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At least 1,027 records · Page 57

Proteome-wide characterization of PTMs reveals host cell responses to viral infection and identifies putative antiviral drug targets

Post-translational modifications (PTMs) are biochemical modifications that can significantly alter protein structure, function, stability, localization, and interactions with other molecules, thereby activating or inactivating intracellular processes. A growing body of research has begun to highlight the role of PTMs, including phosphorylation, ubiquitination, acetylation, and redox modifications, during virus-host interactions. Collectively, these PTMs regulate key steps in mounting the host immune response and control critical host pathways required for productive viral replication. This has led to the conception of antiviral therapeutics that focus on controlling host protein PTMs, potentially offering pathogen-agnostic treatment options and revolutionizing our capacity to prevent virus transmission. On the other hand, viruses can hijack the host cellular PTM machinery to modify viral proteins in promoting viral replication and evading immune surveillance. PTM regulation during virus-host interactions is complex and poorly mapped, and the development of effective PTM-targeted antiviral drugs will require a more comprehensive understanding of the cellular pathways essential for virus replication. In this review, we discuss the roles of PTMs in virus infection and how technological advances in mass spectrometry-based proteomics can capture systems-level PTM changes during viral infection. Additionally, we explore how such knowledge is leveraged to identify PTM-targeted candidates for developing antiviral drugs. Looking ahead, studies focusing on the discovery and functional elucidation of PTMs, either on the host or viral proteins, will not only deepen our understanding of molecular pathology but also pave the way for developing better drugs to fight emerging viruses.

Immunology↗

Understanding and mitigating degradation in amine-based sorbents for CO 2 direct air capture

The success of direct air capture (DAC) of CO 2 depends on sorbents that combine high capacity, low energy requirements, and long-term durability. Amine-based sorbents-including solid-supported aminopolymers, grafted amines, and amine-functionalized resins-remain the leading candidates, but their limited lifetimes drive up costs and constrain deployment. In this review, we outline the current understanding of amine-based sorbent degradation with an emphasis on clearly identifying what is known about structure-property-performance relationships, as well as important knowledge gaps. More specifically, we discuss how polymer chemistry, sorbent design variables, and environmental and process conditions contribute to performance loss. In parallel, we outline how advances in spectroscopy, modeling, and accelerated testing are beginning to illuminate chemical and physical degradation mechanisms. Looking forward, we identify future research directions that will be critical for gaining a deeper understanding of degradation, as well as opportunities for developing innovative mitigation strategies for improving the lifetime of amine-based sorbents.

organic↗

A score-based diffusion model approach for adaptive learning of stochastic partial differential equation solutions

In this paper, we propose a novel framework for adaptively learning the time-evolving solutions of stochastic partial differential equations (SPDEs) using score-based diffusion models within a recursive Bayesian inference setting. SPDEs play a central role in modeling complex physical systems under uncertainty, but their numerical solutions often suffer from model errors and reduced accuracy due to incomplete physical knowledge and environmental variability. To address these challenges, we encode the governing physics into the score function of a diffusion model using simulation data and incorporate observational information via a likelihood-based correction in a reverse-time stochastic differential equation. This enables adaptive learning through iterative refinement of the solution as new data becomes available. To improve computational efficiency in high-dimensional settings, we introduce the ensemble score filter, a training-free approximation of the score function designed for real-time inference. Numerical experiments on benchmark SPDEs demonstrate the accuracy and robustness of the proposed method under sparse and noisy observations.

97 MATHEMATICS AND COMPUTING↗

Systematic Analysis of Drivers and Barriers of Cross-Sectorial Learning Between Nuclear and Oil and Gas Decommissioning Projects - 20139

Project and megaproject management in the energy sector have historically focused on the planning and delivery of the construction of infrastructure. Therefore, policies are predominantly oriented to support the construction of infrastructure rather than its decommissioning. However, globally, several facilities have reached (or will soon reach) their end-of-life and need to be decommissioned. These facilities span across the energy sector, including nuclear power plants and oil and gas rigs, whose decommissioning present unprecedented techno-socio-economic challenges. Moreover, globally, their decommissioning cost is estimated to reach hundreds of billions of US dollars and this budget keeps increasing, with limited knowledge-transfer across industries to mitigate the spiraling increase of this figure. Cross-sectorial knowledge-transfer is a way to tackle this matter and improve the planning and delivery of decommissioning and waste management projects. The aim of this research is to build a road-map based on cross-sectorial industrial experience, designed to promote the sharing of good practices between projects both within and across industries dealing with major decommissioning and waste management challenges. To reach this aim, the tacit knowledge of senior practitioners on several large scale nuclear and oil and gas decommissioning projects is made explicit by the means of semi-structured interviews, systematically analyzed through directed content analysis. The results of this analysis include a list of good practices that could and should be transferred to nuclear decommissioning projects, including the need to promote the adoption of incentives explicitly linked to the project deliverables, and to develop long-term plans to support smooth transition from operations to decommissioning. Suggestions about how the knowledge-transfer can be promoted within and across organizations are also discussed. In this way, this research provides practical guidance for project managers and policymakers on how to support the planning and delivery of projects with improved performance. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Sensitivity-based Similarity Metrics for New Experiment Design Optimization

The nuclear data used in advanced reactor simulations requires validation. Data from nuclear criticality experiments can provide this validation. New nuclear criticality experiment design requires extensive knowledge and expert judgement such that the experimental design parameters are selected in such a way to keep the experiment subcritical. To aide in this experimental design process, professionals can utilize sensitivity and uncertainty analysis. Sensitivity and uncertainty analysis relies on matching new application experiments with currently existing benchmark experiments. Currently, there is functionality in the Whisper 1.1 software package to calculate a similarity metric based on neutron multiplication factor sensitivity coefficients between a new application designed by the user and existing International Criticality Safety Benchmark Experiment Project (ICSBEP) benchmarks. The Whisper 1.1 software package is included in Monte Carlo N-Particle ® Code Version 6.21 (MCNP ® 6.2). This work is geared toward expanding this capability to new similarity metrics based on beta-effective sensitivity coefficients and reactivity coefficient sensitivity coefficients. While the investigation of these sensitivity coefficients is presented in detail in separate works at this same conference, this work will be primarily focused on studying the similarity metrics in more detail. These similarity metrics will then be incorporated into the optimization algorithms used for experiment design in EUCLID (Experiments Underpinned by Computational Learning for Improvements in nuclear Data), which is a Los Alamos National Laboratory (LANL) project designed to constrain nuclear data of interest, such that adjustments can be made to possible inaccuracies. A more detailed optimization can be subsequently performed by breaking down these similarity metrics by isotope, reaction, and energy.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Gradient-Based Novelty Detection Boosted by Self-Supervised Binary Classification

Novelty detection aims to automatically identify out-of-distribution (OOD) data, without any prior knowledge of them. It is a critical step in data monitoring, behavior analysis and other applications, helping enable continual learning in the field. Conventional methods of OOD detection perform multi-variate analysis on an ensemble of data or features, and usually resort to the supervision with OOD data to improve the accuracy. In reality, such supervision is impractical as one cannot anticipate the anomalous data. In this paper, we propose a novel, self-supervised approach that does not rely on any pre-defined OOD data: (1) The new method evaluates the Mahalanobis distance of the gradients between the in-distribution and OOD data. (2) It is assisted by a self-supervised binary classifier to guide the label selection to generate the gradients, and maximize the Mahalanobis distance. In the evaluation with multiple datasets, such as CIFAR-10, CIFAR-100, SVHN and TinyImageNet, the proposed approach consistently outperforms state-of-the-art supervised and unsupervised methods in the area under the receiver operating characteristic (AUROC) and area under the precision-recall curve (AUPR) metrics. We further demonstrate that this detector is able to accurately learn one OOD class in continual learning.

Sun, Jingbo↗

CASTLE: Conflict Analysis Strategy Testing Laboratory Environment v.1.0.0

SAND2024-01743O The Conflict Analysis Strategy Testing Laboratory Environment (CASTLE) is a software framework that enables and simplifies building a novel, turn-based strategy game in which it can define its own rules, maps, pieces, and interactions. The software is for novice to experienced programmers with some knowledge of Unity3D, a tool used in game production. CASTLE includes a library of common game mechanics used for strategic wargames and traditional board games, such as cards, tokens, dice, and grid maps. It follows design principles popularized by the video game industry and uses singletons for managing portions of the code. CASTLE builds on Unity's component-based design and can respond to engine events during execution. Among the numerous user-friendly features: Build games quickly and cost-effectively Network in real-time and apply data to new games developed on the framework Host multiple participants online Connect rule- or machine learning-based agents to a CASTLE game to serve as opponents or to simulate games Collect data collection from players and in-game behaviors Create a survey to gather demographics or opinions from players Store data locally or save it to an external database through Representational State Transfer (REST) functions CASTLE, which was prototyped using Microsoft Azure, is also designed for easily distributing online games using popular cloud services. The multiplayer functionality includes an agent interface, allowing developers to construct AI players that can substitute for humans in any of the games. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Fabian, Nathan↗

Accelerated Materials Deployment in Advanced Nuclear Power Plants

The purpose of this report is to begin the development of a maximally efficient process for licensing and deploying new materials in Advanced Non-Light-Water Reactors (ANLWRs). Some new materials that are to be used in some new plants are seen as possibly introducing risks, because our understanding of those new materials’ behavior in the conditions generated by some novel plant designs is less complete than our understanding of the behavior of materials with long use histories in existing designs. In these cases, an approved code/standard or a code case to support the use of these materials in the novel design’s safety case may not exist for the regulator to utilize as part of the licensing determination. This circumstance creates the potential for an extremely long licensing process for new designs using new materials. The present strategy is to show how to manage these risks proactively, in such a way as to permit licensing decisions to be made in a timely manner, based on this risk management process. The present report outlines the gaps in the current codes to support deployment and use of novel materials and begins the development of the necessary risk management framework that is focused on the subject materials issues; it is based on risk-informed in-service surveillance practices, carried out in such a way as to compensate for current limitations in our state of knowledge. This development will enable licensing and deployment of the subject materials, conditional on the proactive surveillance process to be established. While this report is occasioned by limitations in our knowledge of certain materials issues that may arise in advanced designs, in-service surveillance is always done in order to compensate for a lack of knowledge: if we knew that components were not already failed and not trending toward failure, we would not perform surveillance, even in current-generation plants (except that prescriptive requirements would force us to do so). What is different about the surveillance program discussed here is that the issues are newer and the relevant experience base is less complete, so the surveillance presently contemplated may need to measure new things and/or measure them more often than has been traditional for surveillance coupons. The present report is devoted to the risk management framework and applies American Society of Mechanical Engineers Boiler and Pressure Vessel Code Section XI, Division [1] to establish the structure of a protocol for carrying out the necessary surveillance. These documents are generic: they do not tell us how often to surveille, or what to surveille, or what to measure, but rather how to determine those things, given certain technical inputs. The Regulatory Development R&D Program [2] is currently developing the companion supporting technical basis for the materials surveillance technology that, when completed and validated, can be used by owner/operator and NRC to implement a materials degradation management program for ANLWRs. This report also outlines salient points of discussion, positive potential outcomes, and potential concerns from industry and the USNRC. These aspects of the report intend to inform future work to develop a proposed technical process for adoption by the industry and endorsement by the USNRC to allow developers to propose a risk informed and conservative approach for the use of materials where operating experience/data and codes and standards may not exist for use of a novel material in an operating reactor environment. Additionally, such a technology could be leveraged to potentially reduce part of the upfront materials data requirements from ongoing long-term materials testing so that early action on license application could be undertaken by NRC, in parallel with the continuation of long-term data collection. This could accelerate the schedule for a first-of-a-kind ANLWR deployment or a nth-of-a-kind new materials insertion for established ANLWR designs.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Efficient distributed continual learning for steering experiments in real-time

Deep learning has emerged as a powerful method for extracting valuable information from large volumes of data. However, when new training data arrives continuously (i.e., is not fully available from the beginning), incremental training suffers from catastrophic forgetting (i.e., new patterns are reinforced at the expense of previously acquired knowledge). Training from scratch each time new training data becomes available would result in extremely long training times and massive data accumulation. Rehearsal-based continual learning has shown promise for addressing the catastrophic forgetting challenge, but research to date has not addressed performance and scalability. To fill this gap, we propose an approach based on a distributed rehearsal buffer that efficiently complements data-parallel training on multiple GPUs to achieve high accuracy, short runtime, and scalability. It leverages a set of buffers (local to each GPU) and uses several asynchronous techniques for updating these local buffers in an embarrassingly parallel fashion, all while handling the communication overheads necessary to augment input minibatches using unbiased, global sampling. We further propose a generalization of rehearsal buffers to support both classification and generative learning tasks, as well as more advanced rehearsal strategies (notably Dark Experience Replay, leveraging knowledge distillation). We illustrate this approach with a real-life HPC streaming application from the domain of ptychographic image reconstruction. Furthermore, we run extensive experiments on up to 128 GPUs of the ThetaGPU supercomputer to compare our approach with baselines representative of training-from-scratch (the upper bound in terms of accuracy) and incremental training (the lower bound). Results show that rehearsal-based continual learning achieves a top-5 validation accuracy close to the upper bound, while simultaneously exhibiting a runtime close to the lower bound.

Asynchronous data management↗

Makah Tribe Climate Assessment, Adaptation, and Resilience Planning

Our aim was to develop a Climate Adaptation and Resilience Plan through gathering community input through personal interviews and individual surveys, building from our Climate Impacts Assessment work completed in 2018. This project has collected traditional, cultural, and local knowledge to support the ongoing multi-departmental environmental planning processes of the Makah Tribe. This information was then used to identify specific human wellbeing indicators to inform and enhance Makah tribal policy, management, and decision-making processes. Combined our tribal environmental planning to include the work of the Tribal Resilience Work Group (TRWG) and Oil Spill Work Group (OSWG), which relied on publicly available Western science-based data. While this information provided a strong basis for tribal environmental planning, it does not capture the unique traditional, cultural needs, and local knowledge and tribal voices of the Makah community.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Advanced Energy Scale Correction Techniques for the X-ray Transition Edge Sensors of the Athena mission

The X-ray Integral Field Unit (X-IFU) onboard the future European X-ray telescope Athena will be the first space instrument carrying an array of more than a thousand transition edge sensors. One of the key challenges of the X-IFU is the measurement of narrow X-ray atomic lines to determine velocity shifts at an unprecedented level of accuracy. For this reason, the energy scale of the instrument needs to be known with extreme accuracy, of 0.4 eV (1σ) up to 7 keV. The energy scale will be measured on the ground through a dedicated calibration campaign using fiducial X-ray sources. Though calibrated, the energy scale is extremely sensitive to the environmental conditions around the TES array, and drifts in the readout chain electronics. Uncorrected, the energy scale can naturally drift up to hundreds of eVs. Changes of the TES gain will be monitored via onboard X-ray calibration sources, and the energy scale will be corrected either per pixel, or within a small groups of pixels. Although simulations show that a 0.4 eV level can be achieved, the very high accuracy required by the X-IFU calls for experimental validation. A dedicated measurement campaign has been performed by NASA Goddard Space Flight Center to characterize the energy scale of a prototype kilo-pixel array of X-IFU-representative TESs. The analysis of the data demonstrated the ability to correct for various drifts using two fiducial lines to track the temporal gain variation. In this paper, we propose to extend this study on the same data set by investigating multi-parameter correction techniques based on both the pulse-height of the fiducial line and the prepulse baseline level, using the knowledge of the TES energy scale at reference temperature/magnetic field set points acquired on the ground. Investigations on the co-adding of pixels to perform a joint correction over pools of pixels is also explored.

79 ASTRONOMY AND ASTROPHYSICS↗

Physics-informed KNN milling stability model with process damping effects

This paper describes a k-nearest neighbors, or KNN, model for milling stability including process damping effects. A physics-based, frequency domain milling stability solution is used to generate the training data, but does not incorporate process damping effects. The data set is then updated using limited tests to capture the process damping behavior. A “stair step” approach is used to select the test points, where a first spindle speed-axial depth combination is selected based on the physics-based stability map, subsequent tests are defined using the previous test result, and data points are updated by knowledge of process damping behavior and the test results. Furthermore, the KNN modeling approach demonstrates the ability to predict both stable and unstable results, including process damping behavior.

42 ENGINEERING↗

Climate Leads to Reversed Latitudinal Changes in Chinese Flood Peak Timing

Changes in river floods under a changing climate are of worldwide concerns, but relevant knowledge is limited especially over the East Asia monsoon region. Here we examine changes in flood peak timing based on the most comprehensive flood dataset to date across China during 1961-2017. The temporal shifts of Chinese flood peak timing range from -19.0 days earlier to +14.0 days later per decade. Earlier flood occurrences are mainly observed in northern China, with delayed flood occurrences in the south. The spatial pattern of reversed latitudinal changes in flood timing leads to growing spatial extents of concurrent river floods over China. Soil moisture plays an important role in modulating such changes, despite precipitation determines the climatological mean dates of flood occurrences. Our results highlight a strong climate signal on the changes in flood timing over China, and call for coordinated efforts in alleviating expanding flood hazards related to the changes in flood timing.

54 ENVIRONMENTAL SCIENCES↗

Toward a mechanistic understanding of electrocatalytic nanocarbon

Electrocatalytic nanocarbon (EN) is a class of material receiving intense interest as a potential replacement for expensive, metal-based electrocatalysts for energy conversion and chemical production applications. The further development of EN will require an intricate knowledge of its catalytic behaviors, however, the true nature of their electrocatalytic activity remains elusive. This review highlights work that contributed valuable knowledge in the elucidation of EN catalytic mechanisms. Experimental evidence from spectroscopic studies and well-defined molecular models, along with the survey of computational studies, is summarized to document our current mechanistic understanding of EN-catalyzed oxygen, carbon dioxide and nitrogen electrochemistry. We hope this review will inspire future development of synthetic methods and in situ spectroscopic tools to make and study well-defined EN structures.

36 MATERIALS SCIENCE↗

Terrain-Relative Navigation with Neuro-Inspired Elevation Encoding

Terrain-relative navigation (TRN) encompasses a wide variety of algorithms that perform localization with respect to the terrain below a flying vehicle. In traditional approaches, measurements of the terrain are matched to a map carried onboard. This work presents a terrain-relative navigation filter with a position measurement inspired by neural activity associated with positioning in nature. Here, the filter is shown to produce accurate position measurements that outperform popular optimization and template matching methods given poor prior knowledge of the position. The proposed method is also better-suited to distributed implementation than optimization-based methods.

33 ADVANCED PROPULSION SYSTEMS↗

Structural basis for antibody binding to adenylate cyclase toxin reveals RTX linkers as neutralization-sensitive epitopes

RTX leukotoxins are a diverse family of prokaryotic virulence factors that are secreted by the type 1 secretion system (T1SS) and target leukocytes to subvert host defenses. T1SS substrates all contain a C-terminal RTX domain that mediates recruitment to the T1SS and drives secretion via a Brownian ratchet mechanism. Neutralizing antibodies against the Bordetella pertussis adenylate cyclase toxin, an RTX leukotoxin essential for B . pertussis colonization, have been shown to target the RTX domain and prevent binding to the α M β 2 integrin receptor. Knowledge of the mechanisms by which antibodies bind and neutralize RTX leukotoxins is required to inform structure-based design of bacterial vaccines, however, no structural data are available for antibody binding to any T1SS substrate. Here, we determine the crystal structure of an engineered RTX domain fragment containing the α M β 2 -binding site bound to two neutralizing antibodies. Notably, the receptor-blocking antibodies bind to the linker regions of RTX blocks I–III, suggesting they are key neutralization-sensitive sites within the RTX domain and are likely involved in binding the α M β 2 receptor. As the engineered RTX fragment contained these key epitopes, we assessed its immunogenicity in mice and showed that it elicits similar neutralizing antibody titers to the full RTX domain. The results from these studies will support the development of bacterial vaccines targeting RTX leukotoxins, as well as next-generation B . pertussis vaccines.

59 BASIC BIOLOGICAL SCIENCES↗

Retrospective Analysis of Backwater Habitat Availability Using Remote Sensing

Low-velocity channel-margin habitats serve as important nursery habitats for the endangered Colorado pikeminnow (Ptychocheilus lucius) in the middle Green River between Jensen and Ouray, Utah. These habitats, known as backwaters, are associated with emergent sandbars, and are shaped and reformed annually by peak flows. Our recent knowledge about backwater characteristics and dynamics that is summarized in the synthesis report (Grippo et al. 2015) was based on detailed annual survey data from a relatively small sample of backwaters that were collected from 2003 to 2014 and reach-wide evaluations of backwater surface area based on manual interpretation of aerial and satellite imagery. Methods that bridge the gap between the detailed surveys from a small number of backwaters and the reach-wide assessment of their surface area would enable an assessment of the availability of backwater habitats that meet the minimum depth requirements for suitable habitat for Colorado pikeminnow. In 2015 Argonne National Laboratory (Argonne) tested three regression models—linear, multiple, and partial least square (PLS) regression models—for estimating backwater depth using National Agriculture Imagery Program (NAIP) imagery collected in July 2006 that covered the Jensen-Ouray reach of the Green River (Hamada and LaGory 2016). The results suggested that a PLS regression model showed high correlation with the reference depth (R 2 = 0.69) and had the most unbiased and consistent estimate of backwater depth. The results also indicated that the PLS model would provide reasonable estimates of the amount of habitat providing a minimum suitable depth of 30 cm for young-of-the-year Colorado pikeminnow, even though absolute depth estimates may be uncertain for backwater areas deeper than approximately 40 cm. The study also provided insights regarding the amount and the selection of calibration and validation (cal-val) data needed for improving the accuracy of depth prediction.

54 ENVIRONMENTAL SCIENCES↗