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At least 109 records · Page 6

Structural and functional characterization of NEMO cleavage by SARS-CoV-2 3CLpro

Abstract In addition to its essential role in viral polyprotein processing, the SARS-CoV-2 3C-like protease (3CLpro) can cleave human immune signaling proteins, like NF-κB Essential Modulator (NEMO) and deregulate the host immune response. Here, in vitro assays show that SARS-CoV-2 3CLpro cleaves NEMO with fine-tuned efficiency. Analysis of the 2.50 Å resolution crystal structure of 3CLpro C145S bound to NEMO 226–234 reveals subsites that tolerate a range of viral and host substrates through main chain hydrogen bonds while also enforcing specificity using side chain hydrogen bonds and hydrophobic contacts. Machine learning- and physics-based computational methods predict that variation in key binding residues of 3CLpro-NEMO helps explain the high fitness of SARS-CoV-2 in humans. We posit that cleavage of NEMO is an important piece of information to be accounted for, in the pathology of COVID-19.

60 APPLIED LIFE SCIENCES↗

A Data-driven Phytotechnology Framework for Identification and Remediation of Leached-Metals-Contaminated Soil Near Coal Ash Impoundments

This project developed and evaluated advanced remote sensing and machine learning approaches to identify, monitor, and address environmental contamination associated with coal combustion residual (CCR) impoundments and landfills at coal-fired power plants. In Phase I, historical and multi-temporal Sentinel-2 satellite imagery, groundwater monitoring data, and environmental variables were integrated to detect vegetation stress potentially caused by toxic metal leaching from coal ash disposal sites. Multiple vegetation and biophysical indices were analyzed to determine their effectiveness in identifying abnormal vegetation growth patterns linked to contamination. Results from case studies conducted at coal ash–impacted power plant sites in North Carolina and Virginia demonstrated that satellite-based vegetation monitoring can serve as an effective early indicator of environmental stress associated with metals such as arsenic, cadmium, cobalt, lead, lithium, radium, and thallium.

01 COAL, LIGNITE, AND PEAT↗

NMF-Based Anomaly Detection in CMS 2D Tracking Occupancy Histograms

The CMS experiment relies on Data Quality Monitoring (DQM) to ensure that recorded collision data are suitable for physics analysis. During LHC Run 3, each run contains many lumisections and tracking monitoring elements, making offline inspection challenging, especially for localized detector effects that may appear only for short periods of time. This poster presents an unsupervised machine-learning approach to identify anomalous lumisections in CMS tracking occupancy histograms using Non-Negative Matrix Factorization (NMF). The workflow uses offline CMS DQMIO tracking histograms retrieved with the CMS DIALS API and organized as two-dimensional occupancy maps for each lumisection. After selecting stable lumisections, the occupancy maps are normalized and arranged into a non-negative data matrix. The NMF model learns a compact set of basis patterns describing normal tracking occupancy. Each lumisection is then reconstructed from these learned components, and the reconstruction error is used as an anomaly score. Large residuals indicate occupancy patterns that deviate from normal detector behavior and are flagged for further inspection. This NMF-based approach provides a fast and interpretable way to flag lumisections whose tracking occupancy patterns differ from normal detector behavior. Preliminary studies show sensitivity to known tracking anomalies, and ongoing work is focused on validating the method across additional Run 3 Pixel and Strip detector issues.

Rodríguez Ramos, Iliomar [Puerto Rico U., Mayaguez↗

Analysis Methods for Progressive Damage of Composite Structures

This document provides an overview of recent accomplishments and lessons learned in the development of general progressive damage analysis methods for predicting the residual strength and life of composite structures. These developments are described within their State-of-the-Art (SoA) context and the associated technology barriers. The emphasis of the authors is on developing these analysis tools for application at the structural level. Hence, modeling of damage progression is undertaken at the mesoscale, where the plies of a laminate are represented as a homogenous orthotropic continuum. The aim of the present effort is establish the ranges of validity of available models, to identify technology barriers, and to establish the foundations of the future investigation efforts. Such are the necessary steps towards accurate and robust simulations that can replace some of the expensive and time-consuming "building block" tests that are currently required for the design and certification of aerospace structures.

Rose, Cheryl A.↗

Unlocking the Mysteries of the Moon’s Shadowed Regions

The Moon poles host large quantities of water-ice deposits in the permanently shadowed regions (PSRs), which are vital for enabling sustainable human space exploration, making these regions high-priority targets for upcoming Artemis missions [1]. Unfortunately, today, the best available orbital lunar imagery [2, 3] lacks the meter-scale resolution and signal needed to understand the geomorphology and trafficability of PSRs, complicating the planning and execution of future missions seeking to explore PSRs. We have developed an image enhancement tool called HORUS (Hyper-effective nOise Removal Unet Software) [4, 5], designed to enhance LRO Narrow-Angle Camera (NAC) optical low-light imagery of permanently shadowed regions by effectively removing the CCD-related, photon, and other residual noises that corrupt the images. The tool is composed of two deep learning neural networks trained on environmental metadata and real and synthetic imagery, the latter generated by a physical noise model (LROC). We demonstrated that HORUS effectively produces low-noise, high-resolution images (~1.5m/px), achieving a 5 to 10x improvement over existing long-exposure images of PSRs. HORUS allows scientists and engineers to identify geomorphic features (e.g., craters and boulders) in shadowed regions as small as 3 meters across as well as to peek inside of small shadowed regions, for the first time. The tool was deployed and thoroughly validated for NASA's VIPER mission [6], where it was applied to 20 candidate target regions across the lunar South Pole. Additionally, we conducted different approaches to validate the resulting HORUS-processed images. With HORUS denoised images, VIPER scientists can increase their confidence on what surface features (previously unseen) exist in the shadowed regions, helping them plan rover traverses more safely and efficiently (e.g., Fig. 1) In this manuscript, we will describe how VIPER scientists are utilizing HORUS denoised images to extract new information from the terrain and increase their confidence in what surface features exist in the shadowed regions. In combination with other high-resolution images and digital elevation maps, HORUS images are helping the team analyze potential lading and science sites, as well as planning traverses more safely and efficiently (e.g., Fig. 1). Additionally, we will describe how HORUS tool unlocks a broad range of scientific and exploration applications to other Artemis and CPLS missions to the lunar poles, including (but not limited to) geomorphic analysis, change detection, surface hazard detection, and terrain relative navigation.

artificial intelligence↗

Insights Into the Hydrology of the Congo Peatlands Through Land Surface Modeling and Data Assimilation

The 16.8 million ha of peatlands in the Cuvette Centrale wetland complex in the Congo Basin is one of the largest peatland regions on Earth but still highly understudied. Understanding the hydrological functioning of these peatlands and the effects of external disturbances thereon remains a major challenge. Recent research suggested fundamental hydrological differences between the Congo peatlands and the well-studied Southeast Asian peatlands. The Congo peatlands have a doming gradient that is up to ten times smaller, and they are influenced by river hydrology to some extent. In this study, we explore the Congo peatland hydrology through land surface modeling and data assimilation. We build upon our recently developed tropical PEATCLSM module (Apers et al., 2022) that was parameterized based on data from Southeast Asian peatlands due to the lack of field data from other tropical peatland regions. In a first step, we derive Congo-specific peat hydraulic and discharge function parameters from a scalar parametrization of water level dynamics in the Congo peatlands, using observed water level data at two locations. These Congo-specific parameters differ considerably from the original literature-based parameters from Southeast Asian peatlands. In a second step, we apply our original and Congo-specific parameters in an assimilation scheme for L-band brightness temperature (Tb) data from the Soil Moisture and Ocean Salinity (SMOS) mission. The data assimilation results are used in two ways. First, the effect of these parameters on the simulated peatland hydrology and the observation-minus-forecast Tb residuals is evaluated. It is hypothesized that the new parameters reduce the previously reported modeling errors over the Congo peatlands and reduce the residuals in Tb as well. Second, we analyze the data assimilation diagnostics to learn about other model improvement possibilities. In preliminary results, we found long periods of temporally autocorrelated total water storage increments (difference of pre- and post-update) that coincided with anomalies in river stages measured upstream of the peatlands. Since PEATLCSM neglects possible river influence, this concurrence suggests that the typically used grid-based approach of land surface models should be combined with a river routing scheme over the Congo peatlands.

Sebastian Apers↗

Residuals-based distributionally robust optimization with covariate information

We consider data-driven approaches that integrate a machine learning prediction model within distributionally robust optimization (DRO) given limited joint observations of uncertain parameters and covariates. Our framework is flexible in the sense that it can accommodate a variety of regression setups and DRO ambiguity sets. We investigate asymptotic and finite sample properties of solutions obtained using Wasserstein, sample robust optimization, and phi-divergence-based ambiguity sets within our DRO formulations, and explore cross-validation approaches for sizing these ambiguity sets. Through numerical experiments, we validate our theoretical results, study the effectiveness of our approaches for sizing ambiguity sets, and illustrate the benefits of our DRO formulations in the limited data regime even when the prediction model is misspecified.

97 MATHEMATICS AND COMPUTING↗

Domain-aware Control-oriented Neural Models for Autonomous Underwater Vehicles

Conventional physics-based modeling is a time-consuming bottleneck in control design for complex nonlinear systems like autonomous underwater vehicles (AUVs). In contrast, purely data-driven models, require a large number of observations and lack operational guarantees for safety-critical systems. Data-driven models leveraging available partially characterized dynamics have potential to provide reliable systems models in a typical data-limited scenario for high value complex systems, thereby avoiding months of expensive expert modeling time. In this work we explore this middle-ground between expert-modeled and pure data-driven modeling. We present control-oriented parametric models with varying levels of domain-awareness that exploit known system structure and prior physics knowledge to create constrained deep neural dynamical system models. We employ universal differential equations to construct data-driven blackbox and graybox representations of the AUV dynamics. In addition, we explore a hybrid formulation that explicitly models the residual error related to imperfect graybox models. We compare the prediction performance of the learned models for different distributions of initial conditions and control inputs to assess their suitability for control.

Shaw Cortez, Wenceslao E.↗

SPUS-Small-PDE-U-net-Solver

Small PDE U-Net Solver (SPUS) is a compact and efficient foundation model (FM) designed as a unified neural operator for solving a wide range of partial differentialequations (PDEs). SPUS leverages a lightweight residual U-Net-based architecture as a foundation model architecture. To enable effective learning in this minimalist framework, SPUS utilizes a simple yet powerful auto-regressive pretraining strategy which closely replicates the behavior of numerical solvers to learn the underlying physics. SPUS is designed to be pretrained on a diverse set of fluid dynamics PDEs from public benchmark datasets.

Siddik, Abu↗

Techno Economic Analysis for Production of Renewable Natural Gas and Value-Added Chemicals from Forest Biomass Residues (CRADA Final Report)

West Biofuels - in collaboration with the University of California San Diego, the University of California Davis, the National Laboratory of the Rockies (NLR), the Colorado School of Mines’ Center for Hydrate Research, Placer County Air Pollution Control District, the Sierra Business Council, and the Southern California Gas Company (SoCalGas)-will demonstrate an innovative pathway to convert forest biomass to renewable gas (RG). The project, Production of Pipeline Grade Renewable Natural Gas and Value-Added Chemicals from Forest Biomass Residues, will utilize an existing pilot-scale gasification system and data and lessons learned from a lab-scale catalytic reactor design, develop, and demonstrate an integrated pilot-scale RG process with a scaled-up catalytic reactor and hydrate-based gas separation process. This robust and simple process uses a commercial proven gasifier, a commercially available catalyst that can tolerate gas contaminants, and a gas separation process that simplifies the downstream processing. Current testing has shown that the process can yield a large amount of methane rich renewable gas in addition to a mixture of propanol, ethanol and other higher alcohols and the relative amounts can be controlled by shifting the process conditions. This process is novel and groundbreaking because the product mixture of RG and valuable alcohols byproducts makes RG production economically feasible at $\$$12 per million British thermal units (MMBtu) or less using forest biomass from high hazard zones.

09 BIOMASS FUELS↗

Detecting and Characterizing Fracture Zones Using a Convolutional Neural Network

This project directly supports the Geothermal Technologies Office (GTO) objectives outlined in the Multi-Year Program Plan (MYPP) by advancing two key research areas: “Exploration and Characterization” and “Data, Modeling, and Analysis.” This project has successfully demonstrated a pre-drilling ability to image and characterize the distribution and connectivity of subsurface faults and fractures, key parameters for identifying permeable pathways that enable geothermal fluids to circulate and produce energy. Specifically, we developed and implemented innovative machine learning methodologies to enhance geothermal exploration. Large-scale faults were detected using a Convolutional Neural Network (CNN), while small-scale fractures were characterized using a novel Double-Beam Neural Network (DBNN). These tools have proven both technically effective and cost-efficient by reducing reliance on expensive exploratory drilling. Through collaboration with our geothermal industry partner, this research has significantly advanced techniques for identifying hidden geothermal systems and extending the productive lifespan of existing geothermal fields. We applied our methods to two geothermal fields—Soda Lake (Nevada) and Lightning Dock (New Mexico)—to identify shallow steam-charged fracture zones and characterize deep faults at depths of 1.5-2 km. The steam zone identified at the Soda Lake geothermal field showed excellent agreement with prior drilling data, validating the effectiveness of our approaches. In addition, the analysis revealed three new prospective drilling targets for further development and verification. The outcomes of this project improve our scientific understanding of geothermal reservoir behavior, enhance exploration efficiency, extend the economic life of existing geothermal plants. Ultimately, these advancements contribute to GTO’s goal of achieving more sustainable, affordable, and data-driven geothermal energy development across the United States.

15 GEOTHERMAL ENERGY↗

Application of deep neural networks to improve diagnostic accuracy of rheumatoid arthritis using diffuse optical tomography

A set of deep neural network models for rheumatoid arthritis (RA) classification using a highway network, a convolutional neural network and a residual network is proposed based on the data of diffuse optical tomography (DOT) utilising near-infrared light, which ensures early diagnosis of pathophysiological changes resulting from inflammation. A numerical model of the finger is used to generate images to overcome the inherent problem of insufficient clinical DOT images available. The proposed deep neural network models are applied to automatically classify simulated DOT images of inflamed and non-inflamed joints and transfer learning is also used to improve the performance of the classification. The results demonstrate that all three deep neural network methods improve the diagnostic accuracy as compared to the widely applied support vector machine (SVM), especially for high inter-subject variability databases. In cases of distinct modelled severity of disease, residual network achieved the highest accuracy (> 99 %), and both of highway and convolutional neural networks reached 99 %, respectively. However, as the severity of the modelled disease is reduced, this accuracy is reduced to 75.2 % for residual networks. The results indicate that transfer learning can improve the performance of deep neural network methods on RA classification from DOT data and highlight their potential as a computer aided tool in DOT diagnostic systems. (paper)

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

CoordNet: Data Generation and Visualization Generation for Time-Varying Volumes via a Coordinate-Based Neural Network

Although deep learning has demonstrated its capability in solving diverse scientific visualization problems, it still lacks generalization power across different tasks. To address this challenge, we propose CoordNet, a single coordinate-based framework that tackles various tasks relevant to time-varying volumetric data visualization without modifying the network architecture. The core idea of our approach is to decompose diverse task inputs and outputs into a unified representation (i.e., coordinates and values) and learn a function from coordinates to their corresponding values. We achieve this goal using a residual block-based implicit neural representation architecture with periodic activation functions. We evaluate CoordNet on data generation (i.e., temporal super-resolution and spatial super-resolution) and visualization generation (i.e., view synthesis and ambient occlusion prediction) tasks using time-varying volumetric data sets of various characteristics. Here, the experimental results indicate that CoordNet achieves better quantitative and qualitative results than the state-of-the-art approaches across all the evaluated tasks. Source code and pre-trained models are available at https://github.com/stevenhan1991/CoordNet.

97 MATHEMATICS AND COMPUTING↗

Development and Testing of Data Mining Algorithms for Earth Observation

The new algorithms developed under this project included a principled procedure for classification of objects, events or circumstances according to a target variable when a very large number of potential predictor variables is available but the number of cases that can be used for training a classifier is relatively small. These "high dimensional" problems require finding a minimal set of variables -called the Markov Blanket-- sufficient for predicting the value of the target variable. An algorithm, the Markov Blanket Fan Search, was developed, implemented and tested on both simulated and real data in conjunction with a graphical model classifier, which was also implemented. Another algorithm developed and implemented in TETRAD IV for time series elaborated on work by C. Granger and N. Swanson, which in turn exploited some of our earlier work. The algorithms in question learn a linear time series model from data. Given such a time series, the simultaneous residual covariances, after factoring out time dependencies, may provide information about causal processes that occur more rapidly than the time series representation allow, so called simultaneous or contemporaneous causal processes. Working with A. Monetta, a graduate student from Italy, we produced the correct statistics for estimating the contemporaneous causal structure from time series data using the TETRAD IV suite of algorithms. Two economists, David Bessler and Kevin Hoover, have independently published applications using TETRAD style algorithms to the same purpose. These implementations and algorithmic developments were separately used in two kinds of studies of climate data: Short time series of geographically proximate climate variables predicting agricultural effects in California, and longer duration climate measurements of temperature teleconnections.

Glymour, Clark↗

Learning electric vehicle driver range anxiety with an initial state of charge-oriented gradient boosting approach

This manuscript focuses on the modeling of electric vehicle (EV) driver’s range anxiety, a fear that a vehicle does not have sufficient range, or state of charge (SOC) of the battery pack, to reach its destination and would strand its occupants. Despite numerous research studies on the modeling of charging behaviors, modeling efforts to understand at what battery percentages do EV drivers charge their vehicles, and what are the associated contributing factors, are rather limited. To this end, an ensemble learning model based on gradient boosting is developed. The model sequentially fits new predictors to new residuals of the previous prediction and, then, minimizes the loss when adding the latest prediction. A total of 18 features are defined and extracted from the multisource data, which cover information on driver, vehicles, stations, traffic conditions, as well as spatial-temporal context information of the charging events. The analyzed dataset includes 4.5-year’s charging event log data from 3,096 users and 468 public charging stations in Kansas City Missouri, and the macroscopic travel demand model maintained by the metropolitan planning organization. Here, the result shows the proposed model achieved a satisfactory result with a R square value of 0.54 and root mean square error of 0.14, both better than multiple linear regression model and random forest model. To reduce range anxiety, it is suggested that the priorities of deploying new charging facilities should be given to the areas with higher daily traffic prediction, with more conservative EV users or that are further from residential areas.

33 ADVANCED PROPULSION SYSTEMS↗

Improving Trustworthiness of Data-Driven Power Grid Contingency Analysis With Bayesian Residual Graph Neural Networks

The evolving energy landscape requires novel tools to efficiently perform contingency analysis and reliability assessment of power grids, potentially in real-time. The high computational cost of traditional power flow solvers limits their applicability in practice. Machine learning (ML) surrogates such as deep neural networks (NNs) accelerate power flow solvers computations, enabling high-order contingency analysis and real-time decision-making by learning highly nonlinear functions and integrating grid topology via graph architectures. However, (graph) NNs lack predictive power away from training data and do not provide predictive confidence estimates. Here, we present a Bayesian residual graph NN that integrates knowledge from low-fidelity data via residual training and embeds granular quantification of uncertainties, improving trustworthiness critical for high-consequence decision-making. Applying Bayesian concepts to NNs is challenging due to the high-dimensionality of both the parameter space, complicating derivation of a meaningful prior, and the output space in large grid systems, requiring enhanced techniques to assess the predicted high-dimensional uncertainties. Our contributions include: (1) Deriving a prior for fully connected and graph NNs that leverages low-fidelity data to guide mean predictions and appropriately control prior predictive uncertainty. (2) Integrating this prior within an ensembling with anchoring scheme for efficient approximate posterior inference. (3) Deriving enhanced metrics to assess accuracy of both the mean and uncertainty predictions in high dimensions, appropriately accounting for correlations propagated through graph layers. The resulting Bayesian residual graph NN is tested on a contingency analysis task for 14-bus and 118-bus grids.

24 - POWER TRANSMISSION AND DISTRIBUTION↗

Heterogeneous microstructure of yttrium hydride and its relation to mechanical properties

Here, the goal of this study is to investigate the properties of yttrium hydride materials in relation to the microstructure, especially its homogeneity. High-throughput nanoindentation mapping was used to evaluate hardness distribution. Raman spectral imaging demonstrated its sensitivity to the presence of YH2 and impurities. Raman peak position maps were correlated with residual stress in the specimens. Electron backscatter diffraction mapping provided phase distributions with correlation to high-energy X-ray diffraction analysis. The experimental mapping data were combined and analyzed using unsupervised machine learning cluster procedures. The machine learning analysis revealed that yttrium hydride specimens contained a major δ-YH2 – x phase component and minor α-Y and δ-YH2 – x components with significant residual stress. The minor phase fraction decreased with increasing nominal H/Y ratio, which affected the nanoindentation and Vickers hardness. The multimodal mapping procedures described herein affect developing important microstructure–property relationships, as well as correlations in heterogeneity and mechanical properties.

36 MATERIALS SCIENCE↗

Fuzzy Adaptive Control for Intelligent Autonomous Space Exploration Problems

The principal objective of the research reported here is the re-design, analysis and optimization of our newly developed neural network fuzzy adaptive controller model for complex processes capable of learning fuzzy control rules using process data and improving its control through on-line adaption. The learned improvement is according to a performance objective function that provides evaluative feedback; this performance objective is broadly defined to meet long-range goals over time. Although fuzzy control had proven effective for complex, nonlinear, imprecisely-defined processes for which standard models and controls are either inefficient, impractical or cannot be derived, the state of the art prior to our work showed that procedures for deriving fuzzy control, however, were mostly ad hoc heuristics. The learning ability of neural networks was exploited to systematically derive fuzzy control and permit on-line adaption and in the process optimize control. The operation of neural networks integrates very naturally with fuzzy logic. The neural networks which were designed and tested using simulation software and simulated data, followed by realistic industrial data were reconfigured for application on several platforms as well as for the employment of improved algorithms. The statistical procedures of the learning process were investigated and evaluated with standard statistical procedures (such as ANOVA, graphical analysis of residuals, etc.). The computational advantage of dynamic programming-like methods of optimal control was used to permit on-line fuzzy adaptive control. Tests for the consistency, completeness and interaction of the control rules were applied. Comparisons to other methods and controllers were made so as to identify the major advantages of the resulting controller model. Several specific modifications and extensions were made to the original controller. Additional modifications and explorations have been proposed for further study. Some of these are in progress in our laboratory while others await additional support. All of these enhancements will improve the attractiveness of the controller as an effective tool for the on line control of an array of complex process environments.

Esogbue, Augustine O.↗