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

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All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Identification and Clinical Evaluation of Potential Biomarkers for Breast Cancer Resistance Protein ( BCRP / ABCG2 )

Clinical inhibition and genetic variation of the Breast Cancer Resistance Protein (BCRP/ABCG2) efflux transporter can significantly influence drug exposure, highlighting the need for reliable BCRP functional biomarkers. This study aimed to identify and evaluate biomarkers predictive of BCRP function in humans. A comprehensive analysis of metabolomic genome‐wide association studies (mGWAS) was conducted to discover potential BCRP biomarkers, followed by evaluation inin vitrotransporter assays and a clinical drug–drug interaction (DDI) study. Across multiple mGWAS datasets, plasma concentrations of three herbicide derivatives—4‐hydroxychlorothalonil (4HC), 3‐bromo‐5‐chloro‐2,6‐dihydroxybenzoic acid (BCDBA), and 3,5‐dichloro‐2,6‐dihydroxybenzoic acid (DCDBA)—were significantly elevated (P < 5E‐8) in individuals carrying reduced functionABCG2polymorphisms. These compounds were confirmed as novel BCRP substrates via transporter uptake assays and selected for clinical evaluation alongside riboflavin, a known BCRP substrate and potential BCRP biomarker. In a DDI study with 11 healthy subjects, eltrombopag, a BCRP inhibitor, increased rosuvastatin concentrations by approximately twofold (P = 0.002). No significant changes in the plasma concentrations of organic anion transporting polypeptide 1B (OATP1B) biomarkers (CP‐I and CP‐III) or potential BCRP biomarkers (4HC, BCDBA, DCDBA, or riboflavin) were observed. Notably, two subjects were heterozygous carriers for theABCG2p.Q141K variant and exhibited significantly higher baseline concentrations of 4HC (P = 0.004) and BCDBA (P = 0.0003), consistent with reduced BCRP function. These findings suggest that 4HC and BCDBA are promising biomarkers for baseline BCRP function in specific populations, such as those harboring reduced function genetic polymorphisms, but do not appear suitable for detecting acute BCRP inhibition.

Pharmacology & Pharmacy↗
DOE OSTI2025

Reliable and Efficient Machine Learning (Final Technical Report)

Modern scientific experiments generate massive amounts of data at a pace much faster than humans can manually analyze. While machine learning has revolutionized commercial data analysis (such as recommending movies or recognizing faces), applying these tools to complex scientific discovery is challenging because scientific answers must be precise, interpretable, and adhere to physical laws. The research under this project aims to develop new mathematical tools and computer algorithms specifically designed for scientific applications. Major progress has been made in automatically cleaning and deconstructing messy experimental data, analyzing the visual information of physical phenomena, determining the underlying physical variables, and providing rig orous mathematical analysis of interesting algorithms and concepts widely used in machine learning. This project addressed the critical gap between our ability to generate massive scientific data and our ability to extract interpretable information from it. We established mathematical foundations for Scientific Machine Learning (SciML) aimed at effective data analytics and automated discovery. Our work focused on three core objectives: (1) developing reliable feature extraction methods for dynamic high-dimensional data, (2) establishing mathematical foundations for discovering dynamics via neural networks, and (3) creating rigorous optimization techniques for these models. Key outcomes come from two fronts. On the practical side, they include the development of algorithms that significantly enhance the extraction of signals from field data, as well as the capability to handle situations that exhibit smooth variations or physical stretching due to temperature changes. They also include the creation of an automated framework for discovering fundamental state variables from raw experimental data, demonstrating the ability to identify intrinsic physical dimensions without prior knowledge of the governing laws. On the theoretical front, the research results in theoretical advances in Optimal Transport, a widely used notion in SciML, specifically regarding functions with fixed-size nodal sets, provide sharp bounds relevant to uncertainty quantification. Meanwhile, the outcomes also include the establishment of convergence theories for nonlocal gradient descent methods, enabling robust optimization with noisy data in high-dimensional settings commonly encountered in scientific modeling. The project also helps creating opportunities to train the next generation of researchers, equipping them with the necessary technical skills for today’s workplace and preparing them for future advances.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Optimizing Geospatial Assessments for Nuclear Safeguards Applications with Large Language Models

A multidisciplinary team at Argonne National Laboratory evaluated the ability of large language models (LLMs) to identify geographic locations from open-source text and assessed post-processing measures to strengthen the reliability of those extractions in support of international nuclear safeguards. The study focused on addressing challenges such as toponym ambiguity, imprecise descriptions, and misinformation, which often undermine the accuracy of LLM-derived geospatial assessments. By integrating authoritative geospatial datasets, employing rigorous validation techniques, and leveraging human-in-the-loop processes, the project aimed to enhance the precision, transparency, and reproducibility of geospatial localization workflows. The findings demonstrate that while LLMs exhibit significant potential for accelerating geospatial analysis, their outputs require systematic grounding and verification to ensure reliability in high-stakes applications. This work contributes to the broader field of geospatial intelligence and supports strategic objectives of international organizations such as the International Atomic Energy Agency (IAEA) and the U.S. Department of Energy (DOE).

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Beneficial Use of Harvested Ponded Fly Ash and Landfilled FGD Materials for High-Volume Surface Mine Reclamation

The overall motivation of this project was to demonstrate at laboratory, bench-scale, and full-scale demonstration levels that (a) coal ash surface impoundments can go through closure by removal as per USEPA and state regulations so that the material can be used as is (other than draining free water using CCRs piles) in high-volume beneficial applications, (b) FGD material from closed out FGD facilities can be excavated and recompacted for coal mine reclamation, and (c) harvested CCRs can be beneficially utilized (providing a net environmental gain) in large-volumes for reclamation at abandoned coal mine sites across the US, especially in the Eastern and Midwest coal mining regions. The objectives of this project were to: 1) promote the safe and cost-effective closure by removal of coal ash impoundments, 2) harvest landfilled FGD, and 3) promote the high-volume beneficial use of these harvested CCRs in the reclamation of abandoned surface coal mine sites across the eastern and midwestern coal mining regions of the United States. The major tasks carried out for this project are summarized below: 1) Conesville Full-Scale Demonstration Project: About 2 million tons of harvested CCR materials from the closure by removal of an inactive fly ash pond and an adjacent old FGD landfill were used for the full-scale demonstration project to fully reclaim a nearby partially completed abandoned surface coal mine. Site monitoring for the project duration was carried out and results are discussed. 2) Laboratory Testing: Geotechnical and environmental testing of harvested ponded fly ash and landfilled FGD material at the former Conesville power plant were carried out. Completing the laboratory testing allowed for QA/QC for the full-scale site construction and informed the formulation of the risk analysis. 3) Risk Analysis: We developed a reliable computational model for fate and transport. We used these models and the rich set of monitored data for the Conesville site to analyze risks to human health and ecological risks associated with high-volume surface mine reclamation using harvested CCRs. 4) GIS Siting Study: A Geographic Information System (GIS) study was carried out for three states in the Eastern coal mining region and two states in the Midwest coal region. This effort provided site specific GIS information for five states and allowed us to establish protocols that other states can follow in implementing their own state specific GIS study.

01 COAL, LIGNITE, AND PEAT↗
DOE OSTI2024

Digital risk analysis in nuclear engineering projects: Designing for safety, performance, reliability, and security

Cyber-informed engineering and security-by-design frameworks are important in promoting the need to identify cybersecurity concerns early in the systems engineering lifecycle so risks from adversarial cyber-attacks can be eliminated or reduced through engineering design practices. In addition to adversarial risk, risk in operational technology systems also includes non-adversarial and unintentional risk from other factors such as human performance errors, environmental conditions, design flaws, and device degradation or failure. This paper introduces a new concept for characterizing digital risk, both adversarial and non-adversarial, and provides the basis for initial research into a novel digital risk analysis approach focused on incorporating attack difficulty into a multi-attribute analysis technique using robust decision-making. This digital risk characterization is also used to frame a discussion on the challenges of competing objectives and competing stakeholder requirements in an integrated energy system project that incorporates a small modular reactor and industrial facility.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2024

Generative AI for Power Grid Operations

Generative artificial intelligence (AI) has captured into the mainstream, demonstrating capabilities that once belonged solely to the realm of human cognition. From defeating world champions in complex games to generating human-quality text and images, Generative AI has proven its potential to revolutionize countless industries. The electric power grid is no exception. Generative AI's ability to process vast amounts of data rapidly, assist decision support and identify patterns could significantly enhance power grid operations. For example, Generative AI could improve state estimation where measurements are not available or integrate renewable energy sources more efficiently with probabilistic forecasting. The key contributions of this whitepaper are outlined below: (1) Comprehensive overview of Generative AI's applications in power grid operations: It highlights the opportunities in areas such as forecasting, state estimation, and demonstrating the potential for enhancing efficiency, reliability, and resilience. (2) Expanding Generative AI's impact through synergies with emerging technologies: The paper introduce NREL developed eGridGPT and explores how AI orchestration, multi-agent systems, and Digital Twins can collaborate to optimize grid operations, addressing the complexities of a decarbonized and electrified future. (3) In-depth analysis of challenges in implementing Generative AI: This includes considerations like data availability and quality, model validation, certification, and ethical concerns, ensuring responsible AI deployment. (4) Emphasizing human-AI collaboration: The whitepaper underscores the importance of trustworthy, transparency, and explainability in AI systems to promote seamless interaction between human operators and AI, ultimately improving decision-making. (5) Exploring future research and development: It identifies critical areas for further advancement to fully realize Generative AI's potential in power grid operations. This whitepaper serves as a valuable resource for researchers, practitioners, and policymakers looking to harness Generative AI for a more reliable, stable, and cost-effective power grid.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2026

Enhancing Sensitivity in Targeted Single-Cell Proteomics by Coupling a Dual Ion Funnel Interface with Triple Quadrupole Mass Spectrometer

Single-cell proteomics (SCP) has emerged as a powerful approach for understanding cellular heterogeneity and biological processes at unprecedented resolution. However, the extremely limited protein content of individual cells (femtogram to picogram levels) pushes current mass spectrometry instrumentation to its sensitivity limits, creating a critical analytical bottleneck. While selected reaction monitoring (SRM) using triple quadrupole (QqQ) instruments 1 offers advantages in sensitivity and reproducibility for targeted proteomics quantification, SRM still struggles with sensitivity for quantification of moderate- or low-abundance proteins from single-cell sample amounts. Here, we report the development and systematic evaluation of a dual ion funnel interface designed to address the sensitivity limitation by significantly enhancing ion transmission efficiency in commercial QqQ mass spectrometers. The dual ion funnel interface, composed of a curved S-funnel followed by a conventional ion funnel, improves ion transmission efficiency while reducing chemical noise through selective ion focusing. The performance of the dual ion funnel interface was systematically compared to standard interface on a TSQ Vantage platform across samples with different levels of complexity. The dual funnel interface demonstrated to provide up to 25-fold improvement in sensitivity across a wide range of protein concentrations in different biological matrices (low complex mouse macrophage and high complex human cells). Critically, enhanced sensitivity was accompanied by increased analytical reproducibility with lower coefficient of variations. Most importantly, the dual funnel interface enabled reliable quantification of low-abundance proteins that were barely detectable or not detected by the standard interface, extending analysis to single-cell equivalent amounts while maintaining excellent reproducibility. These results demonstrate that the dual funnel interface addresses the critical bottleneck in quantitative targeted proteomics, providing a technological foundation for ultrasensitive targeted SCP that requires both high sensitivity and robust quantitative performance.

Min, Sehong↗
DOE OSTI2024

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↗
DOE OSTI2024

CrossMP: Enabling Cross-Modality Translation between Single-Cell RNA-Seq and Single-Cell ATAC-Seq through Web-Based Portal

In recent years, there has been a growing interest in profiling multiomic modalities within individual cells simultaneously. One such example is integrating combined single-cell RNA sequencing (scRNA-seq) data and single-cell transposase-accessible chromatin sequencing (scATAC-seq) data. Integrated analysis of diverse modalities has helped researchers make more accurate predictions and gain a more comprehensive understanding than with single-modality analysis. However, generating such multimodal data is technically challenging and expensive, leading to limited availability of single-cell co-assay data. Here, we propose a model for cross-modal prediction between the transcriptome and chromatin profiles in single cells. Our model is based on a deep neural network architecture that learns the latent representations from the source modality and then predicts the target modality. It demonstrates reliable performance in accurately translating between these modalities across multiple paired human scATAC-seq and scRNA-seq datasets. Additionally, we developed CrossMP, a web-based portal allowing researchers to upload their single-cell modality data through an interactive web interface and predict the other type of modality data, using high-performance computing resources plugged at the backend.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

An engineered lactate oxidase based electrochemical sensor for continuous detection of biomarker lactic acid in human sweat and serum

Lactate levels in humans reveal intensity and duration of exertion and provide a critical readout for the severity of life-threatening illnesses such as pediatric sepsis. Using the lactate oxidase enzyme (Lox) from Aerococcus viridians, we demonstrated its functionality for lactate electrochemical sensing in physiological fluids in a lab setting. The structure and dynamics of LOx were validated by crystallography, X-ray scattering, and hydroxyl radical protein footprinting. This provided a validated protein template for understanding and designing an enzyme-based electrochemical sensing elements. Using this template, LOx enzyme variants were generated and compared. Comparison of the variants demonstrates that one exhibits effective lactate sensing at significantly reduced operating voltages. Additionally, we demonstrate that the four hexahistidine-tags on each enzyme tetramer are sufficient for immobilization to create a durable, functional sensor, with no need for a covalent attachment, enabling self-immobilization and eliminating the need for additional immobilization steps. The functionality of the LOx enzyme variants was verified at physiological lactate concentrations in both human serum (0–4 mM) and artificial sweat (0–100 mM) using 3-electrode setups for analysis of the three variants in parallel. Accuracy of measurement in both artificial sweat and human serum were high. Employing a microfluidic flow cell, we successfully monitored varying lactate levels in physiological fluids continuously over a 2h period. Overall, this optimized LOx enzyme, which self-immobilizes onto gold sensing electrodes, facilitates efficient and reliable lactate detection and continuous monitoring at reduced operating voltages suitable for further development towards commercial use.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2026

Performing Numerical Analysis of Cybersecurity Options Using Dynamic Risk Analysis Tool EMRALD

Cyberattacks can have many different attack paths, durations, and goals. There are also many different mitigation options involving hardware, software, and/or humans. Considering a cyber threat should involve defense-in-depth methods and a quantitative or numerical evaluation of overall effectiveness against dynamic, time-dependent attacks to make cost and risk-informed decisions. Typical cyberattack modeling methods only provide a qualitative evaluation. The main areas of cybersecurity are confidentiality, integrity, and availability. For companies with cyber-physical systems such as advanced nuclear reactors, cyber-related safety is a requirement set by North American Electric Reliability and the U.S. Nuclear Regulatory Commission. They are also concerned about availability or reliability as a business case. As cyber threats are evolving to a business-for-hire structure, more attacks may focus on disrupting business success and reliability, causing financial and economic stability risk. Companies want to know business reliability and recovery from those threats, and that requires modeling physical behavior of the targets. Dynamic-state-based and Markov-based modeling provides a method for better cyber scenario modeling with different tools having issues such as state-base explosion. Dynamic modeling enables time and conditional features not found in other numerical evaluation methods. EMRALD (Event Modeling Risk Assessment using Lined Diagrams) is a dynamic risk analysis modeling and simulation tool and has features that reduce modeling issues. It has been used to model different time-dependent events including plant behavior and operator procedures. As a general modeling tool, EMRALD can also be used to model cyberattack scenarios with varying mitigation options and quantify effectiveness, producing numerical data for risk-informed decisions. This paper uses EMRALD to demonstrate that dynamic numerical risk analysis can be used for cyber threat modeling to provide insights for design decision-making and optimize defense strategies. Keywords: cyber modeling; cyber-physical systems; numerical cyber modeling

97 - MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Characterizing Interaction Uncertainty in Human-Machine Teams

With the increasing use and adoption of artificial intelligence (AI), the reliability of modern data systems will be driven by a tighter teaming between human experts and intelligent machine teammates. As in the case of human-human teams, the success of human-machine teams will also rely on clear communication about mutual goals and actions. In this paper, we combine related literature from cognitive psychology, human-machine teaming, uncertainty in data analysis, and multi-agent systems to propose a new form of uncertainty: interaction uncertainty for characterizing bidirectional communication in human-machine teams. We map the causes and effects of interaction uncertainty and outline potential ways to mitigate uncertainty for mutual trust in a high-consequence real-world scenario.

uncertainty, data analytics, interaction, trust, h↗
DOE OSTI2025

NUTRON NESHAPs Dashboard

My project aims to enhance the Nuclear Material Tracking Application (NUTRON) software by integrating a tool for the National Emission Standards for Hazardous Air Pollutants (NESHAP) emissions calculations and presenting this data on a dashboard. Inefficiencies in the current NESHAP calculation process were addressed, which will result in more timely regulatory compliance efforts. Key improvements include revising the transfer request system, incorporating effective dose calculations, and developing a data visualization dashboard into NUTRON. The project involved creating a wireframe, preparing an Engineering Calculations and Analysis Report (ECAR), stakeholder meetings, and providing supplemental documentation. Key findings indicate that the proposed modifications will streamline the NESHAP calculation process, reduce human error, and provide REC personnel with accurate and timely data for material use determinations and dose estimations. Future work focuses on completing the NUTRON modifications and fully integrating the new features, ensuring a more efficient and reliable system for tracking and reporting nuclear material transfers.

99 - GENERAL AND MISCELLANEOUS↗
DOE OSTI2025

Airport Ground Support Equipment Infrastructure & Logistics Electrification Assessment Tool: 2025 Data Development, Modeling and Analysis for DFW

The aviation industry is increasingly turning to modernize freight facilities by integrating electric Ground Support Equipment (eGSE) to enhance operational efficiency of freight facility moving vehicles and equipment. Airports worldwide are adopting eGSE to streamline cargo movement, reduce fuel and maintenance costs, and improve logistics coordination.1 North America, with its advanced aviation infrastructure, leads this transition, leveraging Internet of things (IoT)-enabled automation and zero emission technologies to boost reliability and reduce human errors.2 Electrification of freight facility moving vehicles and equipment boosts turnaround times, improves equipment reliability, and optimizes logistics coordination, giving operators a competitive advantage. With rising fuel price volatility and the pressure to meet stringent performance benchmarks, airports are focusing on cost-effective, scalable solutions for long-term financial and operational gains. To further accelerate electrification, airports are integrating Zero Emission Vehicles (ZEVs) into rental car fleets and deploying electric baggage carts, requiring strategic investments in charging infrastructure. 3 The shift, however, presents challenges, such as limited technical expertise, high capital costs, and complex procurement processes. By forging strategic partnerships, leveraging advanced technologies, and optimizing infrastructure investments, airports can create a resilient, future-ready ecosystem that enhances the movement of people and goods through electrification-driven efficiency. Supported by the U.S. Department of Energy (DOE) Vehicle Technologies Office (VTO), this electrification effort provides a scalable, cost-effective solution to improve airport freight operations. Through targeted investments and innovation, airports enhance efficiency, reduce costs, and meet performance benchmarks while advancing toward a resilient, electrified future.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2025

Electromagnetic Transient Simulation of Photovoltaic Inverter Using Implicit-Explicit Solver

This paper introduces the implementation of electromagnetic transient (EMT) simulations of a photovoltaic (PV) inverter module using the Implicit-Explicit (ImEx) solver in the Suite of Nonlinear and Differential/Algebraic Equation Solvers (SUNDIALS). This study demonstrates the effectiveness of the ImEx solver in overcoming the challenges inherent in simulating the complex dynamics of PV inverter modules. Furthermore, using SUNDIALS’ ImEx solver module ARKODE for EMT simulation automates key aspects of the process, such as numerical integration, providing substantial benefits including enhanced consistency, faster implementation, reduced human error, and the capability to handle the complexities of advanced numerical integration. By conducting comparative simulations with an implicit method used in commercial software, the research showcases the ImEx solver’s capability in achieving high accuracy and reliability. Results indicate that leveraging the ImEx approach significantly enhances modeling fidelity and reduces simulation setup times, offering a promising tool for the EMT analysis of PV inverter systems in power electronics-dominated power grids.

Choi, Jongchan [ORNL] (ORCID:000000025952455X)↗
DOE OSTI2026

CRCNS21 Computational Models of Multisensory Integration by Upper Limb in Humanoids and Amputees

This international collaborative research project between Johns Hopkins University (JHU) and the Technical University of Munich (TUM) investigated how the human brain processes and integrates multiple types of sensory information, such as touch and force, with the goal of improving prosthetic limbs for amputees and advancing sensory capabilities in humanoid robots. The research advanced our understanding of how the brain responds to sensory feedback in upper-limb amputees. Through experiments in which amputees received electrical stimulation while performing phantom hand movements, we demonstrated that sensory feedback activates the cortical sensorimotor and multisensory regions, and that these regions communicate dynamically during stimulation. Experiments with intact-limb participants explored the integration of visual, haptic, and force feedback, as well as in virtual reality motor training, further showing how the brain processes multimodal sensory information. In addition, this research inspired work on examining the reliability of where amputees perceive sensations over time, which contributed to a successful doctoral fellowship for continued investigation. Our collaborators at TUM improved multimodal sensor technology combining tactile and thermal feedback for humanoid robots, demonstrating the feasibility of integrating multiple sensor types into a unified system for detecting and responding to environmental stimuli. The experimental methods and analysis techniques developed across both teams, including functional network analysis and multimodal sensor integration, provide a foundation for future research in prosthetics and robotics. This research benefits the public by generating knowledge about how amputees process restored sensory information. Advances in humanoid sensing contribute to safer human-robot interaction. The project also fostered international collaboration and cross-disciplinary training: one TUM doctoral student spent a summer at JHU working on multimodal sensor integration, while two JHU students traveled to TUM to host workshops on neuromorphic sensory encoding and sensory integration.

42 ENGINEERING↗
DOE OSTI2025

Increased inflammation as well as decreased endoplasmic reticulum stress and translation differentiate pancreatic islets from donors with pre-symptomatic stage 1 type 1 diabetes and non-diabetic donors

Aims/hypothesis Progression to type 1 diabetes is associated with genetic factors, the presence of autoantibodies and a decline in beta cell insulin secretion in response to glucose. Very little is known regarding the molecular changes that occur in human insulin-secreting beta cells prior to the onset of type 1 diabetes. Herein, we applied an unbiased proteomics approach to identify changes in proteins and potential mechanisms of islet dysfunction in islet-autoantibody-positive organ donors with pre-symptomatic stage 1 type 1 diabetes (HbA1c ≤42 mmol/mol [6.0%]). We aimed to identify pathways in islets that are indicative of beta cell dysfunction. Methods Multiple islet sections were collected through laser microdissection of frozen pancreatic tissues from organ donors positive for single or multiple islet autoantibodies (AAb + , n=5), and age (±2 years)- and sex-matched non-diabetic (ND) control donors (n=5) obtained from the Network for Pancreatic Organ donors with Diabetes (nPOD). Islet sections were subjected to MS-based proteomics and analysed with label-free quantification followed by pathway and functional annotations. Results Analyses resulted in ~4500 proteins identified with low false discovery rate (<1%), with 2165 proteins reliably quantified in every islet sample. We observed large inter-donor variations that presented a challenge for statistical analysis of proteome changes between donor groups. We therefore focused on only the donors with stage 1 type 1 diabetes who were positive for multiple autoantibodies (mAAb + , n=3) and genetic risk compared with their matched ND controls (n=3) for the final statistical analysis. Approximately 10% of the proteins (n=202) were significantly different (unadjusted p<0.025, q<0.15) for mAAb + vs ND donor islets. The significant alterations clustered around major functions for upregulation in the immune response and glycolysis, and downregulation in endoplasmic reticulum (ER) stress response as well as protein translation and synthesis. The observed proteome changes were further supported by several independent published datasets, including a proteomics dataset from in vitro proinflammatory cytokine-treated human islets and single-cell RNA-seq datasets from AAb + individuals. Conclusions/interpretation In situ human islet proteome alterations in stage 1 type 1 diabetes centred around several major functional categories, including an expected increase in immune response genes (elevated antigen presentation/HLA), with decreases in protein synthesis and ER stress response, as well as compensatory metabolic response. The dataset serves as a proteomics resource for future studies on beta cell changes during type 1 diabetes progression and pathogenesis. Data availability The LC-MS raw datasets that support the findings of this study have been deposited in the online repository: MassIVE (https://massive.ucsd.edu/ProteoSAFe/static/massive.jsp) with accession no. MSV000090212.

Autoantibody-positive↗
DOE OSTI2024

Assurance of Reasoning Enabled Systems (ARES)

ARES was in part motivated by the determination of President’s Council of Advisors on Science and Technology (PCAST) on May 13th, 2023 that published a set of inquiries: In an era in which convincing images, audio, and text can be generated with ease on a massive scale, how can we ensure reliable access to verifiable, trustworthy information? How can we be certain that a particular piece of media is genuinely from the claimed source? What technologies, policies, and infrastructure can be developed to detect and counter AI-generated disinformation? In an effort to automatically analyze and patch/optimize code the work in this report describes various neural Machine Learning (ML) analysis engine implementations to assist in situations where source code is deficient or completely lacking to decompile (lift) binary code to ’C’. The goal is to gradually reduce human intervention. To this end, two Large Language Model (LLM) variants (Code LLama 2, LLama 3.1 and Starcoder1, Starcoder 2) where finetuned with ’before/after’ code pairs on the OpenBLAS library. LLama trained on the lowering process, Starcoder trained on the lifting process with National Security Agency’s (NSA) open-source Ghidra decompiler assist. The inferencing test results indicate correctness for only very short sequences for Starcoder 2. Moving forward, the experiments conclude with a set of recommendations of required resources and technologies

97 MATHEMATICS AND COMPUTING↗