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At least 793 records · Page 44

Mapping Influenza-Induced Posttranslational Modifications on Histones from CD8+ T Cells

T cell function is determined by transcriptional networks that are regulated by epigenetic programming via posttranslational modifications (PTMs) to histone proteins and DNA. Bottom-up mass spectrometry (MS) can identify histone PTMs, whereas intact protein analysis by MS can detect species missed by bottom-up approaches. We used a novel approach of online two-dimensional liquid chromatography-tandem MS with high-resolution reversed-phase liquid chromatography (RPLC), alternating electron transfer dissociation (ETD) and collision-induced dissociation (CID) on precursor ions to maximize fragmentation of uniquely modified species. The first online RPLC separation sorted histone families, then RPLC or weak cation exchange hydrophilic interaction liquid chromatography (WCX-HILIC) separated species heavily clad in PTMs. Tentative identifications were assigned by matching proteoform masses to predicted theoretical masses that were verified with tandem MS. We used this innovative approach for histone-intact protein PTM mapping (HiPTMap) to identify and quantify proteoforms purified from CD8 T cells after in vivo influenza infection. Activation significantly altered PTMs following influenza infection, histone maps changed as T cells migrated to the site of infection, and T cells responding to secondary infections had significantly more transcription enhancing modifications. Thus, HiPTMap identified and quantified proteoforms and determined changes in CD8 T cell histone PTMs over the course of infection.

mass spectrometry↗

Formation and Evolution of Lakshmi Planum (V-7), Venus: Assessment of Models using Observations from Geological Mapping

Lakshmi Planum is a high-standing plateau (3.5-4.5 km above MPR) surrounded by the highest mountain ranges on Venus. Lakshmi represents a unique type of elevated region different from dome-shaped and rifted rises and tessera-bearing crustal plateaus. The unique characteristics of Lakshmi suggest that it formed by an unusual combination of processes and played an important role in Venus geologic history. Lakshmi was studied with Venera-15/16 and Magellan data, resulting in two classes of models, divergent and convergent, to explain its unusual topographic and morphologic characteristics. Divergent models explain Lakshmi as a site of mantle upwelling due to rising and subsequent collapse of a mantle diapir; such models explain emplacement of a lava plateau inside Lakshmi and, in some circumstances, formation of the mountain ranges. The convergent models consider Lakshmi as a locus of mantle downwelling, convergence, underthrusting, and possible subduction. Key features in these models are the mountain ranges, high topography of Lakshmi interior, and the large volcanic centers in the plateau center. These divergent and convergent models entail principally different mechanisms of formation and suggest different geodynamic regimes on Venus. Almost all models make either explicit or implicit predictions about the type and sequence of major events during formation and evolution of Lakshmi and thus detailed geological mapping can be used to test them. Here we present the results of such geological mapping (the V-7 quadrangle, 50-75degN, 300-360degE; scale 1:5M) that allows testing the proposed models for Lakshmi.

Ivanov, M. A.↗

Simultaneous mapping of the unsteady flow fields by Particle Displacement Velocimetry (PDV)

Current experimental and computational techniques must be improved in order to advance the prediction capability of the longitudinal vortical flows shed by underwater vehicles. The generation, development, and breakdown mechanisms of the shed vortices at high Reynolds numbers are not fully understood. The ability to measure hull separated vortices associated with vehicle maneuvering does not exist at present. The existing point-by-point measurement techniques can only capture approximately the large 'mean' eddies but fail to meet the dynamics of small vortices during the initial stage of generation. A new technique, which offers a previously unavailable capability to measure the unsteady cross-flow distribution in the plane of the laser light sheet, is called Particle Displacement Velocimetry (PDV). PDV consists of illuminating a thin section of the flowfield with a pulsed laser. The water is seeded with microscopic, neutrally buoyant particles containing imbedded fluorescing dye which responds with intense spontaneous fluorescence with the illuminated section. The seeded particles in the vortical flow structure shed by the underwater vehicle are illuminated by the pulse laser and the corresponding particle traces are recorded in a single photographic frame. Two distinct approaches were utilized for determining the velocity distribution from the particle traces. The first method is based on matching the traces of the same particle and measuring the distance between them. The direction of the flow can be identified by keeping one of the pulses longer than the other. The second method is based on selecting a small window within the image and finding the mean shift of all the particles within that region. The computation of the auto-correlation of the intensity distribution within the selected sample window is used to determine the mean displacement of particles. The direction of the flow is identified by varying the intensity of the laser light between pulses. Considerable computational resources are required to compute the auto-correction of the intensity distribution. Parallel processing will be employed to speed up the data reduction. A few examples of measured unsteady vortical flow structures shed by the underwater vehicles will be presented.

Huang, Thomas T.↗

A self-supervised robotic system for autonomous contact-based spatial mapping of semiconductor properties

Integrating robotically driven contact-based material characterization techniques into self-driving laboratories can enhance measurement quality, reliability, and throughput. While deep learning models support robust autonomy, current methods lack reliable pixel-precision positioning and require extensive labeled data. To overcome these challenges, we propose an approach for building self-supervised autonomy into contact-based robotic systems that teach the robot to follow domain expert measurement principles at high throughputs. We demonstrate the performance of this approach by autonomously driving a 4-DOF robotic probe for 24 hours to characterize semiconductor photoconductivity at 3025 uniquely predicted poses across a gradient of drop-casted perovskite film compositions, achieving throughputs of more than 125 measurements per hour. Spatially mapping photoconductivity onto each drop-casted film reveals compositional trends and regions of inhomogeneity, valuable for identifying manufacturing defects. With this self-supervised neural network–driven robotic system, we enable high-precision and reliable automation of contact-based characterization techniques at high throughputs, thereby allowing measurement of previously inaccessible yet important semiconductor properties for self-driving laboratories.

Science & Technology - Other Topics↗

ThermoPore: Predicting part porosity based on thermal images using deep learning

Part qualification is often a critical and labor-intensive process in additive manufacturing, particularly in the detection of defects such as porosity, which stands to benefit significantly from advancements in machine learning. We present a deep learning approach for quantifying and localizing ex-situ porosity within Laser Powder Bed Fusion fabricated samples utilizing in-situ thermal image monitoring data. Our goal is to build the real time porosity map of parts based on thermal images acquired during the build. The quantification task builds upon the established Convolutional Neural Network model architecture to predict pore count and the localization task leverages the spatial and temporal attention mechanisms of the novel Video Vision Transformer model to indicate areas of expected porosity. Our model for porosity quantification achieved a R 2 score of 0.57 and our model for porosity localization produced an average Intersection over Union (IoU) score of 0.32 and a maximum of 1.0. This work is setting the foundations of part porosity “Digital Twins” based on additive manufacturing monitoring data and can be applied downstream to reduce time-intensive post-inspection and testing activities during part qualification and certification. In addition, we seek to accelerate the acquisition of crucial insights normally only available through ex-situ part evaluation by means of machine learning analysis of in-situ process monitoring data.

Deep learning↗

Forecasting Battery Electrode Performance via Electrochemical Fluorescence Microscopy and Machine-Learning

Predicting lithium-ion battery performance is hindered by microscale electrode heterogeneities invisible to conventional diagnostics. Here, we combine electrochemical fluorescence microscopy (EFM), which maps electronic connectivity by visualizing an electrofluorophore reaction distribution, with a multitask ElasticNet regression to forecast discharge capacity from spatial heterogeneity. Analyzing 196 images from six pilot-scale LiNi 0.5 Mn 0.3 Co 0.2 O 2 cathodes with varying carbon loadings, we extract 62 descriptors that capture morphology and texture. A compact five-feature model predicts capacity across eight discharge rates, achieving a per-target R 2 of up to 0.63 and an overall R 2 of 0.92, with a mean absolute percentage error of less than 2%. This performance rivals impedance-based approaches while avoiding their reliance on postformation data and incomplete electronic network information. Our facile and rapid, image-driven method may enable electrode quality control upstream of costly cell assembly to offer a transformative tool for data-driven battery research and manufacturing.

battery electrodes↗

The CHUVA Lightning Mapping Campaign

The primary science objective for the CHUVA lightning mapping campaign is to combine measurements of total lightning activity, lightning channel mapping, and detailed information on the locations of cloud charge regions of thunderstorms with the planned observations of the CHUVA (Cloud processes of tHe main precipitation systems in Brazil: A contribUtion to cloud resolVing modeling and to the GPM (GlobAl Precipitation Measurement) field campaign. The lightning campaign takes place during the CHUVA intensive observation period October-December 2011 in the vicinity of S o Luiz do Paraitinga with Brazilian, US, and European government, university and industry participants. Total lightning measurements that can be provided by ground-based regional 2-D and 3-D total lightning mapping networks coincident with overpasses of the Tropical Rainfall Measuring Mission Lightning Imaging Sensor (LIS) and the SEVIRI (Spinning Enhanced Visible and Infrared Imager) on the Meteosat Second Generation satellite in geostationary earth orbit will be used to generate proxy data sets for the next generation US and European geostationary satellites. Proxy data, which play an important role in the pre-launch mission development and in user readiness preparation, are used to develop and validate algorithms so that they will be ready for operational use quickly following the planned launch of the GOES-R Geostationary Lightning Mapper (GLM) in 2015 and the Meteosat Third Generation Lightning Imager (LI) in 2017. To date there is no well-characterized total lightning data set coincident with the imagers. Therefore, to take the greatest advantage of this opportunity to collect detailed and comprehensive total lightning data sets, test and validate multi-sensor nowcasting applications for the monitoring, tracking, warning, and prediction of severe and high impact weather, and to advance our knowledge of thunderstorm physics, extensive measurements from lightning mapping networks will be collected in conjunction with electric field mills, field change sensors, high speed cameras and other lightning sensors, dual-polarimetric radars, and aircraft in-situ microphysics which will allow for excellent cross-network inter-comparisons, assessments, and physical understanding.

Goodman, Steven J.↗

A Performance Prediction Model for a Fault-Tolerant Computer During Recovery and Restoration

The modeling and design of a fault-tolerant multiprocessor system is addressed. In particular, the behavior of the system during recovery and restoration after a fault has occurred is investigated. Given that a multicomputer system is designed using the Algorithm to Architecture to Mapping Model (ATAMM), and that a fault (death of a computing resource) occurs during its normal steady-state operation, a model is presented as a viable research tool for predicting the performance bounds of the system during its recovery and restoration phases. Furthermore, the bounds of the performance behavior of the system during this transient mode can be assessed. These bounds include: time to recover from the fault (t(sub rec)), time to restore the system (t(sub rec)) and whether there is a permanent delay in the system's Time Between Input and Output (TBIO) after the system has reached a steady state. An implementation of an ATAMM based computer was developed with the Generic VHSIC Spaceborne Computer (GVSC) as the target system. A simulation of the GVSC was also written based on the code used in ATAMM Multicomputer Operating System (AMOS). The simulation is in turn used to validate the new model in the usefulness and accuracy in tracking the propagation of the delay through the system and predicting the behavior in the transient state of recovery and restoration. The model is validated as an accurate method to predict the transient behavior of an ATAMM based multicomputer during recovery and restoration.

Stoughton, John W.↗

Fundamentals of wildlife dosimetry and lessons learned from a decade of measuring external dose rates in the field

Methods for determining the radiation dose received by exposed biota require major improvements to reduce uncertainties and increase precision. We share our experiences in attempting to quantify external dose rates to free-ranging wildlife using GPS-coupled dosimetry methods. The manuscript is a primer on fundamental concepts in wildlife dosimetry in which the complexities of quantifying dose rates are highlighted, and lessons learned are presented based on research with wild boar and snakes at Fukushima, wolves at Chornobyl, and reindeer in Norway. GPS-coupled dosimeters produced empirical data to which numerical simulations of external dose using computer software were compared. Our data did not support a standing paradigm in risk analyses: Using averaged soil contaminant levels to model external dose rates conservatively overestimate the dose to individuals within a population. Following this paradigm will likely lead to misguided recommendations for risk management. The GPS-dosimetry data also demonstrated the critical importance of how modeled external dose rates are impacted by the scale at which contaminants are mapped. When contaminant mapping scales are coarse even detailed knowledge about each animal’s home range was inadequate to accurately predict external dose rates. Importantly, modeled external dose rates based on a single measurement at a trap site did not correlate to actual dose rates measured on free ranging animals. These findings provide empirical data to support published concerns about inadequate dosimetry in much of the published Chernobyl and Fukushima dose-effects research. Furthermore, our data indicate that a huge portion of that literature should be challenged, and that improper dosimetry remains a significant source of controversy in radiation dose-effect research.

61 RADIATION PROTECTION AND DOSIMETRY↗

Regional Subsidence Analysis Through a Multi-Scale Modeling Framework Based on Breakage Mechanics

Although poroelastic models are often used to explain the delay between subsurface fluid depletion and ground subsidence, inelastic compaction involving permanent changes of rock microstructure may exacerbate hydro-mechanical coupling, thus influencing the interpretation of measurements and long-term forecasts. Here, a multi-scale modeling approach is discussed, which accounts for the inherent connection between rock microstructure, hydraulic conductivity, and pore compaction. A constitutive model built within the framework of breakage mechanics is proposed to link the hydraulic conductivity of granular rocks with inelastic deformations and changes in grading caused by injection-depletion cycles at stress levels far from yielding. The proposed model has been incorporated into large-scale simulation frameworks, thus enabling the spatiotemporal mapping of regional subsidence through a hybrid, semi-analytical approach. Numerical results based on this strategy show that the model allows isolating near-field and far-field effects into the computation of land subsidence and can generate forecasts for different modeling scenarios (e.g., elastic and inelastic compaction, constant permeability, and concurrent change of compressibility and permeability). In particular, examples of simulations for the case of the Groningen gas field are discussed, showing the model capabilities to use both field measurements and laboratory tests for the generation of reasonable subsidence maps, without expensive computational costs. Results indicate that ignoring coupled inelastic effects has major consequences on the predicted timescale of subsidence. Specifically, while all the model scenarios produced similar long-term ground settlements, those ignoring breakage-dependent permeability changes result in a variation of the temporal window of residual subsidence of the order of several decades.

58 GEOSCIENCES↗

Subdomain cryo-EM structure of nodaviral replication protein A crown complex provides mechanistic insights into RNA genome replication

For positive-strand RNA [(+)RNA] viruses, the major target for antiviral therapies is genomic RNA replication, which occurs at poorly understood membrane-bound viral RNA replication complexes. Recent cryoelectron microscopy (cryo-EM) of nodavirus RNA replication complexes revealed that the viral double-stranded RNA replication template is coiled inside a 30- to 90-nm invagination of the outer mitochondrial membrane, whose necked aperture to the cytoplasm is gated by a 12-fold symmetric, 35-nm diameter “crown” complex that contains multifunctional viral RNA replication protein A. Here we report optimizing cryo-EM tomography and image processing to improve crown resolution from 33 to 8.5 Å. This resolves the crown into 12 distinct vertical segments, each with 3 major subdomains: A membrane-connected basal lobe and an apical lobe that together comprise the ~19-nm-diameter central turret, and a leg emerging from the basal lobe that connects to the membrane at ~35-nm diameter. Despite widely varying replication vesicle diameters, the resulting two rings of membrane interaction sites constrain the vesicle neck to a highly uniform shape. Labeling protein A with a His-tag that binds 5-nm Ni-nanogold allowed cryo-EM tomography mapping of the C terminus of protein A to the apical lobe, which correlates well with the predicted structure of the C-proximal polymerase domain of protein A. These and other results indicate that the crown contains 12 copies of protein A arranged basally to apically in an N-to-C orientation. Moreover, the apical polymerase localization has significant mechanistic implications for template RNA recruitment and (-) and (+)RNA synthesis.

59 BASIC BIOLOGICAL SCIENCES↗

A Four-Layer Cyber-Physical Security Model for Electric Machine Drives Considering Control Information Flow

Despite the IEEE Power Electronics Society (PELS) establishing Technical Committee 10 on Design Methodologies with a focus on the cyber-physical security of power electronics systems, a holistic design methodology for addressing security vulnerabilities remains underdeveloped. This gap largely stems from the limited integration of computer science and power/control engineering studies in this interdisciplinary field. Addressing the inadequacy of unilateral cyber or control perspectives, this article presents a novel four-layer cyber-physical security model specifically designed for electric machine drives. Central to this model is the innovative control information flow (CIF) model, residing within the control layer, which serves as a pivotal link between the cyber layer's vulnerable resources and the physical layer's state-space models. By mapping vulnerable resources to control variable space and tracing attack propagation, the CIF model facilitates accurate impact predictions based on tainted control laws. The effectiveness and validity of this proposed model are demonstrated through hardware experiments involving two typical cyber-attack scenarios, underscoring its potential as a comprehensive framework for multidisciplinary security strategies.

97 MATHEMATICS AND COMPUTING↗

Real-Time Ecodriving Control in Electrified Connected and Autonomous Vehicles Using Approximate Dynamic Programing

Connected and automated vehicles (CAVs), particularly those with a hybrid electric powertrain, have the potential to significantly improve vehicle energy savings in real-world driving conditions. In particular, the ecodriving problem seeks to design optimal speed and power usage profiles based on available information from connectivity and advanced mapping features to minimize the fuel consumption over an itinerary. This paper presents a hierarchical multilayer model predictive control (MPC) approach for improving the fuel economy of a 48 V mild-hybrid powertrain in a connected vehicle environment. Approximate dynamic programing (DP) is used to solve the receding horizon optimal control problem, whose terminal cost is approximated with the base policy obtained from the long-term optimization. The controller was tested virtually (with deterministic and Monte Carlo simulation) across multiple real-world routes, demonstrating energy savings of more than 20%. The controller was then deployed on a test vehicle equipped with a rapid prototyping embedded controller. In-vehicle testing confirm the energy savings obtained in simulation and demonstrate the real-time ability of the controller.

Automation & Control Systems↗

Symbolic diagnostics to interpret and analyze neural network models

Embedded machine-learned models (EMLMs) have the promise to improve the predictive accuracy of engineering simulators in environments of national interest. EMLMs often comprise complex input-output maps (e.g., neural networks), which make them unamenable to rigorous analysis and generally difficult to interpret. In the face of decades of theory, this lack of interpretability is a significant barrier to building confidence in these models. This work outlines an approach to interpret EMLMs using sparse polynomial regression for comparison with theoretical understanding. To do so, we build on the concept of Locally Interpretable Model-agnostic Explanations (LIME) using physics-informed clustering, prototype selection, and library construction. While general, we demonstrate our method on tensor-basis neural networks used in Reynolds-Averaged Navier-Stokes simulations of hypersonic fluid flows. Results are presented for a simulated toy model and for direct numerical simulations (DNS) of turbulent flows over a flat plate.

97 MATHEMATICS AND COMPUTING↗

Estimating Watershed Subsurface Permeability From Stream Discharge Data Using Deep Neural Networks

Subsurface permeability is a key parameter in watershed models that controls the contribution from the subsurface flow to stream flows. Since the permeability is difficult and expensive to measure directly at the spatial extent and resolution required by fully distributed watershed models, estimation through inverse modeling has had a long history in subsurface hydrology. The wide availability of stream surface flow data, compared to groundwater monitoring data, provides a new data source to infer soil and geologic properties using integrated surface and subsurface hydrologic models. As most of the existing methods have shown difficulty in dealing with highly nonlinear inverse problems, we explore the use of deep neural networks for inversion owing to their successes in mapping complex, highly nonlinear relationships. We train various deep neural network (DNN) models with different architectures to predict subsurface permeability from stream discharge hydrograph at the watershed outlet. The training data are obtained from ensemble simulations of hydrographs corresponding to an permeability ensemble using a fully-distributed, integrated surface-subsurface hydrologic model. The trained model is then applied to estimate the permeability of the real watershed using its observed hydrograph at the outlet. Our study demonstrates that the permeabilities of the soil and geologic facies that make significant contributions to the outlet discharge can be more accurately estimated from the discharge data. Their estimations are also more robust with observation errors. Compared to the traditional ensemble smoother method, DNNs show stronger performance in capturing the nonlinear relationship between permeability and stream hydrograph to accurately estimate permeability. Our study sheds new light on the value of the emerging deep learning methods in assisting integrated watershed modeling by improving parameter estimation, which will eventually reduce the uncertainty in predictive watershed models.

54 ENVIRONMENTAL SCIENCES↗

On the Need to Align Intent and Implementation in Uncertainty Quantification for Machine Learning

Quantifying uncertainties for machine learning (ML) models is a foundational challenge in modern data analysis. This challenge is compounded by at least two key aspects of the field: (a) inconsistent terminology surrounding uncertainty and estimation across disciplines, and (b) the varying technical requirements for establishing trustworthy uncertainties in diverse problem contexts. In this position paper, we aim to clarify the depth of these challenges by identifying these inconsistencies and articulating how different contexts impose distinct epistemic demands. We examine the current landscape of estimation targets (e.g., prediction, inference, simulation-based inference), uncertainty constructs (e.g., frequentist, Bayesian, fiducial), and the approaches used to map between them. Drawing on the literature, we highlight and explain examples of problematic mappings. To help address these issues, we advocate for standards that promote alignment between the \textit{intent} and \textit{implementation} of uncertainty quantification (UQ) approaches. We discuss several axes of trustworthiness that are necessary (if not sufficient) for reliable UQ in ML models, and show how these axes can inform the design and evaluation of uncertainty-aware ML systems. Our practical recommendations focus on scientific ML, offering illustrative cases and use scenarios, particularly in the context of simulation-based inference (SBI).

Trivedi, Shubhendu [MIT] (ORCID:0000000312374301)↗

Overview of a stirling engine test project

Tests were conducted on three Stirling engines ranging in size from 1.33 to 53 horsepower (1 to 40 kW). The tests were directed toward developing alternative, backup component concepts to improve engine efficiency and performance or to reduce costs. Some of the activities included investigating attractive concepts and materials for cooler-regenerator units, installing a jet impingement device on a Stirling engine to determine its potential for improved engine performance, and presenting performance maps for initial characterization of Stirling engines. The experiment results of the tests are presented along with predictions of results of future tests to be conducted on the Stirling engines.

Slaby, J. G.↗

Flow aerodynamics modeling of an MHD swirl combustor - Calculations and experimental verification

This paper describes a computer code for calculating the flow dynamics of constant density flow in the second stage trumpet shaped nozzle section of a two stage MHD swirl combustor for application to a disk generator. The primitive pressure-velocity variable, finite difference computer code has been developed to allow the computation of inert nonreacting turbulent swirling flows in an axisymmetric MHD model swirl combustor. The method and program involve a staggered grid system for axial and radial velocities, and a line relaxation technique for efficient solution of the equations. Turbulence simulation is by way of a two-equation Kappa-epsilon model. The code produces as output the flowfield map of the nondimensional stream function, axial, and swirl velocity. Good agreement was obtained between the theoretical predictions and the qualitative experimental results. The best seed injector location for uniform seed distribution at combustor exit is with injector located centrally on the combustor axis at entrance to the second stage combustor.

Gupta, A. K.↗