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DOE OSTI2017

Patterns of Care in Proton Radiation Therapy for Pediatric Central Nervous System Malignancies

Purpose: Proton beam therapy (PBT) potentially allows for improved sparing of normal tissues, hopefully leading to decreased late side effects in children. Using a national registry, we sought to perform a patterns-of-care analysis for children receiving PBT for primary malignancies of the central nervous system (CNS). Methods and Materials: Using the National Cancer Data Base, we identified pediatric patients with primary CNS malignancies that were diagnosed between 2004 and 2012. We used a standard t test for comparison of means and χ{sup 2} testing to identify differences in demographic and clinical characteristics. Univariate and multivariate logistical regression was applied to identify predictors of PBT use. Results: We identified 4637 pediatric patients receiving radiation therapy from 2004 to 2012, including a subset of 267 patients treated with PBT. We found that PBT use increased with time from <1% in 2004 to 15% in 2012. In multivariate logistical regression, we found the following to be predictors of receipt of PBT: private insurance, the highest income bracket, younger age, living in a metropolitan area, and residing >200 miles from a radiation treatment facility (P<.05). Conclusions: We noted the proportion of children receiving PBT to be significantly increasing over time from <1% to 15% from 2004 to 2012. We also observed important disparities in receipt of PBT based on socioeconomic status. Children from higher-income households and with private insurance were more likely to use this expensive technology. As we continue to demonstrate the potential benefits of PBT in children, efforts are needed to expand the accessibility of PBT for children of all socioeconomic backgrounds and regions of the country.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

DOE OSTI2021

DeepGRN: prediction of transcription factor binding site across cell-types using attention-based deep neural networks

Abstract Background Due to the complexity of the biological systems, the prediction of the potential DNA binding sites for transcription factors remains a difficult problem in computational biology. Genomic DNA sequences and experimental results from parallel sequencing provide available information about the affinity and accessibility of genome and are commonly used features in binding sites prediction. The attention mechanism in deep learning has shown its capability to learn long-range dependencies from sequential data, such as sentences and voices. Until now, no study has applied this approach in binding site inference from massively parallel sequencing data. The successful applications of attention mechanism in similar input contexts motivate us to build and test new methods that can accurately determine the binding sites of transcription factors. Results In this study, we propose a novel tool (named DeepGRN) for transcription factors binding site prediction based on the combination of two components: single attention module and pairwise attention module. The performance of our methods is evaluated on the ENCODE-DREAM in vivo Transcription Factor Binding Site Prediction Challenge datasets. The results show that DeepGRN achieves higher unified scores in 6 of 13 targets than any of the top four methods in the DREAM challenge. We also demonstrate that the attention weights learned by the model are correlated with potential informative inputs, such as DNase-Seq coverage and motifs, which provide possible explanations for the predictive improvements in DeepGRN. Conclusions DeepGRN can automatically and effectively predict transcription factor binding sites from DNA sequences and DNase-Seq coverage. Furthermore, the visualization techniques we developed for the attention modules help to interpret how critical patterns from different types of input features are recognized by our model.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2017

Indirect Validation of Probe Speed Data on Arterial Corridors

This study aimed to estimate the accuracy of probe speed data on arterial corridors on the basis of roadway geometric attributes and functional classification. It was assumed that functional class (medium and low) along with other road characteristics (such as weighted average of the annual average daily traffic, average signal density, average access point density, and average speed) were available as correlation factors to estimate the accuracy of probe traffic data. This study tested these factors as predictors of the fidelity of probe traffic data by using the results of an extensive validation exercise. This study showed strong correlations between these geometric attributes and the accuracy of probe data when they were assessed by using average absolute speed error. Linear models were regressed to existing data to estimate appropriate models for medium- and low-type arterial corridors. The proposed models for medium- and low-type arterials were validated further on the basis of the results of a slowdown analysis. These models can be used to predict the accuracy of probe data indirectly in medium and low types of arterial corridors.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

DOE OSTI2024

Stream water sourcing from high-elevation snowpack inferred from stable isotopes of water: a novel application of d-excess values

About 80 % of the precipitation at the Colorado River's headwaters is snow, and the resulting snowmelt-driven hydrograph is a crucial water source for about 40 million people. Snowmelt from alpine and subalpine snowpack contributes substantially to groundwater recharge and river flow. However, the dynamics of snowmelt progression are not well understood because observations of the high-elevation snowpack are difficult due to challenging access in complex mountainous terrain as well as the cost and labor intensity of currently available methods. We present a novel approach to infer the processes and dynamics of high-elevation snowmelt contributions predicated upon stable hydrogen and oxygen isotope ratios observed in streamflow. We show that deuterium-excess (d-excess) values of stream water could serve as a comparatively cost-effective proxy for a catchment-integrated signal of high-elevation snowmelt contributions to catchment runoff. We sampled stable hydrogen and oxygen isotope ratios of the precipitation, snowpack, and stream water in the East River, a headwater catchment of the Colorado River, and the stream water of larger catchments at sites on the Gunnison River and Colorado River. The d-excess of snowpack increased with elevation; the upper subalpine and alpine snowpack (> 3200 m) had substantially higher d-excess compared to lower elevations (< 3200 m) in the study area. The d-excess values of stream water reflected this because d-excess values increased as the higher-elevation snowpack contributed more to stream water generation later in the snowmelt/runoff season. End-member mixing analyses based on the d-excess data showed that the share of high-elevation snowmelt contributions within the snowmelt hydrograph was on average 44 % and generally increased during melt period progression, up to 70 %. The observed pattern was consistent during 6 years for the East River, and a similar relation was found for the larger catchments on the Gunnison and Colorado rivers. High-elevation snowpack contributions were found to be higher for years with lower snowpack and warmer spring temperatures. Thus, we conclude that the d-excess of stream water is a viable proxy to observe changes in high-elevation snowmelt contributions in catchments at various scales. Inter-catchment comparisons and temporal trends of the d-excess of stream water could therefore serve as a catchment-integrated measure to monitor if mountain systems rely on high-elevation water inputs more during snow drought compared to years of average snowpack depths.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2019

XFEL structures of the human MT2 melatonin receptor reveal the basis of subtype selectivity

The human MT 1 and MT 2 melatonin receptors are G-protein-coupled receptors (GPCRs) that help to regulate circadian rhythm and sleep patterns. Drug development efforts have targeted both receptors for the treatment of insomnia, circadian rhythm and mood disorders, and cancer, and MT 2 has also been implicated in type 2 diabetes. Here in this paper we report X-ray free electron laser (XFEL) structures of the human MT 2 receptor in complex with the agonists 2-phenylmelatonin (2-PMT) and ramelteon6 at resolutions of 2.8 Å and 3.3 Å, respectively, along with two structures of function-related mutants: H208 5.46 A (superscripts represent the Ballesteros–Weinstein residue numbering nomenclature7) and N86 2.50 D, obtained in complex with 2-PMT. Comparison of the structures of MT 2 with a published structure of MT 1 reveals that, despite conservation of the orthosteric ligand-binding site residues, there are notable conformational variations as well as differences in [ 3 H]melatonin dissociation kinetics that provide insights into the selectivity between melatonin receptor subtypes. A membrane-buried lateral ligand entry channel is observed in both MT 1 and MT 2 , but in addition the MT 2 structures reveal a narrow opening towards the solvent in the extracellular part of the receptor. We provide functional and kinetic data that support a prominent role for intramembrane ligand entry in both receptors, and suggest that there might also be an extracellular entry path in MT 2 . Our findings contribute to a molecular understanding of melatonin receptor subtype selectivity and ligand access modes, which are essential for the design of highly selective melatonin tool compounds and therapeutic agents.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Towards replacing physical testing of granular materials with a Topology-based Model

In the study of packed granular materials, the performance of a sample (e.g., the detonation of a high-energy explosive) often correlates to measurements of a fluid flowing through it. The “effective surface area,” the surface area accessible to the airflow, is typically measured using a permeametry apparatus that relates the flow conductance to the permeable surface area via the Carman-Kozeny equation. This equation allows calculating the flow rate of a fluid flowing through the granules packed in the sample for a given pressure drop. However, Carman-Kozeny makes inherent assumptions about tunnel shapes and flow paths that may not accurately hold in situations where the particles possess a wide distribution in shapes, sizes, and aspect ratios, as is true with many powdered systems of technological and commercial interest. To address this challenge, we replicate these measurements virtually on micro-CT images of the powdered material, introducing a new Pore Network Model based on the skeleton of the Morse-Smale complex. Pores are identified as basins of the complex, their incidence encodes adjacency, and the conductivity of the capillary between them is computed from the cross-section at their interface. We build and solve a resistive network to compute an approximate laminar fluid flow through the pore structure. Here, we provide two means of estimating flow-permeable surface area: (i) by direct computation of conductivity, and (ii) by identifying dead-ends in the flow coupled with isosurface extraction and the application of the Carman-Kozeny equation, with the aim of establishing consistency over a range of particle shapes, sizes, porosity levels, and void distribution patterns.

36 MATERIALS SCIENCE↗

DOE OSTI2025

VA Determinants of Health Data Curation Documentation FY25-Q2

The U.S. Department of Veterans Affairs (VA) places the health and well-being of our nation’s veterans as its top priority. VA is dedicated to offering timely access to high-quality, evidence-based mental health care that meets the needs of veterans and supports their reintegration into society. One of our core missions is to prevent suicide among veterans through innovative approaches and resources. With funding from the VA Office of Mental Health and Suicide Prevention (OMHSP), the Determinants of Health (EDH) project has developed innovative datasets associated with specific health outcomes, a methodology for transforming spatiotemporal data from one spatial reference (e.g., a 1km grid) to another (e.g., US Census Tracts), and capabilities for modeling health outcomes. These datasets represent an enhancement of the Agency for Healthcare Research and Quality (AHRQ), addressing key gaps by introducing finer spatial resolution (Census Tract) and additional geographical covariates into existing data. The curation and standardization of these datasets is a complex task since they often originate from various sources and are measured at different spatial and temporal resolutions. For example, US Census data products typically use census blocks, block groups, or counties, while data like weather data are available on 1km grids. Some economic data may only be available at the zip code level. In this context, ‘standardized’ means that all datasets share the same spatial extent (e.g., US Census Tract and/or County), and ‘curated’ implies a repeatable process with data provenance and the use of appropriate methodologies for covariate conversion. The Determinants of Health datasets draw from multiple sources, resulting in variables with varying degrees of availability, patterns of missing data, and methodological considerations across different sources, geographies, and years.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

VA Determinants of Health Data Curation Documentation FY25-Q3

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

VA Community Determinants of Health Data Curation Documentation FY25-Q4

The U.S. Department of Veterans Affairs (VA) places the health and well-being of our nation’s veterans as its top priority. VA is dedicated to offering timely access to high-quality, evidence-based mental health care that meets the needs of veterans and supports their reintegration into society. One of our core missions is to prevent suicide among veterans through innovative approaches and resources. With funding from the VA Office of Mental Health and Suicide Prevention (OMHSP), the Determinants of Health (EDH) project has developed innovative datasets associated with specific health outcomes, a methodology for transforming spatiotemporal data from one spatial reference (e.g., a 1km grid) to another (e.g., US Census Tracts), and capabilities for modeling health outcomes. These datasets represent an enhancement of the Agency for Healthcare Research and Quality (AHRQ), addressing key gaps by introducing finer spatial resolution (Census Tract) and additional geographical covariates into existing data. The curation and standardization of these datasets is a complex task since they often originate from various sources and are measured at different spatial and temporal resolutions. For example, US Census data products typically use census blocks, block groups, or counties, while data like weather data are available on 1km grids. Some economic data may only be available at the zip code level. In this context, standardized’ means that all datasets share the same spatial extent (e.g., US Census Tract and/or County), and ‘curated’ implies a repeatable process with data provenance and the use of appropriate methodologies for covariate conversion. The Determinants of Health datasets draw from multiple sources, resulting in variables with varying degrees of availability, patterns of missing data, and methodological considerations across different sources, geographies, and years.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

VA Community Determinants of Health Data Curation Documentation FY26-Q1

The U.S. Department of Veterans Affairs (VA) places the health and well-being of our nation’s veterans as its top priority. VA is dedicated to offering timely access to high-quality, evidence-based mental health care that meets the needs of veterans and supports their reintegration into society. One of our core missions is to prevent suicide among veterans through innovative approaches and resources. With funding from the VA Office of Mental Health and Suicide Prevention (OMHSP), the Community Determinants of Health (EDH) Data project has developed innovative datasets associated with specific health outcomes, a methodology for transforming spatiotemporal data from one spatial reference (e.g., a 1km grid) to another (e.g., US Census Tracts), and capabilities for modeling health outcomes. These datasets represent an enhancement of the Agency for Healthcare Research and Quality (AHRQ), addressing key gaps by introducing finer spatial resolution (Census Tract) and additional geographical covariates into existing data. The curation and standardization of these datasets is a complex task since they often originate from various sources and are measured at different spatial and temporal resolutions. For example, US Census data products typically use census blocks, block groups, or counties, while data like weather data are available on 1km grids. Some economic data may only be available at the zip code level. In this context, ‘standardized’ means that all datasets share the same spatial extent (e.g., US Census Tract and/or County), and ‘curated’ implies a repeatable process with data provenance and the use of appropriate methodologies for covariate conversion. The Community Determinants of Health datasets draw from multiple sources, resulting in variables with varying degrees of availability, patterns of missing data, and methodological considerations across different sources, geographies, and years.

99 GENERAL AND MISCELLANEOUS↗

NASA NTRSDate not supplied

NASA GeneLab Multi-study Visualization Portal

NASA GeneLab has helped advance the field of Space Biology by providing a public repository where researchers can store, share, analyze and visualize the results of space flight related omics experiments. The GeneLab data visualization portal allows any user, regardless of bioinformatics knowledge or access to computational resources, to interact with the experimental data, draw their own conclusions, and gain insights about the effects of space on living systems. These tools help democratize scientific research and foster the NASA Open Science initiative. The new multi-study feature of the GeneLab visualization platform allows users to mine study metadata from RNA sequencing (RNA-seq) experiments to identify samples of interest by filtering datasets based on organism, tissue, assay technology type, and/or factor. Once samples are selected from multiple datasets, users can combine and normalize the sample data, then utilize the visualization displays, including Principal Component Analysis (PCA) plots, to assess sample distributions. Finally, users can perform differential gene expression analysis on the combined data and visualize the results through PCA plots, Volcano plots, Pair plots, Heatmap, Ideogram and Gene Set Enrichment Analysis. All user-generated results and visualizations will be available for download. Here, we present a biological study using samples from multiple GeneLab RNA-seq datasets and analyzed using the multi-study visualization platform to demonstrate inter- and intra-study variability, as well as commonly differentially expressed genes between spaceflight and ground control conditions across datasets. This new feature opens a wide range of possibilities and opportunities for further development including combining other assay technology types and integration with batch effect correction techniques and machine learning applications. Overall, this tool allows users to increase the statistical power of individual experiments, validate hypothesis, identify patterns, and opens the door to new and exciting research.

space biology↗

DOE OSTI2026

VA Community Determinants of Health Data Curation Documentation FY26-Q2

The U.S. Department of Veterans Affairs (VA) places the health and well-being of our nation’s veterans as its top priority. VA is dedicated to offering timely access to high-quality, evidence-based mental health care that meets the needs of veterans and supports their reintegration into society. One of our core missions is to prevent suicide among veterans through innovative approaches and resources. With funding from the VA Office of Mental Health and Suicide Prevention (OMHSP), the Community Determinants of Health (EDH) Data project has developed innovative datasets associated with specific health outcomes, a methodology for transforming spatiotemporal data from one spatial reference (e.g., a 1 km grid) to another (e.g., U.S. Census Tracts), and capabilities for modeling health outcomes. These datasets represent an enhancement of the Agency for Healthcare Research and Quality (AHRQ), addressing key gaps by introducing finer spatial resolution (Census Tract) and additional geographical covariates into existing data. The curation and standardization of these datasets is a complex task since they often originate from various sources and are measured at different spatial and temporal resolutions. For example, U.S. Census data products typically use census blocks, block groups, or counties, while data like weather data are available on 1 km grids. Some economic data may only be available at the ZIP code level. In this context, ‘standardized’ means that all datasets share the same spatial extent (e.g., U.S. Census Tract and/or County), and ‘curated’ implies a repeatable process with data provenance and the use of appropriate methodologies for covariate conversion. The Community Determinants of Health datasets draw from multiple sources, resulting in variables with varying degrees of availability, patterns of missing data, and methodological considerations across different sources, geographies, and years.

99 GENERAL AND MISCELLANEOUS↗

DOE OSTI2021

Phasor-Measurement-Unit-Based Data Analytics Using Digital Twin and PhasorAnalytics Software

A major objective of this project was to apply GE’s commercial machine learning and data analytics toolsets to large-scale, real-world, anonymized Phasor Measurement Unit (PMU) datasets in order to extract signatures, correlated and/or causal factors, and precursor patterns associated with significant power system phenomena. The project had a particular emphasis on extraction of insights relevant to asset health monitoring, real-time load modeling and cybersecurity monitoring. Additionally, the team was directed to undertake a comprehensive data quality analysis for the provided datasets and encouraged to estimate the ‘machine-learning readiness’ of the datasets by documenting any major obstacles to the application of commercial machine learning algorithms. To accomplish the aforementioned objectives, the project team’s work centered around the identification of key event signatures and application of the identified event signatures for event detection and event classification. The industry-validated, semi-supervised machine learning strategy employed for event signature identification involved several major tasks, including data-preprocessing, generation of an overabundance of features, normal data identification, normality modeling, and event signature identification through a methodical, quantitative ranking of features in order of relevance to each studied event type. Throughout the project, data quality issues and mitigation techniques were investigated. In this report, insights are provided regarding the readiness of the provided synchrophasor datasets for application of machine learning and data analytics. The methodologies employed for this technical strategy are summarized in this report. With regards to data preprocessing and feature generation, the provided Training and Test Datasets were ingested into GE’s big data environment. Subsequently, the team applied bad data cleansing and data imputation scripts, event detection scripts, and application programming interfaces (APIs) to the datasets for convenient data access. The project team completed development and validation of dozens of physics-based, statistics-based and transformation-based feature functions used for the extraction of over 60 synchrophasor features. Using a new parallel feature generation technology developed on this project, over 60 features have been rapidly generated for the full two years’ worth of Training and Test Dataset data associated with both the Eastern and Western interconnects. Even accommodating for temporal down-sampling inherent to the feature extraction procedure, this parallel feature generation activity resulted in a massive feature set with a storage requirement approximately equal to that of the raw training dataset itself. With regards to normal data identification and normality modeling, a normality model was built using the feature data extracted from the Training Dataset and iteratively refined subsequent to incremental adjustments and expansions of the Training Dataset feature data. With respect to event characterization and signature identification, an event signature identification pipeline was developed and used in conjunction with the normality model to identify over 15 event signatures for key event categories within the Training Dataset. The identified event signatures were used to characterize hundreds of key events in terms of relative severity, duration, and location of the event. An investigation was undertaken to identify correlated and causal factors involved in transformer events. A separate investigation into temporal trends in ring-down analysis results was undertaken to determine possible associations between system dynamics and various other factors such as loading, season or year. To validate the identified event signatures, additional work was undertaken to develop signature-based anomaly detection and classification tools suitable for convenient application to the synchrophasor datasets. The anomaly detection and classification tools, suitable for online application, were then applied to the entirety of the Eastern Interconnect Training and Test Datasets. Performance of the event detection and classification tools was evaluated upon receipt of the Test Dataset event logs (i.e., the labels for events contained in the Test Dataset), and promising results were obtained despite several challenges (documented herein) associated with application of supervised or semi-supervised machine learning methods to large-scale, anonymized datasets. Finally, the detection and classification tools were used to detect, classify, and characterize thousands of new events not included in the original event logs provided by the DOE within both the Training and Test Datasets.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2025

DOE Repository Metadata Profile (DRMP): A Metadata Framework for Advancing Interoperability and AI Readiness Across Scientific Repositories

The Department of Energy (DOE) funds a diverse and distributed ecosystem of repositories that steward scientific data, publications, and software across its research programs, user facilities, and national laboratories. While significant progress has been made in standardizing dataset-level metadata, the metadata describing repositories themselves (their identity, governance, access interfaces, policies, and technical capabilities) remains inconsistent and fragmented across DOE-funded systems. This variability limits discoverability, interoperability, automated validation, and AI-driven analysis, all of which are increasingly essential for modern scientific workflows. To address this gap, the DOE Data Curation Working Group (DCWG) developed the DOE Repository Metadata Profile (DRMP). The DRMP is a practical, community-driven framework that defines how repositories can describe themselves in a consistent, machine-actionable, and scalable manner. The DRMP is not a new metadata schema. Instead, it is a mapping profile and structured element set capturing the essential characteristics of DOE repositories. It harmonizes repository-level metadata across six widely adopted community schemas: RE3Data; DCAT-US v3; Schema.org; Dublin Core; DataCite 4.6; and PREMIS 3.0. This harmonization eliminates reinvention and enables interoperability within DOE and across the broader scientific ecosystem. A core objective of the DRMP is to reduce burden on repositories by allowing them to reuse their existing metadata through a Rosetta-style crosswalk rather than redesigning local implementations. The profile introduces a three-level conformance model that supports incremental adoption: • Level 1 – Minimum Viable Record (MVR): foundational identification elements required for workflows, project registration, and basic repository presence. • Level 2 – Interoperable: structured metadata enabling alignment with national and international discovery systems. • Level 3 – AI-Ready: enhanced provenance, policy transparency, fixity, semantic context, and capabilities that support automated reasoning, model training governance, and machine-assisted curation. To support implementation, the DRMP includes JSON Schema definitions, OpenAPI patterns, and MCP templates that allow repositories to publish machine-readable metadata directly within existing platforms. These resources are modular and lightweight, enabling adoption without major architectural change. Adopting the DRMP enables repositories to: • Enhance discoverability and interoperability by aligning identifiers, classifications, and descriptive elements across widely used schema standards. • Support federated discovery and cross-registration across DOE systems, Data.gov, and international catalogs. • Enable AI agents and workflow orchestration systems to interpret repository-level metadata within the American Science Cloud (AmSC) through Model Context Protocol (MCP)-based context publication. • Demonstrate alignment with DOE’s open science, stewardship, and FAIR data priorities. This guidance represents a community-driven step forward. Through voluntary adoption and continued feedback, the DRMP advances a cohesive, machine-actionable description of DOE repositories that supports FAIR data practices, preparing the infrastructure for AI-enabled research, and strengthening the discoverability and reuse of DOE’s scientific outputs.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

DOE OSTI2023

Transforming our understanding of chloroplast-associated genes through comprehensive characterization of protein localizations and protein-protein interactions

Bioenergy crops are a renewable source of fuels and are a critical base for building a carbon-neutral economy. Rational engineering of bioenergy crops has the potential to enhance the yields. However, our ability to engineer plants is limited because the functions of most genes remain unknown. Systematic characterization of gene function in plants thus has the potential to greatly accelerate bioenergy research. Here, we focus on the chloroplast, an underexplored energy-producing organelle that is a hallmark of plants. The chloroplast is one of the promising targets of biofuel crop engineering efforts because of its central role in photosynthesis, metabolism, and intracellular signaling. However, the protein composition of the chloroplast and the functions of most of its proteins remain poorly characterized. At the core of this project, we sought to comprehensively determine the localization of chloroplast-associated proteins and generate a spatially defined protein-protein interaction network for chloroplast. For this purpose, we used the leading model alga Chlamydomonas reinhardtii, which greatly increased experimental speed and throughput. We illustrated the value of our findings to land plants by determining the localization of Arabidopsis thaliana land plant homologs of the Chlamydomonas proteins. Altogether, we were successful in determining the localization of 1,034 chloroplast-associated proteins in Chlamydomonas. The localizations provide numerous insights into the spatial organization of chloroplasts and how they function to support photosynthesis. The localization patterns of distinct proteins revealed new chloroplast structures and revealed new spatial organization inside the chloroplast. We also identified new components of known chloroplast structures, such as the chloroplast envelope, nucleoid, plastoglobuli, and pyrenoid. We identified these new components by investigating the interacting partners of known proteins. Many proteins localized in both the chloroplast and other cellular structures, thereby hinting at new functions and communication between cellular structures. We also applied machine learning on the atlas to generate predictions for the location of all of the proteins in Chlamydomonas. This enabled us to assign putative functions to many uncharacterized proteins based on their cellular location. Altogether, this research establishes a rich resource that opens new avenues of investigation and guides future work in deciphering and manipulating chloroplast function. Next, we developed an extensive protein-protein interaction network for the chloroplast by performing affinity purification-mass spectrometry on ~1,150 tagged chloroplast-associated proteins, the first such large-scale study in any photosynthetic organism. This dataset reveals 4,694 high-confidence protein-protein interactions, offering insights into the functions of thousands of conserved poorly-characterized chloroplast proteins. This systematic identification of protein-protein interactions in the chloroplast also provides multiple exciting new research directions and a detailed blueprint of the chloroplast's operation. This research lays the groundwork to decipher the inner workings of the chloroplast, the cell structure at the heart of photosynthesis. The spatial atlas and protein-protein interactions reveal chloroplast organizational features that would not have been accessible with traditional approaches. The localization mapping, insights into the function, and research materials generated further provide a rich resource for the research community to advance the understanding of how the chloroplast is organized to enable engineering of enhanced photosynthetic organisms.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRSDate not supplied

Transcriptomic Analysis of Irradiated Mouse Retina Following Readaptation

Rodent models are used as analogs for studying the effects of spaceflight. NASA GeneLab provides access to relevant omics datasets generated from spaceflight and ground-based experiments allowing for additional retrospective analysis. In this study, we used GeneLab’s GLDS-203, a dataset generated by researchers at Loma Linda University to study the impact of prolonged unloading and/or low-dose radiation on mouse retina. We analyzed transcriptomics data from retina of mice irradiated with gamma-rays for 21 days followed by 7 days, 1 month, or 4 months of readaptation. We obtained raw gene counts from GeneLab and performed differential gene expression analysis after data normalization. For each of the three timepoints, we performed differential expression analysis to compare transcriptional profiles for retina from irradiated vs. non-irradiated (controls) mice, all exposed to gravity. We observed the highest number of differentially expressed genes at 7 days, followed by 1 month and 4 months. Enrichment analysis showed top pathways (adjusted p-value < 0.05) were related to transport along microtubule and photoreceptor cell development in the 7-day readaptation group. Fewer significantly enriched pathways were observed for the 1-month group and included mRNA metabolic processes and neuron differentiation. No significantly enriched pathways were found in the 4-month group. The Gene Ontology biological processes common between the 7 days and 1-month groups include visual perception, synapse organization, and perception of light stimulus. This analysis is part of a larger effort to characterize the molecular mechanisms involved in retinal readaptation following radiation exposure. Future analyses will include other related retina datasets in GeneLab repository to assess whether gene expression patterns are consistent across different study cohorts.

Prachi Kothiyal↗

DOE OSTI2023

ESnet Requirements Review Program Through the IRI Lens: A Meta-Analysis of Workflow Patterns Across DOE Office of Science Programs (Final Report)

The Department of Energy (DOE) ensures America’s security and prosperity by addressing its energy, environmental, and nuclear challenges through transformative science and technology solutions. The DOE’s Office of Science (SC) delivers groundbreaking scientific discoveries and major scientific tools that transform our understanding of nature and advance the energy, economic, and national security of the United States. The SC’s programs advance DOE mission science across a wide range of disciplines and have developed the research infrastructure needed to remain at the forefront of scientific discovery. The DOE SC’s world-class research infrastructure — exemplified by the 28 SC scientific user facilities — provides the research community with premier observational, experimental, computational, and network capabilities. Each user facility is designed to provide unique capabilities to advance core DOE mission science for its sponsor SC program and to stimulate a rich discovery and innovation ecosystem. Research communities gather and flourish around each user facility, bringing together diverse perspectives. A hallmark of many facilities is the large population of students, postdoctoral researchers, and early-career scientists who contribute as full-fledged users. These facility staff and users collaborate over years to devise new approaches to utilizing the user facility’s core capabilities. The history of the SC user facilities has many examples of wildly inventive researchers challenging operational orthodoxy to pioneer new vistas of discovery; for example, the use of the synchrotron X-ray light sources for study of proteins and other large biological molecules. This continual reinvention of the practice of science — as users and staff forge novel approaches expressed in research workflows — unlocks new discoveries and propels scientific progress. Within this research ecosystem, the high-performance computing (HPC) and networking user facilities stewarded by SC’s Advanced Scientific Computing Research (ASCR) program play a dynamic cross-cutting role, enabling complex workflows demanding high performance data, networking, and computing solutions. The DOE SC’s three HPC user facilities and the Energy Sciences Network (ESnet) high-performance research network serve all of the SC’s programs as well as the global research community. Argonne Leadership Computing Facility (ALCF), the National Energy Research Scientific Computing Center (NERSC), and Oak Ridge Leadership Computing Facility (OLCF) conceive, build, and provide access to a range of supercomputing, advanced computing, and large-scale data-infrastructure platforms, while ESnet interconnects DOE SC research infrastructure and enables seamless exchange of scientific data. All four facilities operate testbeds to expand the frontiers of computing and networking research. Together, the ASCR facilities enterprise seeks to understand and meet the needs and requirements across SC and DOE domain science programs and priority efforts, highlighted by the formal requirements reviews (RRs) methodology. In recent years, the research communities around the SC user facilities have begun experimenting with and demanding solutions integrated with HPC and data infrastructure. This rise of integrated-science approaches is documented in many community and high-level government reports. At the dawn of the era of exascale science and the acceleration of artificial intelligence (AI) innovation, there is a broad need for integrated computational, data, and networking solutions. In response to these drivers, DOE has developed a vision for an Integrated Research Infrastructure (IRI): To empower researchers to meld DOE’s world-class research tools, infrastructure, and user facilities seamlessly and securely in novel ways to radically accelerate discovery and innovation.

42 ENGINEERING↗

DOE OSTI2020

GEANT4 parameter tuning using Professor

The GEANT4 toolkit is used extensively in high energy physics to simulate the passage of particles through matter and to predict effects such as detector efficiencies and smearing. GEANT4 uses many underlying models to predict particle interaction kinematics, and uncertainty in these models leads to uncertainty in high energy physics measurements. The GEANT4 collaboration recently made free parameters in some models accessible through partnership with GEANT4 developers. We present a study of the impact of varying parameters in three GEANT4 hadronic physics models on agreement with thin target datasets and describe fits to these datasets using the Professor model tuning framework [1]. We find that varying parameters produces substantially better agreement with some datasets, but that more degrees of freedom are required for full agreement. This work is a first step towards a common framework for propagating uncertainties in GEANT4 models to high energy physics measurements, and we outline future work required to complete that goal.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗