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WEBINAR, May 6: New Discoveries Using GeneLab

The NASA GeneLab project capitalizes on multi-omic technologies to maximize the return on spaceflight experiments. To do this, GeneLab maintains a publicly accessible database (GLDS) that houses spaceflight and spaceflight relevant multi-omics data and collaborates with NASA principal investigators and projects to generate additional omics data. GeneLab houses more than 220 transcriptomic, proteomic, metabolomic and epigenomic datasets from plant, animal and microbial experiments, with a growing number of these having been produced by the GeneLab sample processing lab. The GLDS contains rich metadata about each experiment and has recently integrated radiation dosimetry data from experiments flown on the Space Shuttle. GeneLab has also recently implemented an effort to present processed data in the GLDS in addition to the raw omics data. The processed data will enable interpretation of the data by a larger group of students, scientists and the general public. Standard pipelines for the transformation of raw data into visualizations were developed by four GeneLab Analysis Working Groups (animals, plants, microbes, multi-omics) comprised of over 120 scientists from NASA, industry, and academia. To explore the data, the GLDS provides users various tools for data analysis, collaborative workspace for file storage and sharing, and a visualization portal. The analysis platform built using the Galaxy toolshed provides access to a broad variety of users including those with limited bioinformatics experience and students to learn how to analyze spaceflight omics data. The visualization portal takes GeneLab one step closer to data democratization by removing all bioinformatics requisites to interpret transcriptomics data hosted in the repository. Discoveries made using GeneLab have begun and will continue to deepen our understanding of biology, advance the field of genomics, and help to discover cures for diseases, create better diagnostic tools, and ultimately allow astronauts to better withstand the rigors of long-duration spaceflight.

Sylvain V. Costes↗

NASA GeneLab: Open Science for Life in Space

The NASA GeneLab project capitalizes on multi-omic technologies to maximize the return on spaceflight experiments. To do this, GeneLab maintains a publicly accessible database (GLDS) that houses spaceflight and spaceflight relevant multi-omics data and collaborates with NASA principal investigators and projects to generate additional omics data. GeneLab houses more than 350 transcriptomic, proteomic, metabolomic and epigenomic datasets from plant, animal and microbial experiments, with a growing number of these having been produced by the GeneLab Sequencing Lab. The GLDS contains rich metadata about each experiment and has integrated radiation dosimetry data from experiments flown on the Space Shuttle, International Space Station, and Free Flying spacecrafts. With the increasing amount and complexity of omics data being generated, GeneLab utilizes community-defined, common models for metadata and terminology so that omics data and results are discoverable and reliably reproducible. GeneLab uses the ISA-Tab specification and semantic model for organizing and representing omics metadata. In addition to metadata standards, data files must be open-source file or common exchange formats to ensure accessibility and usability by all users. To ease data ingestion and transfer, the web-based submission tool allows PIs a user-friendly user interface to curate, organize, and publish their space relevant omics data. In the more recent years, data curation and submission portal has incorporated the FAIR principles making data findable, accessible, interoperable, and reusable. To increase reusability of data, GeneLab has implemented an effort to present processed data in the GLDS in addition to the raw omics data. The processed data will enable interpretation of the data by a larger group of students, scientists and the general public. Standard pipelines for the transformation of raw data into visualizations were developed by four GeneLab Analysis Working Groups (animals, plants, microbes, multi-omics) comprised of over 200 scientists from NASA, industry, and academia. To explore the data, the GLDS provides users various tools for data analysis, collaborative workspace for file storage and sharing, and a visualization portal. The analysis platform built using the Galaxy toolshed provides access to a broad variety of users including those with limited bioinformatics experience and students to learn how to analyze spaceflight omics data. The visualization portal takes GeneLab one step closer to data democratization by removing all bioinformatics requisites to interpret transcriptomics data hosted in the repository. To train the next generation of scientists, NASA offers training programs such as GeneLab 4 High School (GL4HS) and GeneLab 4 Universities. NLM Curation at a Scale Workshop 2022 | NASA GeneLab (GL4U) to teach students bioinformatics and computational biology methods to analyze omics data. Discoveries made using GeneLab have begun and will continue to deepen our understanding of biology, advance the field of genomics, and help to discover cures for diseases, create better diagnostic tools, and ultimately allow astronauts to better withstand the rigors of long-duration spaceflight.

GeneLab↗

Central Valley Water Resources II: Groundwater Sustainability Management Support in the California Central Valley using GRACE and InSAR Datasets

California’s Central Valley is one of the most productive agricultural regions in the United States, producing a fourth of the nation’s food supply. The water demand in this region is heavily dependent on groundwater resources, resulting in over pumping of aquifers at unsustainable rates during recent periods of severe drought. Over the past century, Central Valley aquifers have experienced a significant decline in groundwater levels, resulting in land subsidence and irreversible loss in groundwater storage. In 2014, the state enacted the Sustainable Groundwater Management Act, requiring high and medium priority subbasins to suspend overdraft and achieve sustainable levels of pumping and recharge by 2042.The California Department of Water Resources (DWR) oversees subbasin groundwater management; however, monitoring remains challenging due to sparse and inconsistent in situ data. To assist the DWR, this project developed a user-friendly executable application and an interactive visualization tool to quantify groundwater storage and land subsidence trends using remotely sensed and in situ data. The team utilized NASA’s Gravity Recovery and Climate Experiment (GRACE), GRACE Follow-On (GRACE-FO), Sentinel-1 C-band Synthetic Aperture Radar (C-SAR) interferograms, and Advanced Land Observing Satellite 2 (ALOS-2) Phased Array L-band Synthetic Aperture Radar 2 (PALSAR-2) interferograms in conjunction with well and GPS measurements to analyze groundwater and subsidence trends. GRACE and well data returns produced a strong Pearson correlation of .84, while Sentinel-1 and GPS data returns produced a Pearson correlation of .41 over the entire Central Valley. These findings suggest remotely sensed GRACE and interferometric SAR data can be used in the absence of in situ data.

DEVELOP Project Summary↗

Building a FAIR data ecosystem for incorporating single-cell transcriptomics data into agricultural genome to phenome research

Introduction The agriculture genomics community has numerous data submission standards available, but the standards for describing and storing single-cell (SC, e.g., scRNA- seq) data are comparatively underdeveloped. Methods To bridge this gap, we leveraged recent advancements in human genomics infrastructure, such as the integration of the Human Cell Atlas Data Portal with Terra, a secure, scalable, open-source platform for biomedical researchers to access data, run analysis tools, and collaborate. In parallel, the Single Cell Expression Atlas at EMBL-EBI offers a comprehensive data ingestion portal for high-throughput sequencing datasets, including plants, protists, and animals (including humans). Developing data tools connecting these resources would offer significant advantages to the agricultural genomics community. The FAANG data portal at EMBL-EBI emphasizes delivering rich metadata and highly accurate and reliable annotation of farmed animals but is not computationally linked to either of these resources. Results Herein, we describe a pilot-scale project that determines whether the current FAANG metadata standards for livestock can be used to ingest scRNA-seq datasets into Terra in a manner consistent with HCA Data Portal standards. Importantly, rich scRNA-seq metadata can now be brokered through the FAANG data portal using a semi-automated process, thereby avoiding the need for substantial expert curation. We have further extended the functionality of this tool so that validated and ingested SC files within the HCA Data Portal are transferred to Terra for further analysis. In addition, we verified data ingestion into Terra, hosted on Azure, and demonstrated the use of a workflow to analyze the first ingested porcine scRNA-seq dataset. Additionally, we have also developed prototype tools to visualize the output of scRNA-seq analyses on genome browsers to compare gene expression patterns across tissues and cell populations. This JBrowse tool now features distinct tracks, showcasing PBMC scRNA-seq alongside two bulk RNA-seq experiments. Discussion We intend to further build upon these existing tools to construct a scientist-friendly data resource and analytical ecosystem based on Findable, Accessible, Interoperable, and Reusable (FAIR) SC principles to facilitate SC-level genomic analysis through data ingestion, storage, retrieval, re-use, visualization, and comparative annotation across agricultural species.

Genetics & Heredity↗

Direct evidence from STXM analysis of enhanced oxygen storage capacity in ceria through the addition of Cu and Mg: Correlation of HT-WGS reaction performance

Here, scanning transmission X-ray microscopy (STXM) analysis was utilized to directly present visual evidence of changes in oxygen storage capacity (OSC) when small amounts of an additive were incorporated into CeO2. Specifically, the chemical map measured by STXM analysis differentiated between Cu-rich and Ce-rich areas to derive the proportion of Ce3+. Additionally, we found that the dispersion of Cu significantly influenced the formation of OSC. The findings were applied to the high-temperature water–gas shift reaction for producing high-purity hydrogen from waste-derived syngas, establishing a correlation with catalyst performance. Consequently, the CCM75 (Ce/Mg = 75/25) catalyst demonstrated the highest Cu dispersion and OSC values (6.9 %, 800.3 μmolO/gcat), and it also showed the highest CO conversion (79 % at 450 °C) and stability (−7.7 % at 450 °C after 50 h), attributed to the significant presence of active Cu. This study confirms previously reported interactions between Cu and CeO2 and uncovers the significant roles of Cu and Mg in this catalysis system, providing new understanding of the mechanisms that facilitate OSC improvement.

Lee, Ru-Ri↗

Modeling a Transient Pressurization with Active Cooling Sizing Tool

As interest in the area of in-space zero boil-off cryogenic propellant storage develops, the need to visualize and quantify cryogen behavior during ventless tank self-pressurization and subsequent cool-down with active thermal control has become apparent. During the course of a mission, such as the launch ascent phase, there are periods that power to the active cooling system will be unavailable. In addition, because it is not feasible to install vacuum jackets on large propellant tanks, as is typically done for in-space cryogenic applications for science payloads, instances like the launch ascent heating phase are important to study. Numerous efforts have been made to characterize cryogenic tank pressurization during ventless cryogen storage without active cooling, but few tools exist to model this behavior in a user-friendly environment for general use, and none exist that quantify the marginal active cooling system size needed for power down periods to manage tank pressure response once active cooling is resumed. This paper describes the Transient pressurization with Active Cooling Tool (TACT), which is based on a ventless three-lump homogeneous thermodynamic self-pressurization model1 coupled with an active cooling system estimator. TACT has been designed to estimate the pressurization of a heated but unvented cryogenic tank, assuming an unavailable power period followed by a given cryocooler heat removal rate. By receiving input data on the tank material and geometry, propellant initial conditions, and passive and transient heating rates, a pressurization and recovery profile can be found, which establishes the time needed to return to a designated pressure. This provides the ability to understand the effect that launch ascent and unpowered mission segments have on the size of an active cooling system. A sample of the trends found show that an active cooling system sized for twice the steady state heating rate would results in a reasonable time for tank pressure recovery with ZBO of a liquid oxygen propellant tank.

Guzik, Monica C.↗

Spatial orientation of the vestibular system

1. A simplified three-dimensional state space model of visual vestibular interaction was formulated. Matrix and dynamical system operators representing coupling from the semicircular canals and the visual system to the velocity storage integrator were incorporated into the model. 2. It was postulated that the system matrix for a tilted position was a composition of two linear transformations of the system matrix for the upright position. One transformation modifies the eigenvalues of the system matrix while another rotates the pitch and roll eigenvectors with the head, while maintaining the yaw axis eigenvector approximately spatially invariant. Using this representation, the response characteristics of the pitch, roll, and yaw eye velocity were obtained in terms of the eigenvalues and associated eigenvectors. 3. Using OKAN data obtained from monkeys and comparing to the model predictions, the eigenvalues and eigenvectors of the system matrix were identified as a function of tilt to the side or of tilt to the prone positions, using a modification of the Marquardt algorithm. The yaw eigenvector for right-side-down tilt and for downward pitch cross-coupling was approximately 30 degrees from the spatial vertical. For the prone position, the eigenvector was computed to be approximately 20 degrees relative to the spatial vertical. For both side-down and prone positions, oblique OKN induced along eigenvector directions generated OKAN which decayed to zero along a straight line with approximately a single time constant. This was verified by a spectral analysis of the residual sequence about the straight line fit to the decaying data. The residual sequence was associated with a narrow autocorrelation function and a wide power spectrum. 4. Parameters found using the Marquardt algorithm were incorporated into the model. Diagonal matrices in a head coordinate frame were introduced to represent the direct pathway and the coupling of the visual system to the integrator. Model simulations predicted the behavior of yaw and pitch OKN and OKAN when the animal was upright, as well as the cross-coupling in the tilted position. The trajectories in velocity space were also accurately simulated. 5. There were similarities between the monkey eigenvectors and human perception of the spatial vertical. For side-down tilts and downward eye velocity cross-coupling, there was only an Aubert (A) effect. For upward eye velocity cross-coupling there were both Muller (E) and Aubert (A) effects. The mean of the eigenvectors for upward and downward eye velocities overlay human 1 x g perceptual data.(ABSTRACT TRUNCATED AT 400 WORDS).

NASA Discipline Neuroscience↗

Electroless Formation of Hybrid Lithium Anodes for Fast Interfacial Ion Transport

Abstract Rechargeable batteries based on metallic anodes are of interest for fundamental and application‐focused studies of chemical and physical kinetics of liquids at solid interfaces. Approaches that allow facile creation of uniform coatings on these metals to prevent physical contact with liquid electrolytes, while enabling fast ion transport, are essential to address chemical instability of the anodes. Here, we report a simple electroless ion‐exchange chemistry for creating coatings of indium on lithium. By means of joint density functional theory and interfacial characterization experiments, we show that In coatings stabilize Li by multiple processes, including exceptionally fast surface diffusion of lithium ions and high chemical resistance to liquid electrolytes. Indium coatings also undergo reversible alloying reactions with lithium ions, facilitating design of high‐capacity hybrid In‐Li anodes that use both alloying and plating approaches for charge storage. By means of direct visualization, we further show that the coatings enable remarkably compact and uniform electrodeposition. The resultant In‐Li anodes are shown to exhibit minimal capacity fade in extended galvanostatic cycling when paired with commercial‐grade cathodes.

Choudhury, Snehashis↗

Electroless Formation of Hybrid Lithium Anodes for Fast Interfacial Ion Transport

Abstract Rechargeable batteries based on metallic anodes are of interest for fundamental and application‐focused studies of chemical and physical kinetics of liquids at solid interfaces. Approaches that allow facile creation of uniform coatings on these metals to prevent physical contact with liquid electrolytes, while enabling fast ion transport, are essential to address chemical instability of the anodes. Here, we report a simple electroless ion‐exchange chemistry for creating coatings of indium on lithium. By means of joint density functional theory and interfacial characterization experiments, we show that In coatings stabilize Li by multiple processes, including exceptionally fast surface diffusion of lithium ions and high chemical resistance to liquid electrolytes. Indium coatings also undergo reversible alloying reactions with lithium ions, facilitating design of high‐capacity hybrid In‐Li anodes that use both alloying and plating approaches for charge storage. By means of direct visualization, we further show that the coatings enable remarkably compact and uniform electrodeposition. The resultant In‐Li anodes are shown to exhibit minimal capacity fade in extended galvanostatic cycling when paired with commercial‐grade cathodes.

Choudhury, Snehashis↗

EDX ClaiMM

EDX ClaiMM is a centralized data & analytical platform designed to revolutionize U.S. critical minerals and materials (CMM) activities. By providing a robust digital infrastructure, ClaiMM will accelerate the combination, leveraging, and rapid utilization of vital data, advanced tools, and cutting-edge research advancements in CMM. This adaptive digital research hub connects the CMM community to essential knowledge products and offers access to interoperable datasets, databases, models, software, and tools from the National Energy Technology’s (NETL’s) Energy Data eXchange (EDX) and other authoritative sources, serving both public and private sectors. EDX ClaiMM delivers AI-informed solutions to address fundamental knowledge gaps and fosters the innovation of new techniques for enhanced characterization and recovery of CMMs within the U.S. By leveraging cloud-hosted, scalable digital infrastructure, ClaiMM meets public–private applied energy needs. It equips the CMM community with priority digital resources that harness on-site and cloud compute capabilities, enabling big data storage, advanced processing, analytics, and visualization.

Critical Materials; Critical Minerals; Rare Earth ↗

Energy Systems Integration Facility (ESIF): World-Class Systems Integration Capabilities and Research

The Energy Systems Integration Facility (ESIF), located at the National Renewable Energy Laboratory (NREL) South Table Mountain campus, is a world-renowned user facility for research and development of modern, advanced, and clean energy technologies. ESIF is distinguished by its continuously evolving, highly integrated systems that span throughout the building, connecting research capabilities across multiple laboratories and test areas. The primary ESIF research systems include: [1] data, cyber, and control networks, [2] research electrical distribution buses (REDB), [3] thermal integration infrastructure, and [4] hydrogen systems. The data, cyber, and control networks provide monitoring, control, communication, automation, visualization, and time series data storage and tagging capabilities for research projects and ESIF systems, including facility safety functions. The REDB system consists of four dedicated AC and DC electrical power networks that can connect devices located across the facility through versatile, automatic circuit configuration to support complex power electronics experiments up to the megawatt-scale. The thermal integration infrastructure consists of three temperature-conditioned water loops that provide heating and cooling interfaces and capabilities for thermal energy research. The hydrogen systems provide megawatt-scale hydrogen production, drying, compression, high-pressure storage, and delivery to laboratory end uses, including hydrogen fuel cell vehicle fueling. The ESIF research systems interconnect and extend throughout the various lab areas of the facility to create elaborate networks composed of diverse technologies for cutting-edge research. The ESIF capabilities are operated and stewarded by the ESIF Research Operations group, who also actively upgrade and advance the systems to ensure they remain ahead of anticipated research - enabling the success of many pioneering energy integration projects. The poster, created by members of the ESIF Research Operations team, highlights and summarizes the four core integrated systems at ESIF. The poster was first presented at the internal NREL Energize Forum on May 13th, 2024, and received the "Best Poster" award.

capabilities↗

Method and apparatus for filtering visual documents

A method and apparatus for producing an abstract or condensed version of a visual document is presented. The frames comprising the visual document are first sampled to reduce the number of frames required for processing. The frames are then subjected to a structural decomposition process that reduces all information in each frame to a set of values. These values are in turn normalized and further combined to produce only one information content value per frame. The information content values of these frames are then compared to a selected distribution cutoff point. This effectively selects those values at the tails of a normal distribution, thus filtering key frames from their surrounding frames. The value for each frame is then compared with the value from the previous frame, and the respective frame is finally stored only if the values are significantly different. The method filters or compresses a visual document with a reduction in digital storage on the ratio of up to 700 to 1 or more, depending on the content of the visual document being filtered.

Rorvig, Mark E.↗

Uncovering I/O demands on HPC platforms: Peeking under the hood of Santos Dumont

High-Performance Computing (HPC) platforms are required to solve the most diverse large-scale scientific problems in various research areas, such as biology, chemistry, physics, and health sciences. Researchers use a multitude of scientific softwares, which have different requirements. These include input and output operations, which directly impact performance due to the existing difference in processing and data access speeds. Thus, supercomputers must efficiently handle mixed workload when storing data from the applications. Understanding the set of applications and their performance running in a supercomputer is paramount to understanding the storage system's usage, pinpointing possible bottlenecks, and guiding optimization techniques. This research proposes a methodology and visualization tool to evaluate a supercomputer's data storage infrastructure's performance, taking into account the diverse workload and demands of the system over a long period of operation. As a study case, we focus on the Santos Dumont supercomputer, identifying inefficient usage, problematic performance factors, and providing guidelines on how to tackle those issues.

97 MATHEMATICS AND COMPUTING↗

CO2 Storage Site Analysis, Screening, and Resource Estimation for Cenozoic Offshore Reservoirs in the Central Gulf of Mexico

The storage potential of hydrocarbon reservoirs in the central Gulf of Mexico (GOM) makes future development of CO2 storage projects in those areas promising for secure, large-scale, and long-term storage purposes. Focusing on the producing and depleted hydrocarbon fields in the continental slope of the central GOM, this paper analyzed, assessed, and screened the producing sands and evaluated their CO2 storage potential. A live interactive CO2 storage site screening system was built in the SAS® Viya system with a broad range of screening criteria combined from published studies. This offers the users a real-time assessment of the storage sites and enables them to adjust the filters and visualize the results to determine the most suitable filter range. The CO2 storage resources of the sands were estimated using a volumetric equation and the correlation developed by the National Energy Technology Laboratory (NETL). The results of this study indicate that 1.05 gigatons of CO2 storage resources are available in the developed reservoirs at the upper slope area of the central GOM. The Mississippi Canyon and Green Canyon protraction areas contain the fields with the largest storage resources.

Hu, Xitong↗

ParaView Catalyst: Enabling In Situ Data Analysis and Visualization

Computer simulations are growing in sophistication and producing results of ever greater fidelity. This trend has been enabled by advances in numerical methods and increasing computing power. However these advances come with several costs including massive increases in data size, difficulties examining output data, challenges in configuring simulation runs, and difficulty debugging running codes. Interactive visualization tools, like ParaView, have been used for post-processing of simulation results. However, the increasing data sizes, and limited storage and bandwidth make high fidelity post-processing impractical. In situ analysis is recognized as one of the ways to address these challenges. In situ analysis moves some of the post-processing tasks in line with the simulation code thus short circuiting the need to communicate the data between the simulation and analysis via storage. ParaView Catalyst is a data processing and visualization library that enables in situ analysis and visualization. Built on and designed to interoperate with the standard visualization toolkit VTK and the ParaView application, Catalyst enables simulations to intelligently perform analysis, generate relevant output data, and visualize results concurrent with a running simulation. Here, we provide an overview of the Catalyst framework and some of the success stories.

97 MATHEMATICS AND COMPUTING↗

Probing local electrochemistry via mechanical cyclic voltammetry curves

Understanding the mechanical response of an electrode during electrochemical cycling and its correlation to the device electrochemical performance is crucial to improving the performance of insertion-type energy storage devices, electrochemical actuators, water purification, ion separation and neuromorphic computing applications. Here, we visualized the electro-chemo-mechanical coupling behaviors during charge storage of anhydrous and hydrated WO 3 electrodes via in situ atomic force microscopy (AFM) and developed the concept of mechanical cyclic voltammetry (mCV) curves. The relationship between electrochemical current and strain was investigated with simplified models and the results revealed that the proton insertion/deinsertion process could be described through potential-dependent electro-chemo-mechanical coupling coefficients which might indicate changes in insertion processes during electrode cycling. The mCV mapping results highlight the local heterogeneity and show that the charging processes varied across the electrode. These local variations could be further correlated to local morphology, crystal orientations or chemical compositions with proper electrode designs.

36 MATERIALS SCIENCE↗

Flow visualization using a computerized data acquisition system

A computer-driven traversing mechanism combined with mass data storage, data reduction programs, and general-purpose graphics programs permits a visualization of complex flows. A unique seven-hole probe is used which permits reasonably accurate measurements of all average flow properties if the local flow angle does not exceed 80 degrees. A description is given of the wake of a lifting canard surface as this wake passes over a wing. The flow includes concentrated and dissipating vortices, large regions of reduced total pressure, and local flow angles up to 60 deg. All these features can be clearly seen and accurately located in the graphical output.

Gallington, R.↗

Destructive examination of shipping package 9975-02101

Destructive and non-destructive examinations have been performed on the components of shipping package 9975-02101 as part of the comprehensive Model 9975 package surveillance program. This package is one of ten high-wattage packages that were selected for field surveillance in FY15, and was identified to contain several non-conforming conditions. Most of these conditions (mold, stains, drum corrosion, calculated fiberboard dimensions and fiberboard damage) relate to the accumulation of water in the outer and lower portions of the cane fiberboard assembly. In the short term, this causes local but reversible changes in the fiberboard properties. Long-term effects can include the permanent loss of fiberboard properties (thus far observed only in the bottom fiberboard layers) and reduced drum integrity due to corrosion. The observed conditions must be fully evaluated by KAC to ensure the safety function of the package is being maintained. Three of the other nine FY15 high-wattage packages examined in the K-Area Complex showed similar behavior. Corrosion of the overpack drum has been seen primarily in those packages with relatively severe fiberboard degradation. Visual examination of the drums in storage for external corrosion should be considered as a screening tool to identify additional packages with potential fiberboard degradation. Where overpack drum corrosion has been observed, it is typically heaviest adjacent to the stitch welds along the bottom edge. It is possible that changes to the stitch weld design would reduce the degree of corrosion in this area, but would not eliminate it. Several factors can contribute to the concentration of moisture in the fiberboard, including higher than average initial moisture content, higher internal temperature (due to internal heat load and placement with the array of packages), and the creation of additional moisture as the fiberboard begins to degrade.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗