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At least 307 records · Page 17

National Cancer Institute Think-Tank Meeting Report on Proteomic Cartography and Biomarkers at the Single-Cell Level: Interrogation of Premalignant Lesions

A Think-Tank Meeting was convened by the National Cancer Institute (NCI) to solicit experts’ opinion on the development and application of multi-omic single-cell analyses, and especially single-cell proteomics, to improve the development of a new generation of biomarkers for cancer risk, early detection, diagnosis, prognosis as well as to discuss the discovery of new targets for prevention and therapy. It is anticipated that such markers and targets will be based on cellular, subcellular, molecular and functional aberrations within the lesion and within individual cells. Additionally, single-cell proteomic data will be essential for the establishment of new tools that with searchable and scalable features that include spatial and temporal cartographies of premalignant and malignant lesions. Challenges and potential solutions that were discussed included: • The best way/s to analyze single-cells from fresh and preserved tissue • Detection and analysis of secreted molecules and from single cells, especially from a tissue slice • Detection of new, previously undocumented cell type/s in the premalignant and early stage cancer tissue microenvironment • Multi-omic integration of data to support and inform proteomic measurements • Subcellular organelles – identifying abnormal structure, function, distribution and location within individual premalignant and malignant cells • How to improve the dynamic range of single-cell proteomic measurements for discovery of differentially expressed proteins and their post translational modifications (PTM) • The depth of coverage measured concurrently using single-cell techniques • Quantitation - absolute or semiquantitative? • Single methodology or multiplexed combinations? • Application of analytical methods for identification of biologically significant subsets • Data visualization of N-dimensional datasets • How to construct intercellular signaling networks in individual cells within premalignant tumor microenvironments (TME) • Associations between intrinsic cellular processes and extrinsic stimuli • How to predict cellular responses to stress inducing stimuli • Identification of new markers for prediction of progression from precursor, benign and localized lesions to invasive cancer, based on spatial and temporal changes within individual cells • Identification of new targets for immunoprevention or immunotherapy – identification of neoantigens and surfactome of individual cells within a lesion

59 BASIC BIOLOGICAL SCIENCES↗

mvBayes

SAND2026-16980O mvBayes implements multivariate Bayesian regression using MATLAB and decomposes a multivariate or functional response into components based on a user-specified orthogonal basis. This allows for independent modeling of each component with any chosen univariate Bayesian regression model. This tool includes methods for prediction and visualization, facilitating the evaluation of Bayesian surrogate models through the application of Bayesian theory and Markov Chain Monte Carlo (MCMC) sampling techniques. 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.

Tucker, J. Derek [Sandia National Lab. (SNL-CA), L↗

Approach for energy efficient building design during early phase of design process

Energy consumption in the building sector is about 40% of total energy consumed globally and is trending upwards, along with its contribution to greenhouse gas (GHG) emissions. Given the adverse impacts of GHG emissions, it is crucial to integrate energy efficiency into building designs. The most significant opportunities for enhancing energy performance are present during the initial phases of building design, when there is less impact of other design constraints. Various tools exist for simulating different design options and providing feedback in terms of energy consumption and comfort parameters. These simulation outputs must then be analyzed to derive design solutions. This paper presents an innovative approach that utilizes user input parameters, processes them through cloud computing, and outputs easily understandable strategies for energy-efficient building design. The methodology employs Asynchronous Distributed Task Queues (DTQ) - a more scalable and reliable alternative to conventional speedup techniques-for conducting parametric energy simulations in the cloud. The goal of this approach is to assist design teams in identifying, visualizing, and prioritizing energy-saving design strategies from a range of possible solutions for each project. Furthermore, a tool ‘eDOT’ has been developed utilizing the discussed methodology. Unlike existing tools, eDOT leverages artificial intelligence to dynamically generate and provide design strategies during the early phases of design process. By simplifying the simulation process, eDOT enables design teams to make informed, data-driven decisions without needing to interpret complex simulation outputs. A case study simulated for two locations is provided in this paper to demonstrate the effectiveness of eDOT, further underscoring its practical impact on energy-efficient building design.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Exploring Explicit Uncertainty for Binary Analysis (EUBA)

Reverse engineering (RE) analysts struggle to address critical questions about the safety of binary code accurately and promptly, and their supporting program analysis tools are simply wrong sometimes. The analysis tools have to approximate in order to provide any information at all, but this means that they introduce uncertainty into their results. And those uncertainties chain from analysis to analysis. We hypothesize that exposing sources, impacts, and control of uncertainty to human binary analysts will allow the analysts to approach their hardest problems with high-powered analytic techniques that they know when to trust. Combining expertise in binary analysis algorithms, human cognition, uncertainty quantification, verification and validation, and visualization, we pursue research that should benefit binary software analysis efforts across the board. We find a strong analogy between RE and exploratory data analysis (EDA); we begin to characterize sources and types of uncertainty found in practice in RE (both in the process and in supporting analyses); we explore a domain-specific focus on uncertainty in pointer analysis, showing that more precise models do help analysts answer small information flow questions faster and more accurately; and we test a general population with domain-general sudoku problems, showing that adding "knobs" to an analysis does not significantly slow down performance. This document describes our explorations in uncertainty in binary analysis.

97 MATHEMATICS AND COMPUTING↗

Unified Language Frontend for Physic-Informed AI/ML

Artificial intelligence and machine learning (AI/ML) are becoming important tools for scientific modeling and simulation as in several other fields such as image analysis and natural language processing. ML techniques can leverage the computing power available in modern systems and reduce the human effort needed to configure experiments, interpret and visualize results, draw conclusions from huge quantities of raw data, and build surrogates for physics based models. Domain scientists in fields like fluid dynamics, microelectronics and chemistry can automate many of their most difficult and repetitive tasks or improve the design times by use of the faster ML-surrogates. However, modern ML and traditional scientific highperformance computing (HPC) tend to use completely different software ecosystems. While ML frameworks like PyTorch and TensorFlow provide Python APIs, most HPC applications and libraries are written in C++. Direct interoperability between the two languages is possible but is tedious and error-prone. In this work, we show that a compiler-based approach can bridge the gap between ML frameworks and scientific software with less developer effort and better efficiency. We use the MLIR (multi-level intermediate representation) ecosystem to compile a pre-trained convolutional neural network (CNN) in PyTorch to freestanding C++ source code in the Kokkos programming model. Kokkos is a programming model widely used in HPC to write portable, shared-memory parallel code that can natively target a variety of CPU and GPU architectures. Our compiler-generated source code can be directly integrated into any Kokkosbased application with no dependencies on Python or cross-language interfaces.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Landscaper v1

Understanding the inner workings of machine learning models through their loss landscapes offers crucial insights into model properties, optimization dynamics, and generalizability. However, accessing these insights has traditionally required specialized mathematical expertise, limiting broader adoption. Landscaper is an open-source Python package designed to bridge this gap. Landscaper seamlessly integrates a suite of multi-dimensional loss landscape analyses with cutting-edge topological data analysis (TDA) methods. This powerful combination makes both fundamental loss landscape analysis and advanced TDA techniques accessible to the broader scientific ML community, without requiring deep pre-existing mathematical knowledge. Landscaper offers three key functionalities: * Construction: Builds detailed loss landscape representations through versatile low and high-dimensional sampling techniques. * Quantification: Applies advanced metrics, including a novel topological data analysis (TDA) based smoothness metric, enabling new perspectives on model behavior. * Visualization: Offers intuitive tools to visualize and interpret loss landscapes, providing actionable insights beyond traditional performance metrics.

Weber, Gunther [Lawrence Berkeley National Laborat↗

Adaptive Spatially Aware I/O for Multiresolution Particle Data Layouts

Large-scale simulations on nonuniform particle distributions that evolve over time are widely used in cosmology, molecular dynamics, and engineering. Such data are often saved in an unstructured format that neither preserves spatial locality nor provides metadata for accelerating spatial or attribute subset queries, leading to poor performance of visualization tasks. Furthermore, the parallel I/O strategy used typically writes a file per process or a single shared file, neither of which is portable or scalable across different HPC systems. We present a portable technique for scalable, spatially aware adaptive aggregation that preserves spatial locality in the output. We evaluate our approach on two supercomputers, Stampede2 and Summit, and demonstrate that it outperforms prior approaches at scale, achieving up to 2.5× faster writes and reads for nonuniform distributions. Furthermore, the layout written by our method is directly suitable for visual analytics, supporting low-latency reads and attribute-based filtering with little overhead.

Usher, Will↗

The effect of lighting environment on task performance in buildings – A review

The effects of indoor environmental conditions on human health, satisfaction, and performance have been the focal point of research for decades. This paper reviews and summarizes the impact of lighting environment on task performance, specifically for the built environment audience. Existing studies included a variety of performance tests on cognitive performance and perception, visual acuity and reaction, memory, reasoning, and labor productivity. Illuminance, luminance ratio and correlated color temperature were found to affect performance in different ways, reflecting the impact of experimental techniques, conditions, performance evaluation methods used and data analysis methods. These were reviewed and categorized, with discussion on limitations related to sample size, modeling approach, carryover effects and other factors affecting individual differences in performance, with recommendations for future improvement. Although no universal conclusions can be made, in general, task performance seems to improve with higher illuminances, contrast ratios in the range of 7–11:1 (while always making sure that glare will not occur in the space) and higher correlated color temperature, while spectral tuning in the red or blue wavelengths has also shown positive effects. To obtain more generic evidence, future studies should be more consistent in terms of experimental procedures and overall light conditions, and also consider the effects of vertical illuminance, daylight provision/control, and outside views on task performance. Finally, studying performance with multi-factorial designs in a human-centered optimized manner (such as deploying variable lighting scenarios optimized for various tasks) can lead to deeper understanding of lighting effects on task performance, and ultimately to improved lighting design and operation in buildings overall.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Dimensionally Aligned Signal Projection Algorithms Library

Dimensionally aligned signal projection (DASP) algorithms are used to analyze fast Fourier transforms (FFTs) and generate visualizations that help focus on the harmonics for specific signals. At a high level, these algorithms extract the FFT segments around each harmonic frequency center, and then align them in equally sized arrays ordered by increasing distance from the base frequency. This allows for a focused view of the harmonic frequencies, which, among other use cases, can enable machine learning algorithms to more easily identify salient patterns. This work seeks to provide an effective open-source implementation of the DASP algorithms proposed by Vann et al. (2018) as well as functionality to help explore and test how these algorithms work with an interactive dashboard and signal-generation tool. The DASP library is implemented in Python and contains four types of algorithms for implementing these feature engineering techniques: fixed harmonically aligned signal projection (HASP), decimating HASP, interpolating HASP, and frequency aligned signal projection (FASP). Each algorithm returns a numerical array, which can be visualized as an image. The HASP algorithms are variations of the algorithms originally presented by Vann et al. (2018). For consistency, FASP, which is the terminology used for the short-time Fourier transform (STFT), has been implemented as part of the library to provide a similar interface to the STFT of the raw signal. Additionally, the library contains an algorithm to generate artificial signals with basic customizations such as the base frequency, sample rate, duration, number of harmonics, noise, and number of signals. Finally, the library provides multiple interactive visualizations, each of which is implemented using IPyWidgets and works in a Jupyter environment. A dashboard-style visualization is provided, which contains some common signal-processing visual components (signal, FFT, spectogram) updating in unison with the HASP functions (see Figure 1 below). Separate from the dashboard, an independent visualization is provided for each of the DASP algorithms as well as for the artifical signal generator. These visualizations are included in the library to aid in developing an intuitive understanding how the algorithms are affected by different input signals and parameter selections.

harmonics↗

Topological superconductivity in skyrmion lattices

Atomic manipulation and interface engineering techniques have provided an intriguing approach to custom-designing topological superconductors and the ensuing Majorana zero modes, representing a paradigm for the realization of topological quantum computing and topology-based devices. Magnet-superconductor hybrid (MSH) systems have proven to be experimentally suitable to engineer topological superconductivity through the control of both the complex structure of its magnetic layer and the interface properties of the superconducting surface. Here, we demonstrate that two-dimensional MSH systems containing a magnetic skyrmion lattice provide an unprecedented ability to control the emergence of topological phases. By changing the skyrmion radius, which can be achieved experimentally through an external magnetic field, one can tune between different topological superconducting phases, allowing one to explore their unique properties and the transitions between them. In these MSH systems, Josephson scanning tunneling spectroscopy spatially visualizes one of the most crucial aspects underlying the emergence of topological superconductivity, the spatial structure of the induced spin–triplet correlations.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Automated pipeline processing X-ray diffraction data from dynamic compression experiments on the Extreme Conditions Beamline of PETRA III

Presented and discussed here is the implementation of a software solution that provides prompt X-ray diffraction data analysis during fast dynamic compression experiments conducted within the dynamic diamond anvil cell technique. It includes efficient data collection, streaming of data and metadata to a high-performance cluster (HPC), fast azimuthal data integration on the cluster, and tools for controlling the data processing steps and visualizing the data using the DIOPTAS software package. This data processing pipeline is invaluable for a great number of studies. The potential of the pipeline is illustrated with two examples of data collected on ammonia–water mixtures and multiphase mineral assemblies under high pressure. The pipeline is designed to be generic in nature and could be readily adapted to provide rapid feedback for many other X-ray diffraction techniques, e.g. large-volume press studies, in situ stress/strain studies, phase transformation studies, chemical reactions studied with high-resolution diffraction etc.

97 MATHEMATICS AND COMPUTING↗

Comparative study between experimental measurements and model predictions of bubble rise velocity in molten LiCl-KCl

This research investigated the shape and rise velocities of gas bubbles (helium, nitrogen, argon, and krypton) in molten LiCl-KCl at 500 °C using a specialized optical visualization apparatus. The apparatus features a custom quartz rectangular prism cell housed in a furnace, enabling the application of the shadowgraph measurement technique. Bubbles with diameters between 0.45 and 3.2 mm were produced via a capillary, and their equivalent diameters and rise velocities were analyzed using high-resolution imaging and centroid tracking algorithms. Important non-dimensional parameters were calculated to characterize behavior. Bubbles with 0.03 < Eo < 1.32, 17 < Re < 718, and Mo order of 10 -11 were generated in the molten LiCl-KCl, revealing that bubbles with diameters less than 1.46 mm remain spherical, whereas those with larger diameters are ellipsoidal. The transition and oscillation onset for bubble shape occurred at larger diameters than those previously observed in air–water systems. Comparative analysis of the gas-molten salt data against existing air–water bubble rise velocity correlations highlighted inaccuracies in predictions, particularly across the different bubble regimes. An existing correlation was calibrated to the molten salt data to improve the bubble velocity predictions. In conclusion, this study contributes essential experimental data for the design and safety evaluation of molten salt reactors and offers insights for the optimization of sparge systems for fission product removal.

Bubble rise velocity↗

Multidisciplinary concurrent optimization framework for multi-phase building design process

Modern day building design projects require multidisciplinary expertise from architects and engineers across various phases of the design (conceptual, preliminary, and detailed) and construction processes. The Architecture Engineering and Construction (AEC) community has recently shifted gears toward leveraging design optimization techniques to make well-informed decisions in the design of buildings. However, most of the building design optimization efforts are either multidisciplinary optimization confined to just a specific design phase (conceptual/preliminary/detailed) or single disciplinary optimization (structural/thermal/daylighting/energy) spanning across multiple phases. Complexity in changing the optimization setup as the design progresses through subsequent phases, interoperability issues between modeling and physics-based analysis tools used at later stages, and the lack of an appropriate level of design detail to get meaningful results from these sophisticated analysis tools are few challenges that limit multi-phase multidisciplinary design optimization (MDO) in the AEC field. Here this paper proposes a computational building design platform leveraging concurrent engineering techniques such as interactive problem structuring, simulation-based optimization using meta models for energy and daylighting (machine learning based) and tradespace visualization. The proposed multi-phase concurrent MDO framework is demonstrated by using it to design and optimize a sample office building for energy and daylighting objectives across multiple phases. Furthermore, limitations of the proposed framework and future avenues of research are listed.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Material Control and Accounting Regulatory and Technical Considerations for Microreactors

New microreactors must comply with the Material Control and Accounting (MC&A) regulations in 10CFR74. The objective of MC&A is to verify that the nuclear material is not stolen or diverted to unauthorized users. Microreactors have unique features which pose new challenges to addressing these regulations. This work considers general approaches and methods for microreactor MC&A based on the reactor life cycles which have been proposed by microreactor vendors. One key aspect of MC&A is measurement of the nuclear material. Measurement of microreactor fuel could be especially important because the cores may be sealed for up to 20 years, preventing direct visual confirmation. Measurements could also be especially challenging due to the thick shielding designed around microreactors. This work evaluates a range of techniques used in medical, industrial, and nuclear fields. The cost, time, and performance of the techniques were estimated. Finally, for a promising technique of using in-core neutron detectors, the feasibility was analyzed in detail.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Feasible Actuator Range Modifier (FARM), a Tool Aiding the Solution of Unit Dispatch Problems for Advanced Energy Systems

Integrated energy systems (IESs) seek to minimize power generating costs in future power grids through the coupling of different energy technologies. To accommodate fluctuations in load demand due to the penetration of renewable energy sources, flexible operation capabilities must be fully exploited, and even power plants that are traditionally considered as base-load units need to be operated according to unconventional paradigms. Thermomechanical loads induced by frequent power adjustments can accelerate the wear and tear. If a unit is flexibly operated without respecting limits on materials, the risk of failures of expensive components will eventually increase, nullifying the additional profits ensured by flexible operation. In addition to the bounds on power variations (explicit constraints),the solution of the unit dispatch problem needs to meet the limits on the variation of key process variables, including temperature, pressure and flow rate (implicit constraints).The FARM (Feasible Actuator Range Modifier) module was developed to enable existing optimization algorithms to identify solutions to the unit dispatch problem that are both economically favorable and technologically sustainable. Thanks to the iterative dispatcher–validator scheme, FARM permits addressing all the imposed constraints without excessively increasing the computational costs. In this work, the algorithms constituting the module are described, and the performance was assessed by solving the unit dispatch problem for an IES composed of three units, i.e., balance of plant, gas turbine, and high-temperature steam electrolysis. Finally, the FARM module provides dedicated tools for visualizing the response of the constrained variables of interest during operational transients and a tool aiding the operator at making decisions. These techniques might represent the first step towards the deployment of an ecological interface design (EID) for IES units.

47 OTHER INSTRUMENTATION↗

In Situ Chemical Monitoring and Imaging of Contents within Microfluidic Devices Having a Porous Membrane Wall Using Liquid Microjunction Surface Sampling Probe Mass Spectrometry

The ability to observe dynamic chemical processes (e.g., signaling, transport, etc.) in vivo or in situ using nondestructive chemical imaging opens a new door to understanding the complex dynamics of developing biological systems. With the advent of “biology-on-a-chip” devices has come the ability to monitor dynamic chemical processes in a controlled environment, using these engineered habitats to capture key features of natural systems while allowing visual observation of system development. Having the capability to spatially and temporally map the chemical signals within these devices may yield new insights into the forces that drive biosystem development. Here, a porous membrane sealed microfluidic device was designed to allow normal microfluidic operation while enabling continuous, location specific sampling and chemical characterization by liquid microjunction surface sampling probe mass spectrometry (LMJ-SSP MS). LMJ-SSP was used to extract fluids with nL-to-μL/min flow rates directly from selected areas of the microfluidic device without negatively impacting the device function. These extracts were subsequently characterized using MS. This technique was used to acquire MS images of the entirety of several multi-input microfluidic devices having different degrees of fluid mixing. LMJ-SSP MS imaging visualized the spatial distribution of chemical components within the microfluidic channels and could visualize chemical reactions occurring in the device. These microfluidic devices with a porous membrane wall are wholly compatible with the construction of biology-on-a-chip devices. This ultimately would enable correlation of biosystem physical structure with an evolving chemical environment

47 OTHER INSTRUMENTATION↗

Nanoscale Conductivity Imaging of Correlated Electronic States in WSe 2 /WS 2 Moiré Superlattices

We report the nanoscale conductivity imaging of correlated electronic states in angle-aligned WSe 2 /WS 2 heterostructures using microwave impedance microscopy. Here, the noncontact microwave probe allows us to observe the Mott insulating state with one hole per moiré unit cell that persists for temperatures up to 150 K, consistent with other characterization techniques. In addition, we identify for the first time a Mott insulating state at one electron per moiré unit cell. Appreciable inhomogeneity of the correlated states is directly visualized in the hetero-bilayer region, indicative of local disorders in the moiré superlattice potential or electrostatic doping. Our work provides important insights on 2D moiré systems down to the microscopic level.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Electron Microscopy Studies of Soft Nanomaterials

This review highlights recent efforts on applying electron microscopy (EM) to soft (including biological) nanomaterials. We will show how developments of both the hardware and software of EM have enabled new insights into the formation, assembly, and functioning (e.g., energy conversion and storage, phonon/photon modulation) of these materials by providing shape, size, phase, structural, and chemical information at the nanometer or higher spatial resolution. Specifically, we first discuss standard real-space two-dimensional imaging and analytical techniques which are offered conveniently by microscopes without special holders or advanced beam technology. The discussion is then extended to recent advancements, including visualizing three-dimensional morphology of soft nanomaterials using electron tomography and its variations, identifying local structure and strain by electron diffraction, and recording motions and transformation by in situ EM. On these advancements, we cover state-of-the-art technologies designed for overcoming the technical barriers for EM to characterize soft materials as well as representative application examples. Here, the even more recent integration of machine learning and its impacts on EM are also discussed in detail. With our perspectives of future opportunities offered at the end, we expect this review to inspire and stimulate more efforts in developing and utilizing EM-based characterization methods for soft nanomaterials at the atomic to nanometer length scales in academic research and industrial applications.

Imaging↗