated systems applies to microbiomes is unclear. Investigating the metabolic strategies found in microbiomes are particularly informative for testing the universality of ecological theories because microorganisms have far wider metabolic capacity than plants and animals. We used metagenomic analyses to explore the relationships between the energy and physicochemical gradients in Lake Fryxell and the metabolic capacity of its benthic microbiome. Statistical analysis of the relative abundance of metabolic marker genes and gene family diversity shows that oxygenic photosynthesis, carbon fixation, and flavin-based electron bifurcation differentiate mats growing in different environmental conditions. The pattern of gene family diversity points to the likely importance of temporal environmental heterogeneity in addition to resource gradients. Overall, we found that the environmental heterogeneity of photosynthetically active radiation (PAR) and oxygen concentration ([O2]) in Lake Fryxell provide the framework by which metabolic diversity and composition of the community is structured, in accordance with its phylogenetic structure. The organization of the resulting microbial ecosystems are consistent with the maximum power principle and the species sorting model.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Supervised extraction of near-complete genomes from metagenomic samples: A new service in PATRIC

Large amounts of metagenomically-derived data are submitted to PATRIC for analysis. In the future, we expect even more jobs submitted to PATRIC will use metagenomic data. One in-demand use case is the extraction of near-complete draft genomes from assembled contigs of metagenomic origin. The PATRIC metagenome binning service utilizes the PATRIC database to furnish a large, diverse set of reference genomes. We provide a new service for supervised extraction and annotation of high-quality, near-complete genomes from metagenomically-derived contigs. Reference genomes are assigned to putative draft genome bins based on the presence of single-copy universal marker roles in the sample, and contigs are sorted into these bins by their similarity to reference genomes in PATRIC. Each set of binned contigs represents a draft genome that will be annotated by RASTtk in PATRIC. A structured-language binning report is provided containing quality measurements and taxonomic information about the contig bins. The PATRIC metagenome binning service emphasizes extraction of high-quality genomes for downstream analysis using other PATRIC tools and services. Due to its supervised nature, the binning service is not appropriate for mining novel or extremely low-coverage genomes from metagenomic samples.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

CDR3α drives selection of the immunodominant Epstein Barr virus (EBV) BRLF1-specific CD8 T cell receptor repertoire in primary infection

The T cell receptor (TCR) repertoire is an essential component of the CD8 T-cell immune response. Here, we seek to investigate factors that drive selection of TCR repertoires specific to the HLA-A2-restricted immunodominant epitope BRLF1 109-117 (YVLDHLIVV) over the course of primary Epstein Barr virus (EBV) infection. Using single-cell paired TCRαβ sequencing of tetramer sorted CD8 T cells ex vivo , we show at the clonal level that recognition of the HLA-A2-restricted BRLF1 (YVL-BR, BRLF-1109) epitope is mainly driven by the TCRα chain. For the first time, we identify a CDR3α (complementarity determining region 3 α) motif, KDTDKL, resulting from an obligate AV8.1-AJ34 pairing that was shared by all four individuals studied. This observation coupled with the fact that this public AV8.1-KDTDKL-AJ34 TCR pairs with multiple different TCRβ chains within the same donor (median 4; range: 1–9), suggests that there are some unique structural features of the interaction between the YVL-BR/MHC and the AV8.1-KDTDKL-AJ34 TCR that leads to this high level of selection. Newly developed TCR motif algorithms identified a lysine at position 1 of the CDR3α motif that is highly conserved and likely important for antigen recognition. Crystal structure analysis of the YVL-BR/HLA-A2 complex revealed that the MHC-bound peptide bulges at position 4, exposing a negatively charged aspartic acid that may interact with the positively charged lysine of CDR3α. TCR cloning and site-directed mutagenesis of the CDR3α lysine ablated YVL-BR-tetramer staining and substantially reduced CD69 upregulation on TCR mutant-transduced cells following antigen-specific stimulation. Reduced activation of T cells expressing this CDR3 motif was also observed following exposure to mutated (D4A) peptide. In summary, we show that a highly public TCR repertoire to an immunodominant epitope of a common human virus is almost completely selected on the basis of CDR3α and provide a likely structural basis for the selection. These studies emphasize the importance of examining TCRα, as well as TCRβ, in understanding the CD8 T cell receptor repertoire.

Microbiology↗
DOE OSTI2020

“The structure of the Type III secretion system export gate with CdsO, an ATPase lever arm”

Type III protein secretion systems (T3SS) deliver effector proteins from the Gram-negative bacterial cytoplasm into a eukaryotic host cell through a syringe-like, multi-protein nanomachine. Cytosolic components of T3SS include a portion of the export apparatus, which traverses the inner membrane and features the opening of the secretion channel, and the sorting complex for substrate recognition and for providing the energetics required for protein secretion. Two components critical for efficient effector export are the export gate protein and the ATPase, which are proposed to be linked by the central stalk protein of the ATPase. We present the structure of the soluble export gate homo-nonamer, CdsV, in complex with the central stalk protein, CdsO, of its cognate ATPase, both derived from Chlamydia pneumoniae. This structure defines the interface between these essential T3S proteins and reveals that CdsO engages the periphery of the export gate that may allow the ATPase to catalyze an opening between export gate subunits to allow cargo to enter the export apparatus. We also demonstrate through structure-based mutagenesis of the homologous export gate in Pseudomonas aeruginosa that mutation of this interface disrupts effector secretion. These results provide novel insights into the molecular mechanisms governing active substrate recognition and translocation through a T3SS.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

GPFA-AB_Phase1UtilizationTask4DataUpload

This submission of Utilization Analysis data to the Geothermal Data Repository (GDR) node of the National Geothermal Data System (NGDS) is in support of Phase 1 Low Temperature Geothermal Play Fairway Analysis for the Appalachian Basin (project DE-EE0006726). The submission includes data pertinent to the methods and results of an analysis of the Surface Levelized Cost of Heat (SLCOH) for US Census Bureau ‘Places’ within the study area. This was calculated using a modification of a program called GEOPHIRES, available at http://koenraadbeckers.net/geophires/index.php. The MATLAB modules used in conjunction with GEOPHIRES, the MATLAB data input file, the GEOPHIRES output data file, and an explanation of the software components have been provided. Results of the SLCOH analysis appear on 4 .png image files as mapped ‘risk’ of heat utilization. For each of the 4 image (.png) files, there is an accompanying georeferenced TIF (.tif) file by the same name. In addition to calculating SLCOH, this Task 4 also identified many sites that may be prospects for use of a geothermal district heating system, based on their size and industry, rather than on the SLCOH. An industry sorted listing of the sites (.xlsx) and a map of these sites plotted as a layer onto different iterations of maps combining the three geological risk factors (Thermal Quality, Natural Reservoir Quality, and Risk of Seismicity) has been provided. In addition to the 6 image (.png) files of the maps in this series, a shape (.shp) file and 7 associated files are included as well. Finally, supporting files (.pdf) describing the utilization analysis methodology and summarizing the anticipated permitting for a deep district heating system are supplied.

15 GEOTHERMAL ENERGY↗
DOE OSTI2015

Utilization Analysis in Low-Temperature Geothermal Play Fairway Analysis for the Appalachian Basin (GPFA-AB)

This submission of Utilization Analysis data to the Geothermal Data Repository (GDR) node of the National Geothermal Data System (NGDS) is in support of Phase 1 Low Temperature Geothermal Play Fairway Analysis for the Appalachian Basin. The submission includes data pertinent to the methods and results of an analysis of the Surface Levelized Cost of Heat (SLCOH) for US Census Bureau Places within the study area. This was calculated using a modification of a program called GEOPHIRES, available at http://koenraadbeckers.net/geophires/index.php. The MATLAB modules used in conjunction with GEOPHIRES, the MATLAB data input file, the GEOPHIRES output data file, and an explanation of the software components have been provided. Results of the SLCOH analysis appear on 4 .png image files as mapped risk of heat utilization. For each of the 4 image (.png) files, there is an accompanying georeferenced TIF (.tif) file by the same name. In addition to calculating SLCOH, this Task 4 also identified many sites that may be prospects for use of a geothermal district heating system, based on their size and industry, rather than on the SLCOH. An industry sorted listing of the sites (.xlsx) and a map of these sites plotted as a layer onto different iterations of maps combining the three geological risk factors (Thermal Quality, Natural Reservoir Quality, and Risk of Seismicity) has been provided. In addition to the 6 image (.png) files of the maps in this series, a shape (.shp) file and 7 associated files are included as well. Finally, supporting files (.pdf) describing the utilization analysis methodology and summarizing the anticipated permitting for a deep district heating system are supplied. UPDATE: Newer version of the Utilization Analysis has been added here: https://gdr.openei.org/submissions/878

15 GEOTHERMAL ENERGY↗
DOE OSTI2016

Appalachian Basin Play Fairway Analysis Analyses and Results

*This submission updates a 2015 submission for the utilization analysis (https://gdr.openei.org/submissions/623)* The files document the analysis of utilization potential in support of Phase 1 Low Temperature Geothermal Play Fairway Analysis for the Appalachian Basin. This 2016 submission includes data pertinent to the methods and results of an analysis of the Surface Levelized Cost of Heat (SLCOH) for US Census Bureau 'Places' within the study area. The SLCOHis was calculated using a modification of a program called GEOPHIRES, available at http://koenraadbeckers.net/geophires/index.php. In addition to calculating SLCOH, this task also identified many industrial sites that may be prospects for use of a geothermal district heating system, based on their size and industry, rather than on the SLCOH. An industry sorted listing and maps of the sites have been plotted as a layer onto different iterations of maps combining the three geologic risk factors (Thermal Quality, Natural Reservoir Quality, and Risk of Seismicity). In addition, a shapefile of the industrial sites is also included with 7 associated files. Supporting files are also supplied.

15 GEOTHERMAL ENERGY↗
DOE OSTI2021

Brady Geodatabase for Geothermal Exploration Artificial Intelligence

These files contain the geodatabases related to Brady's Geothermal Field. It includes all input and output files for the Geothermal Exploration Artificial Intelligence. Input and output files are sorted into three categories: raw data, pre-processed data, and analysis (post-processed data). In each of these categories there are six additional types of raster catalogs which are titled Radar, SWIR, Thermal, Geophysics, Geology, and Wells. These inputs and outputs were used with the Geothermal Exploration Artificial Intelligence to identify indicators of blind geothermal systems at the Brady Hot Springs Geothermal Site. The included zip file is a geodatabase to be used with ArcGIS and the tar file is an inclusive database that encompasses the inputs and outputs for the Brady Hot Springs Geothermal Site.

15 GEOTHERMAL ENERGY↗
DOE OSTI2021

Salton Sea Geodatabase for Geothermal Exploration Artificial Intelligence

These files contain the geodatabases related to Salton Sea Geothermal Field. It includes all input and output files used with the Geothermal Exploration Artificial Intelligence. Input and output files are sorted into three categories: raw data, pre-processed data, and analysis (post-processed data). In each of these categories there are six additional types of raster catalogs which are titled Radar, SWIR, Thermal, Geophysics, Geology, and Wells. The files are used with the Geothermal Exploration Artificial Intelligence for the Salton Sea Geothermal Site to identify indicators of blind geothermal systems. The included zip file is a geodatabase to be used with ArcGIS and the tar file is an inclusive database that encompasses the inputs and outputs for the Salton Sea Geothermal Site.

15 GEOTHERMAL ENERGY↗
DOE OSTI2021

Nutrient and stress tolerance traits linked to fungal responses to global change: Four case studies

In this case study analysis, we identified fungal traits that were associated with the responses of taxa to 4 global change factors: elevated CO2, warming and drying, increased precipitation, and nitrogen (N) enrichment. We developed a trait-based framework predicting that as global change increases limitation of a given nutrient, fungal taxa with traits that target that nutrient will represent a larger proportion of the community (and vice versa). In addition, we expected that warming and drying and N enrichment would generate environmental stress for fungi and may select for stress tolerance traits. We tested the framework by analyzing fungal community data from previously published field manipulations and linking taxa to functional gene traits from the MycoCosm Fungal Portal. Altogether, fungal genera tended to respond similarly to 3 elements of global change: increased precipitation, N enrichment, and warming and drying. The genera that proliferated under these changes also tended to possess functional genes for stress tolerance, which suggests that these global changes—even increases in precipitation—could have caused environmental stress that selected for certain taxa. In addition, these genera did not exhibit a strong capacity for C breakdown or P acquisition, so soil C turnover may slow down or remain unchanged following shifts in fungal community composition under global change. Since we did not find strong evidence that changes in nutrient limitation select for taxa with traits that target the more limiting nutrient, we revised our trait-based framework. The new framework sorts fungal taxa into Stress Tolerating versus C and P Targeting groups, with the global change elements of increased precipitation, warming and drying, and N enrichment selecting for the stress tolerators.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Quantitative analysis of mammalian translation initiation sites by FACS -seq

An approach combining fluorescence-activated cell sorting and high-throughput DNA sequencing (FACS-seq) was employed to determine the efficiency of start codon recognition for all possible translation initiation sites (TIS) utilizing AUG start codons. Using FACS-seq, we measured translation from a genetic reporter library representing all 65,536 possible TIS sequences spanning the -6 to +5 positions. We found that the motif RYMRMVAUGGC enhanced start codon recognition and translation efficiency. However, dinucleotide interactions, which cannot be conveyed by a single motif, were also important for modeling TIS efficiency. Our dataset combined with modeling allowed us to predict genome-wide translation initiation efficiency for all mRNA transcripts. Additionally, we screened somatic TIS mutations associated with tumorigenesis to identify candidate driver mutations consistent with known tumor expression patterns. Finally, we implemented a quantitative leaky scanning model to predict alternative initiation sites that produce truncated protein isoforms and compared predictions with ribosome footprint profiling data. The comprehensive analysis of the TIS sequence space enables quantitative predictions of translation initiation based on genome sequence.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Field and Model Data Associated with the Manuscript “Drivers of Streamflow Intermittency in Humid Regions: 2. Evaluating Controls on Flow Persistence in an Urbanized Catchment”

This package contains field data, modeling files, and scripts supporting the investigation of the drivers of streamflow intermittency in an urbanized catchment. It includes the field data collected from electrical resistivity tomography (ERT) surveys, distributed temperature sensing (DTS), continuous self-potential (SP) monitoring, groundwater and stilling well. In addition, it contains the data and results of the coupled water- and electrical-flow model developed using the COMSOL Multiphysics and Advanced Terrestrial Simulator (ATS), as well as software files and Jupyter notebooks used to process the data and generate figures in the manuscript submitted for peer review. The data archive is organized in the following directories: 1) Climate Includes hourly precipitation and daily evapotranspiration time series (2024 – 2025) provided as CSV files, alongside a text file detailing dataset units. 2) Coupled_model Field_Application subfolder contains the ATS XML input scripts, data files, output data for the SP site. It also contains the Jupyter notebook (Plot_final_calib.ipynb) to visualize the results of the modeled SP, stream-groundwater exchange and moisture content. The flow model simulation is executed using the ATS XML scripts and the included Python script (generate_data_set.py) to convert ATS output to COMSOL-ready input. COMSOL Multiphysics template (.m can only be used with COMSOL with MATLAB) is executed using the ATS output data to simulate the potential field. 3) Discharge Includes the electrical conductivity (EC) time series (provided as CSV files) from salt slug injections. It also includes the Jupyter notebook (Discharge_process.ipynyb) used to estimate discharge. All discharge measurements collated into rating_curve_processed.csv 4) DTS Contains collated DTS data including raw Stokes and anti-Stokes measurement (provided as .h5 file). It also includes DTS processing.ipynb, a Jupyter notebook for calibrating the DTS data using dts_calibration Python package. cooler_calibration.csv is the DTS calibration CSV used in the calibration sequence. 5) ERT Contains raw resistivity data (provided as CSV files), spatial location of each of the electrodes (provided as CSV files), and files used for the resistivity inversion. 6) Slug_test Includes the slug test data at all the groundwater wells provided as CSV files, as well as the Jupyter notebook (Slug_test.ipynb) for calculating hydraulic conductivity. 7) SP Contains the SP data collected in field at the SP sites (provided as CSV files). 8) Well_data Contains two subfolders: 1) Raw, which provides unprocessed pressure, electrical conductivity and temperature timeseries downloaded from the loggers in all the groundwater and stilling wells, and 2) Processed, which contains sorted, QA/QC timeseries data for each well. The data archive also contains data_process.ipynb, a Jupyter notebook used for field data analysis and generating figures (plotting well, SP, climate, and discharge data, as well as calculating head gradient at sites with nested groundwater wells). Note: Code files (.ipynb, .py, .xml) can be opened in any standard code editor, .exo file can be viewed using Paraview, .h5 files can be opened using HDFView software and h5py Python package, and .resipy file can be opened with the open-source ResIPy software.

ATS↗
DOE OSTI2026

Field and Model Data Associated with the Manuscript “Drivers of Streamflow Intermittency in Humid Regions: 1. Evaluating Above- and Below-ground Controls of Flow Persistence in a Forested Catchment”

This package contains field data, modeling files, and scripts supporting the investigation of the drivers of streamflow intermittency in a forested catchment. It includes the field data collected from electrical resistivity tomography (ERT) surveys, ground penetrating radar (GPR), continuous self-potential (SP) monitoring, electromagnetic (EM) imaging, groundwater and stilling well. In addition, it contains the data and results of the coupled water- and electrical-flow model developed using the COMSOL Multiphysics and Advanced Terrestrial Simulator (ATS), as well as software files and Jupyter notebooks used to process the data and generate figures in the manuscript submitted for peer review. The data archive is organized in the following directories: 1) Climate Includes hourly precipitation and daily evapotranspiration time series (2024 – 2025) provided as CSV files, alongside a text file detailing dataset units. 2) Coupled_model Contains two subfolders: Synthetic and Field_Application subfolder. Synthetic subfolder contains the ATS XML input script (can be opened using any code editor) for the four synthetic hydrological cases tested (Connected and gaining, Connected and losing, Disconnected and losing, and dry stream). It also includes other experimental cases to test the influence of precipitation and concentration gradient. For each synthetic case, the flow model simulation is executed using the ATS XML scripts and the included Python script (generate_data_set.py) to convert ATS output to COMSOL-ready input. COMSOL Multiphysics template (.mph can be opened with the commercial software COMSOL and requires a license) is executed using the ATS output data to simulate the potential field. It also includes the Synthetic_model_plot.ipynb (can be opened using any code editor) to visualize the SP result and generate manuscript figures. The data subfolder contains mesh files to run both the ATS (.exo and .stl files can be viewed using Paraview; .h5 files can be opened using HDFView software and h5py Python package) and COMSOL models. Field_Application subfolder contains two subfolders: ES_MDA_inversion and Final_Model. ES_MDA_inversion contains the Python script (.py can be opened using any code editor) and SP observation data used to run the Ensemble Smoother with Multiple Data Assimilation (ES-MDA) inversion sequence to get the optimal model parameters. The Final_model subfolder contains the ATS XML input scripts, data files, output data for the two SP sites. The same workflow steps outlined for the Synthetic subfolder apply here. It also contains the Jupyter notebook (Plot_final_calib.ipynb) to visualize the results of the modeled SP, stream-groundwater exchange and moisture content. 3) Discharge Includes the electrical conductivity (EC) time series (provided as CSV files) from salt slug injections. It also includes the Jupyter notebook (Discharge_process.ipynyb) used to estimate discharge. All discharge measurements collated into rating_curve_processed.csv 4) EM Contains the CSV file of the EM data from the DUALEM-42, including spatial coordinates (x, y, z), apparent conductivity, and in-phase measurements at 2 m coil separations for horizontal coplanar (HCP) and perpendicular (PRP) geometries. 5) ERT Contains raw resistivity data (provided as CSV files), spatial location of each of the electrodes (provided as CSV files), and files used for the resistivity inversion (.resipy can be opened with the open-source ResIPy software). 6) GPR Includes GPR field datasets collected at 100 MHz and 250 MHz antenna frequencies, along with the processing/interpretation project file (GPR_process.gpz can be viewed using EKKO_Project 6, a commercial software by Sensors & Software that requires a license). 7) Slug_test Includes the slug test data at all the groundwater wells provided as CSV files, as well as the Jupyter notebook (Slug_test.ipynb) for calculating hydraulic conductivity. 8) SP Contains the SP data collected in field at the two SP sites (one in the perennial reach and the other in the intermittent reach), provided as DAT files. 9) Well_data Contains two subfolders: 1) Raw, which provides unprocessed pressure, electrical conductivity and temperature timeseries downloaded from the loggers in all the groundwater and stilling wells, and 2) Processed, which contains sorted, QA/QC timeseries data for each well. The data archive also contains data_process.ipynb, a Jupyter notebook used for field data analysis and generating figures (plotting well, SP, climate, and discharge data, as well as calculating head gradient at sites with nested groundwater wells). It also includes DTW.ipynb, a Jupyter notebook containing the code for the dynamic time warping (DTW) with sliding window to evaluate SP signal synchronicity.

ATS↗