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At least 37 records · Page 2

Structural characterization of influenza group 1 chimeric hemagglutinins as broad vaccine immunogens

Chimeric hemagglutinins (cHA) appear to be promising for the design and development of universal influenza vaccines. Influenza A group 1 cHAs, cH5/1, cH8/1, and cH11/1, comprising an H1 stem attached to either an H5, H8, or H11 globular head, have been used sequentially as vaccine immunogens in human clinical trials and induced high levels of broadly protective antibodies. Using X-ray crystallography and negative-stain electron microscopy, we determined structures of cH5/1, cH8/1, and cH11/1 HAs in their apo (unliganded) and antibody Fab-bound states. Stem-reactive antibodies 3E1 and 31.b.09 recognize their cognate epitopes in cH5/1, cH8/1, and cH11/1 HAs. However, with cH5/1, the head domains are rotated by 35 to 45° around the threefold axis of the HA trimer compared to native HA with a more splayed-open conformation at the stem base. cH11/1 with 3E1 is structurally more native-like but resembles cH5/1 with 31.b.09, whereas cH8/1 with 31.b.09 exhibited a range of closed-to-open stem configurations with some separation of head and stem domains. Furthermore, all of these group 1 cHAs effectively bound a broad head trimer interface antibody and other broad stem antibodies. Thus, the cHAs exhibit structural plasticity without compromising the stem and head trimer interface epitopes for elicitation of influenza A group 1 cross-reactive antibodies.

Science & Technology - Other Topics↗

Isopropyl 3-deoxy-α- D - ribo -hexopyranoside (isopropyl 3-deoxy-α-D-glucopyranoside): evaluating trends in structural parameters

Isopropyl 3-de­oxy-α-D-ribo-hexo­pyran­oside (isopropyl 3-de­oxy-α-D-gluco­py­ran­oside), C 9 H 18 O 5 , (I), crystallizes from a methanol–ethyl acetate solvent mixture at room temperature in a 4C1 chair con­form­ation that is slightly dis­torted towards the C5 S C1 twist-boat form. A com­parison of the structural parameters in (I), methyl α-D-gluco­pyran­oside, (II), α-D-gluco­pyranosyl-(1→4)-D-glucitol (maltitol), (III), and 3-de­oxy-α-D-ribo-hexo­pyran­ose (3-de­oxy-α-D-gluco­pyran­ose), (IV), shows that most endocyclic and exocyclic bond lengths, valence bond angles and torsion angles in the aldohexo­pyranosyl rings are more affected by anomeric configuration, aglycone structure and/or the con­form­ation of exocyclic substituents, such as hy­droxy­methyl groups, than by mono­deoxy­genation at C3. The structural effects observed in the crystal structures of (I)–(IV) were confirmed though density functional theory (DFT) calculations in com­puted structures (I) c –(IV) c . Exocyclic hy­droxy­methyl groups adopt the gauche–gauche (gg) con­form­ation (H5 anti to O6) in (I) and (III), and the gauche–trans (gt) con­form­ation (C4 anti to O6) in (II) and (IV). The O-glycoside linkage con­form­ations in (I) and (III) resemble those observed in disaccharides containing β-(1→4) linkages.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Identifying the Best High‐Biomass Sorghum Hybrids Based on Biomass Yield Potential and Feedstock Quality Affected by Nitrogen Fertility Management Under Various Environments

The growing interest in high-biomass sorghum ( Sorghum bicolor L. Moench), hereafter referred to as sorghum, as a bioenergy feedstock in the United States requires an understanding of geographical adaptation to identify the most suitable hybrids for the Midwest. In this study, 13 sorghum hybrids (H1–H13) were evaluated for biomass yield potential in central and southern IL over two growing seasons (2022 and 2023). In addition to biomass yield, the effects of nitrogen (N) fertilization on yield, nutrient removal (N, P, and K), and feedstock composition (cellulose, hemicellulose, lignin, and soluble fractions) were determined to identify the best-performing sorghum hybrid across environmental gradients. The experimental design was a split-plot arrangement within a randomized complete block design with four replications at each of two locations: N rates (0 and 112 kg-N ha −1 ) as a whole plot factor and 13 sorghum hybrids as a subplot factor. As a result, complex genotypes (13 hybrids) by environment (2 sites and 2 years) and management (2 N rates) interactions were observed in biomass yield. The best hybrids at both sites were H1 (ATx2932/F10702_PSL) and H13 (TX08001), which were very photoperiod sensitive (PS). These hybrids produced superior biomass yield, and they also exhibited less nutrient removal and high energy-rich feedstock compositions (cellulose, hemicellulose, and lignin). Biomass yield potential was associated with morphological and phenological traits according to environmental conditions. Low-yielding hybrids were short-stature (H5 and H6) with pollinators (F10801_PSL-3dw and F10805_PSL-3dw) that are recessive at the Dw3 locus. Moderate PS hybrids (H7, H8, H11, and H12) that produced grain panicles at harvest showed high biomass yield plasticity and excessive nutrient removal as they accumulated high K concentrations in biomass tissues and high N and P in grain panicles.

09 BIOMASS FUELS↗

Focused‐beam X‐ray fluorescence and diffraction microtomographies for mineralogical and chemical characterization of unsectioned extraterrestrial samples

Abstract This study describes the application of new synchrotron X‐ray fluorescence (XRF) and diffraction (XRD) microtomographies for the 3‐D visualization of chemical and mineralogical variations in unsectioned extraterrestrial samples. These improved methods have been applied to three compositionally diverse chondritic meteorite samples that were between 300 and 400 μm in diameter, including samples prepared from fragments of the CR2 chondrite LaPaz Icefield (LAP) 02342, H5 chondrite MacAlpine Hills (MAC) 88203, and the CM2 chondrite Murchison. The synchrotron‐based XRF and XRD tomographies used are focused‐beam techniques that measure the intensities of fluorescent and diffracted X‐rays in a sample simultaneously during irradiation by a high‐energy microfocused incident X‐ray beam. Measured sinograms of the emitted and diffracted intensities were then tomographically reconstructed to generate 2‐D slices of XRF and XRD intensity through the sample, with reconstructed pixel resolution of 1–2 μm, defined by the resolution of the focused incident X‐ray beam. For sample LAP 02342, primary mineral phases that were visualized in reconstructed slices using these techniques included isolated grains of α‐Fe, orthopyroxene, and olivine. For our sample of MAC 88203, XRF/XRD tomography allowed visualization of forsteritic olivine as a primary mineral phase, a vitrified fusion crust at the sample surface, identification of localized Cr‐rich spinels at spatial resolutions of several micrometers, and imaging of a plagioclase‐rich glassy matrix. In the sample of Murchison, major identifiable phases include clinoenstatite‐ and olivine‐rich chondrules, variable serpentine matrix minerals and small Cr‐rich spinels. Most notable in the tomographic analysis of Murchison is the ability to quantitatively distinguish and visualize the complex mixture of serpentine‐group minerals and associated tochilinite–cronstedtite intergrowths. These methods provide new opportunities for spatially resolved characterization of sample texture, mineralogy, crystal structure, and chemical state in unsectioned samples. This provides researchers an ability to characterize such samples internally with minimal disruption of sample micro‐structures and chemistry, possibly without the need for sample extraction from some types of sampling and capture media.

Geochemistry & Geophysics↗

Influenza A Virus Multicycle Replication Yields Comparable Viral Population Emergence in Human Respiratory and Ocular Cell Types

While primarily considered a respiratory pathogen, influenza A virus (IAV) is nonetheless capable of spreading to, and replicating in, numerous extrapulmonary tissues in humans. However, within-host assessments of genetic diversity during multicycle replication have been largely limited to respiratory tract tissues and specimens. As selective pressures can vary greatly between anatomical sites, there is a need to examine how measures of viral diversity may vary between influenza viruses exhibiting different tropisms in humans, as well as following influenza virus infection of cells derived from different organ systems. Here, we employed human primary tissue constructs emulative of the human airway or corneal surface, and we infected both with a panel of human- and avian-origin IAV, inclusive of H1 and H3 subtype human viruses and highly pathogenic H5 and H7 subtype viruses, which are associated with both respiratory disease and conjunctivitis following human infection. While both cell types supported productive replication of all viruses, airway-derived tissue constructs elicited greater induction of genes associated with antiviral responses than did corneal-derived constructs. We used next-generation sequencing to examine viral mutations and population diversity, utilizing several metrics. With few exceptions, generally comparable measures of viral diversity and mutational frequency were detected following homologous virus infection of both respiratory-origin and ocular-origin tissue constructs. Expansion of within-host assessments of genetic diversity to include IAV with atypical clinical presentations in humans or in extrapulmonary cell types can provide greater insight into understanding those features most prone to modulation in the context of viral tropism.

59 BASIC BIOLOGICAL SCIENCES↗

Diffraction imaging of light induced dynamics in xenon-doped helium nanodroplets

Time-resolved wide-angle coherent diffraction imaging of individual helium nanodroplets, doped with xenon and excited with an 800 nm NIR laser pulse. Raw and preprocessed pattern, together with useful metadata, are contained in HDF5 files. Every field in the H5 container comes with a description, under the field "description", and the actual data under the field "data". For further information about the dataset see the [ArXiv article](https://arxiv.org/abs/2205.04154 ) and Bruno Langbehn's [PhD thesis](https://depositonce.tu-berlin.de/handle/11303/13189).

FERMI FEL-1↗

Diffraction imaging of light induced dynamics in xenon-doped helium nanodroplets

Time-resolved wide-angle coherent diffraction imaging of individual helium nanodroplets, doped with xenon and excited with an 800 nm NIR laser pulse. Raw and preprocessed pattern, together with useful metadata, are contained in HDF5 files. Every field in the H5 container comes with a description, under the field "description", and the actual data under the field "data". For further information about the dataset see the [ArXiv article](https://arxiv.org/abs/2205.04154 ) and Bruno Langbehn's [PhD thesis](https://depositonce.tu-berlin.de/handle/11303/13189).

FERMI FEL-1↗

XRFtomo

Based on [1], XRFtomo brings together a variety of image processing tools used for preparing, processing and reconstructing 3D renditions of samples imaged using a synchrotron-based x-ray fluorescence (XRF) microprobe or nanoprobe at the Advanced Photon Source (APS). This software bridges the gap between data acquisition and visualization by providing tools to adjust for misalignment in the imaging process and tools for running reconstructions[2], all with the use of a GUI or command line. XRFtomo accepts .h5 files processed through MAPS[3] and it outputs reconstructed cross-sections, projections, sinograms, metadata, and a configuration file with last-used parameters for rapid processing the next time the program is launched. These images serve as inputs for other 3D visualization software for generating volumetric renderings and animations.

Marin, Fabrico↗

SEM and STEM X-ray spectrum images

This is supplemental information to a paper tentatively titled Applying Data Analytics Methods to X-ray Spectrum Images. Datasets are in the format of .h5 in the pyUSID flavor. SEM_small.h5 is 5 keV beam energy map of a TiB2 ceramic puck. SEM_large.h5 is a 20 keV map of the same sample. STEM.h5 is a STEM 200 keV map of neutron-irradiated tungsten (due to transmutation burnout, it has become a W-Re-Os alloy).

36 MATERIALS SCIENCE↗

Imperial Valley Dark Fiber Project Continuous DAS Data

The Imperial Valley Dark Fiber Project acquired Distributed Acoustic Sensing (DAS) seismic data on a ~28 km segment of dark fiber between the cities of Calipatria and Imperial in the Imperial Valley, Southern California. Dark fiber refers to unused optical fiber cables in telecommunications networks and is repurposed in this project for DAS applications. The objective, which is further detailed in the attached journal article from Ajo-Franklin et al., is to demonstrate dark fiber DAS as a tool for basin-scale geothermal exploration and monitoring. The included DAS data were recorded during two days at the beginning the project. Data is stored in the .h5 (HDF5) file format, readable using various software tools, including the 'h5read' and 'h5info' functions in Matlab. Provided here are examples of methods to read and use the data with the 'h5py' package in Python.

15 GEOTHERMAL ENERGY↗

Data and scripts associated with the manuscript evaluating the hydrologic responses of the Pacific Northwest watersheds to wildfires (v2)

This data package is associated with the publication “Evaluating Post-fire Watershed Response to Varying Burn Severity and Precipitation Regimes Using Fully-distributed and Integrated Hydrologic Models” submitted to Journal of Hydrology (Li et al. 2025). In this study, we employed the Advanced Terrestrial Simulator (ATS), an integrated watershed model that couples surface flow, subsurface flow, and canopy biophysical processes, to investigate post-fire hydrologic responses in a few selected watersheds with varying burn severity.The data package contains the required input data (meteorological forcing, Leaf Area Index, wildfire burn severities, etc.) to run the model, configuration files, the Jupyter notebooks in Python to pre-process and post-process data, the figures in the manuscript, and the modeling output files. The variables include watershed-averaged evapotranspiration, watershed-averaged surface/subsurface/canopy water content, and river discharge at watershed outlet.The data package contains a file-level metadata that lists and describes all the files contained in the data package (ATS_flmd.csv), a data dictionary file that defines columns headers across all csv files contained in the data package (ATS_dd.csv), a data package level readme file (the current file), and four zipped folders.The ‘data’ folder provides data needed to run the model in .h5, .i2s, .xyz, .shp, and .exo formats. The sub-folders are for each data types. The ‘model’ folder provides input files (.xml format) and essential model outputs. Each sub-folder provides the files from each simulated watershed. The ‘notebooks’ folder provides the Jupyter notebooks (.ipynb format) for pre- and post- processing model files, and for producing the figures in the manuscript. The ‘figures’ folder provides the figures associated with manuscript in .pdf and .png formats.The ‘model’ folder and the ‘data’ folder have been split into 5GB-large pieces using the Linux command ‘split -b 5120m model.zip model.zip.’ and ‘split -b 5120m data.zip data.zip.’, respectively. They can be merged back using the Linux command ‘cat model.zip.* > model.zip’ and ‘cat data.zip.* > data.zip’, respectively.

54 ENVIRONMENTAL SCIENCES↗

Dataset: "Widespread Drought-driven Declines in Streamflows and Water quality in the Upper Colorado River Basin (1998-2022)"

This data package contains the associated data and scripts for Nagamoto, E., Ombadi, M., Ciulla, F. et al. Widespread drought-driven declines in streamflows and water quality in the Upper Colorado River Basin during 1998-2022. Commun Earth Environ 7, 734 (2026). https://doi.org/10.1038/s43247-026-03890-5. This purpose of this study was to investigate the impact of the 21st century drought on water quantity and quality at catchments throughout the Upper Colorado River Basin (UCRB). We used stream flow, water temperature, specific conductance, air temperature, precipitation, and catchment attribute data for over 200 sites in the UCRB, collected from the National Water Information System using Basin3D (Varadharajan, 2023), GAGESII (Falcone, 2010), and the Google Earth Engine. We identified years of severe drought between 1998 and 2022 using the Standardized Precipitation Evaporation Index (SPEI), then calculated the relative change percentage of the stream flow, water temperature, and specific conductance from drought versus non-drought years. We used the attribute information from GAGESII to investigate what physical traits of catchments are associated streamflow vulnerability (greater relative change) or resilience to drought. We used land cover data from the National Land Cover Database (USGS, 2024) to assess any changes to physical attributes that may not be represented in the static attributes information in GAGESII. To increase data availability, we modeled stream temperature using methods from Willard, 2023. While the study period is water years 1998 to 2022, the raw water quantity and quality data extends to 1950 and the meteorological data extends to 1980. The data and code can be downloaded via the UCRB_drought.zip. Within the zip, the files are organized as follows: - INPUTS: Contains all input data used in UCRB_Drought_Workflow.ipynb - OUTPUTS: Contains all intermediate data created from UCRB_Drought_Workflow.ipynb as well as final products including the calculated Standardized Evapotranspiration Index (SPEI) - climatic_variables: The code used to collect meteorologic data from Google Earth Engine - feature_importance: The code used for the catchment attributes analysis - preprocessing: Code used in UCRB_Drought_Workflow_Preprocessing.ipynb - pyeto: Code used in UCRB_Drought_Workflow_Preprocessing.ipynb - calculations: Code used in UCRB_Drought_Workflow_Impacts.ipynb - plotting: Code used in UCRB_Drought_Workflow_Impacts.ipynb - README.md - UCRB_Drought_Workflow_Preprocessing.ipynb: The code used to prep raw data for the analysis - UCRB_Drought_Workflow_Impact.ipynb: The code which uses the prepped raw data for analysis, and plots all figures - requirements_ucrb-drought_v2.yml: The requirements file to create a virtual environment and Jupyter Lab kernel to run the code The INPUTS folder is organized into the following major directories and sub-directories. The "RDC_WT_SC_RAW" folder contains raw data for streamflow, water temperature, and specific conductance in a ".h5" file. The "NLCD_RAW" folder contains ".csv" files with annual land cover percentages for counties within the UCRB. The "MET_RAW" folder contains a ".csv" file with monthly meteorological data (air temperature and precipitation) for the sites in the UCRB which was obtained from code in the climatic_variables folder. The "GAGESII" folder contains ".csv" files with physical catchment attribute variables for catchments across the country. The "WT_LSTM_data" folder contains ".csv" files with calculated WT (Willard, 2023) and the associated RMSEs. The "Upper_Colorado_River_Basin_Boundary" folder contains geographic data including a shapefile for plotting in the UCRB_Drought_Workflow.ipynb. The "RESERVOIRS_RAW" folder contains ".csv" files for each reservoir in the UCRB with daily reservoir storage. There are also two files in the INPUTS folder that have combined reservoir storage data and reservoir metadata. The OUTPUTS folder is organized into the following major directories and sub-directories. The "RDC_WT_SC_data" folder contains a folder "Water_year" with the associated cleaned data, metadata, and data availability information in ".csv" files, a folder "Median_Relchange" with the relative change comparing drought to non-drought years in ".csv" files, and a folder "Peak95_Min5_Relchange" that has ".csv" files for the relative change in peak (95th %) and minimum (5th %) variables. The "NLCD_data" folder contains the difference in land cover from the beginning to end of the study period and the percentage of the county that is within UCRB bounds can be found in Nagamoto et al (2025)). The "MET_data" folder contains separated monthly air temperature and precipitation data and the calculated PET in ".csv" files. The "SPEI_data" folder contains ".csv" files with calculated SPEI values (one restricted to the study period and the other with information from the entire MET data period). The "Paper_Tables" folder contains two ".csv" files containing site information and data availability and information about the GAGESII trait aggregated categories. The base directory includes the file “flmd.csv” for a list and description of all files and the file “dd.csv” for data dictionaries. Scripts for preprocessing, analysis, and figure generation are located in the associated GitHub repository found at [https://github.com/iNAIADS/drought-impacts/tree/develop/UCRB-drought]. UPDATE 1: Title and code file updated to match submitted manuscript 10-15-2025. UPDATE 2: Code and data files updated to match revised manuscript 3-4-2026. UPDATE 3: Code and data files updated to match revised manuscript 6-7-2026. ** NOTE: DD and FLMD have not been updated yet. UPDATE 4: Added associated Manuscript information and DD and FLMD have been updated. To cite this code, please use the following BibTeX: @misc{nagamoto2025drought, author = {Emily Nagamoto and Fabio Ciulla and Mohammad Ombadi and Jared Willard and Rosemary Carroll and Charuleka Varadharajan}, title = {Dataset: "Widespread Drought-driven Declines in Streamflows and Water quality in the Upper Colorado River Basin (1998-2022)"}, year = {2025}, doi = {10.15485/2551894}, publisher = {ESS-DIVE Repository}, url = {https://data.ess-dive.lbl.gov/datasets/doi:10.15485/2551894} }

54 ENVIRONMENTAL SCIENCES↗

Hydrologic Model Data for the East Fork Poplar Creek Watershed Simulated with the Advanced Terrestrial Simulator (ATS): Streamflow and Network Expansion–Contraction Dynamics

This dataset supports hydrologic modeling and stream network expansion–contraction analysis for the East Fork Poplar Creek (EFPC) Watershed in Tennessee. It includes a Jupyter notebook for model setup, model configuration files, simulation outputs, and derived products used to evaluate model performance and investigate stream dynamics under varying hydrologic conditions. The dataset was generated using the Watershed Workflow Python package and the Advanced Terrestrial Simulator (ATS), enabling integrated surface–subsurface hydrologic simulations using a stream-aligned mesh. Outputs include high-resolution time series of streamflow, active network length, water table depth, and related hydrologic variables. Also included are spatially explicit stream persistency indices and classifications of reaches as perennial or non-perennial. These data facilitate reproducibility and support further research on stream intermittency and variability in network extent.The model data archive is organized in following directories:1) model_setup_inputsContains the Watershed Workflow Jupyter notebooks (accessed through any open source code editor), selected input datasets, and resulting ATS input files, including XML files (access through any open source code editor), computational mesh (.exo files can be viewed using Paraview), and meteorological forcing files (.h5 files can be accessed through h5py python package and HDFView open source software). 2) model_outputsIncludes ATS simulation outputs relevant to this study. Time series of spatially integrated or averaged variables (e.g., streamflow, water table depth) are provided as CSV files. Select spatial fields (e.g., ponded depth and water table depth) are saved as pickled Python objects to reduce file size, and can be accessed through pickle package in Python. Key geometry objects from Watershed Workflow—such as the surface mesh and river tree—are also included to support analysis of streamflow persistency and expansion–contraction dynamics. These files can also be accessed through Watershed Workflow Python package.3) model_evaluationProvides observed streamflow time series and field survey-based flow regime classifications used to evaluate model performance. Jupyter notebooks for processing ATS outputs and comparing model predictions with observations to build confidence in the model prior to scientific analysis are also included.4) Q_L_relationshipsContains workflows for generating time series of discharge, active network length, and related hydrologic variables used in the stream network expansion–contraction analysis. Includes routines for delineating baseflow-dominated periods. For each catchment, notebooks and processed data (as pickled DataFrames accessed through Pandas Python package) are provided. 5) figure_scriptsProvides the Jupyter notebooks used to generate the figures presented in the paper.

54 ENVIRONMENTAL SCIENCES↗

PFLOTRAN modeling data and scripts associated with “Refining the Hydrogeologic Framework of a Large River Corridor Model Using Waterborne Transient Electromagnetics”

NOTE: The manuscript associated with this data package is currently in review. The data may be revised based on reviewer feedback. Upon manuscript acceptance, this data package will be updated with the final dataset and additional metadata. This data package is associated with the publication “Refining the Hydrogeologic Framework of a Large River Corridor Model Using Waterborne Transient Electromagnetics” submitted to Water Resources Research (Terry et al. 2025). The data package contains the groundwater modeling dataset from PFLOTRAN software. It includes the python script for mesh generation, boundary condition setting, PFLOTRAN input deck formation and postprocessing. It couples groundwater flow and species transport for Hanford Reach river corridor and pipelines the model generation and processing. This model can be used to easily generate the model and analysis for Hanford site. It can also be adjusted to other hydrologic area with ease. For details on how to navigate data packages generated by this project, see https://data.ess-dive.lbl.gov/portals/PNNLRiverCorridorSFA/About. The data package consists of 6 folders: (1) “data” contains all necessary data as input and intermediate data for processing; (2) “mesh” contains all mesh related files to generate mesh in Hanford Reach river corridor; (3) “model_run” contains the generated script for PFLOTRAN modeling; (4) “notebooks” contains all the Python script to generate the model; (5) “output” contains all the output from the computation; (6) “postprocessing” contains the Python script to generate scientific figure for manuscript. All files are .csv (comma-separated values), .h5 (HDF5 format), .in (input files), .ipynb (Jupyter notebooks), .p (Python pickle), .png (images), .PNG (images), .py (Python scripts), .pyc (Python bytecode), .r (R scripts), .sh (shell scripts), .txt (text files), .vtu (3D mesh/visualization format), .xz (compressed archive), or .zip (compressed archive).

54 ENVIRONMENTAL SCIENCES↗

Data, model inputs, and analysis scripts associated with a manuscript on stream intermittency controls across spatial scales in Pacific Northwest watersheds

NOTE: The manuscript associated with this data package is currently in review. The data may be revised based on reviewer feedback. Upon manuscript acceptance, this data package will be updated with the final dataset and additional metadata. This data package is associated with the manuscript "Hydroclimatic Memory and Watershed Template Shape Stream Intermittency: Multi-scale Attribution Using Process-based Simulation and Explainable ML" by Niroula et al. (2026), submitted to Water Resources Research (WRR). The study investigates the dominant controls on stream intermittency across local, reach, and watershed scales using a coupled process-based simulation and explainable machine-learning framework. Long-term daily simulations from the Advanced Terrestrial Simulator (ATS) were used to generate wetness states and ponded-depth responses over river-corridor cells. These ATS outputs were then aggregated across scales and used to train XGBoost (eXtreme Gradient Boosting) models. SHAP (SHapley Additive exPlanations) was applied to quantify the relative importance of hydroclimatic forcings, watershed template attributes, and antecedent-memory effects in shaping intermittency behavior. The analysis is carried out for three contrasting Pacific Northwest watersheds: Oak Creek (OCW), American River Watershed (ARW), and H.J. Andrews (HJA). Across these testbeds, the package contains ATS-ready watershed inputs, ATS run configuration and selected output files, model-evaluation data products, intermittency-analysis datasets, machine-learning target-feature tables, SHAP outputs, and notebooks used to organize, analyze, and visualize results. At a high level, the package documents a workflow in which ATS provides the physically based simulation backbone and explainable machine learning is used as a post-processing attribution tool. The contents are intended to support interpretation of the manuscript figures and results, provide context for how intermittency metrics were generated at multiple scales, and preserve the key artifacts needed to understand and reuse the analysis workflow. The package contains a high-level directory summary file (`summary.txt`) and four main content folders (1) `evaluation_plots` contains evaluation figures and supporting evaluation datasets; (2) `intermittency_plots` contains intermittency-focused analysis notebook and prepared datasets; (3) `ml-training-and-shap_values_plots` contains ML training inputs, SHAP outputs, and figure-generation notebooks; and (4) `watershed_mesh_and_ats_input` contains ATS model setup materials, forcing inputs, geometry, and selected run files. More specifically, the `evaluation_plots` folder contains the notebook used for ATS evaluation plotting and site-specific evaluation datasets. These include evapotranspiration and water-balance products for three watersheds, as well as an Oak Creek field-measurement discharge file. The `intermittency_plots` folder contains the notebook used for intermittency analysis and the prepared datasets used to analyze intermittent and non-intermittent wetness behavior across the study watersheds. The `ml-training-and-shap_values_plots` folder contains notebooks and outputs for the machine-learning and explainability workflow. This includes the main XGBoost and SHAP notebook(s), a beeswarm plotting notebook, target-feature tables for machine-learning training, SHAP summary tables, and per-sample SHAP value archives. The `watershed_mesh_and_ats_input` folder contains ATS-related watershed inputs and supporting materials. This includes mesh and shape products, ATS-readable LAI and meteorological forcing inputs, selected ATS spinup and transient-run files, and a watershed workflow example notebook. Subdirectories are organized by watershed where applicable.All files are .cpg (codepage files), .csv (comma-separated values), .dbf (database files), .exo (Exodus mesh format), .h5 (HDF5 format), .ipynb (Jupyter notebooks), .pkl (Python pickle), .prj (projection files), .sh (shell scripts), .shp (shapefile geometry), .shx (shapefile index), .txt (text files), or .xml (markup data).

Advanced Terrestrial Simulator↗

A bespoke model of Arctic river basins based on hillslope delineation: Model Archive

This dataset is a model archive of the paper A bespoke model of Arctic river basins based on hillslope delineation (in prep), which introduces a watershed decomposition and parameterization method for large scale permafrost hydrology simulation. With this dataset, this study aims to address the research question: whether a computationally efficient hillslope-based modeling framework can reliably simulate discharge at Arctic river-basin scales. This dataset contains model input and output data for five modeling scenarios at a study site located in the Sagavanirktok River basin. The five modeling scenarios include three modeling cases under temperate conditions using full 3D, decomposed 3D, and decomposed 2D modeling strategies; and two modeling cases under actual Arctic conditions with permafrost using full 3D and decomposed 2D modeling strategies. Simulations were performed using the Advanced Terrestrial Simulator (ATS, v1.6 for three temperate scenarios and v1.5 for two Arctic scenarios), a physics-rich integrated surface–subsurface hydrologic model with cryo-hydrology features. For the three temperate models, simulations were conducted for the period of 10/01/1993 - 09/30/2002; and for the two Arctic models, simulations were conducted for the period of 01/01/1994 - 12/31/2002. To facilitate reproducibility of simulations, all datasets are organized hierarchically. The dataset contains: (1) Mesh files (.exo) for full 3D model, decomposed 3D models, and decomposed 2D models, located in huc/190604020802_gauge15906000/mesh/. Mesh files can be visualized through Paraview or read by Python. (2) Climate forcings (.h5) for full 3D model and decomposed 3D/2D models are located in huc/190604020802_gauge15906000/daymet_onePiece/, and huc/190604020802_gauge15906000/vp_pr_revised_daymet_1980_2006_with_wind/ separately. Accessible by Python. (3) Raw measured gage discharge (.csv) from USGS, located in huc/190604020802_gauge15906000/gaged_basin15906000_discharge_usgs/. Accessible by Python. (4) Delineated subdomain raster (.tif) and shape files (.shp), and the final parameterized results (.npy) for decomposed models, located in huc/190604020802_gauge15906000/data_preprocessed-meshing. Accessible by Python. (5) Temperate models are located in nonpermaf_huc190604020802_gauge15906000/, which includes three cases: decomposed 2D models (inside model_0*-hillslope_*), decomposed 3D models (inside model_1*-subcatchment_*), and full 3D model (inside model_2*-onepiece_*). Two step spin-up results (checkpoint_final.h5) are located in model_*1-*_spinup_steadystate and model_*2-*_spinup_cycle, separately, which are used to initialize real transient models. The input files (.xml) and output results (.dat) of the real transient models are located in model_*3-*_transient/. Especially, for two example hillslope models (ID=-11 and 11), additional h5py files are included in model_03-hillslope_transient/hillslope-11/, model_03-hillslope_transient/hillslope11, model_13-subcatchment_transient/subcatchment-11/, model_13-subcatchment_transient/subcatchment/11, respectively, which are used to plot the saturation figure (Figure 5) in the manuscript. Accessible by Python. (6) Arctic models are located in huc190604020802_gauge15906000/, which includes two cases: decomposed 2D models (inside model_04-hillslope_transient), and full 3D model (inside model_05-onepiece_transient_mannp1_ra). Three step spin-up results (checkpoint_final.h5) are located in model_01-column_freezeup/, model_02-column_spinup/, model_03-hillslope_spinup/, respectively, which are used to initialize real 2D transient hillslope models. The input files (.xml) and output results (.dat) of transient 2D hillslope models are located in model_04-hillslope_transient/. The input files (.xml) and output results (.dat) of the full 3D transient model is located in model_05-onepiece_transient_mannp1_ra/. The full 3D transient model is initialized by model_02-column_spinup/. Accessible by Python. (7) The MOSART routed discharge results (.csv) under Arctic conditions is located in huc190604020802_gauge15906000/MOSART/. Accessible by Python. (8) All Python codes (.py) used to parameterize full 3D model to decomposed 2D models are located in script/. These codes fit with watershed workflow (a watershed delineation tool) v1.4 under the branch gaob/v1.4 from https://github.com/gaobhub/watershed-workflow.git.

EARTH SCIENCE > CRYOSPHERE↗

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↗

Materials Data on BH5C4(N2O)2 by Materials Project

(B)6(CN)4(H5(C2N)2)2(CNH2)4(CHNO2)4(N2H)4(H(CO)2)2H2 crystallizes in the orthorhombic Pnn2 space group. The structure is zero-dimensional and consists of six boron molecules; four carbamic acid molecules; four diazene molecules; two formalin formaldehyde molecules; two hydrogen molecules; four hydrogen cyanide molecules; four methylamine molecules; and two n,n'-dimethylethylenediamine molecules.

36 MATERIALS SCIENCE↗