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DOE OSTI2015

Vision 20/20: Mammographic breast density and its clinical applications

Breast density is a strong predictor of the failure of mammography screening to detect breast cancer and is a strong predictor of the risk of developing breast cancer. The many imaging options that are now available for imaging dense breasts show great promise, but there is still the question of determining which women are “dense” and what imaging modality is suitable for individual women. To date, mammographic breast density has been classified according to the Breast Imaging-Reporting and Data System (BI-RADS) categories from visual assessment, but this is known to be very subjective. Despite many research reports, the authors believe there has been a lack of physics-led and evidence-based arguments about what breast density actually is, how it should be measured, and how it should be used. In this paper, the authors attempt to start correcting this situation by reviewing the history of breast density research and the debates generated by the advocacy movement. The authors review the development of breast density estimation from pattern analysis to area-based analysis, and the current automated volumetric breast density (VBD) analysis. This is followed by a discussion on seeking the ground truth of VBD and mapping volumetric methods to BI-RADS density categories. The authors expect great improvement in VBD measurements that will satisfy the needs of radiologists, epidemiologists, surgeons, and physicists. The authors believe that they are now witnessing a paradigm shift toward personalized breast screening, which is going to see many more cancers being detected early, with the use of automated density measurement tools as an important component.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2019

Pore-scale hydrodynamics influence the spatial evolution of bacterial biofilms in a microfluidic porous network

Bacteria occupy heterogeneous environments, attaching and growing within pores in materials, living hosts, and matrices like soil. Systems that permit high-resolution visualization of dynamic bacterial processes within the physical confines of a realistic and tractable porous media environment are rare. In this paper, we use microfluidics to replicate the grain shape and packing density of natural sands in a 2D platform to study the flow-induced spatial evolution of bacterial biofilms underground. We discover that initial bacterial dispersal and grain attachment is influenced by bacterial transport across pore space velocity gradients, a phenomenon otherwise known as rheotaxis. We find that gravity-driven flow conditions activate different bacterial cell-clustering phenotypes depending on the strain’s ability to product extracellular polymeric substances (EPS). A wildtype, biofilm-producing bacteria formed compact, multicellular patches while an EPS-defective mutant displayed a linked-cell phenotype in the presence of flow. Finally, these phenotypes subsequently influenced the overall spatial distribution of cells across the porous media network as colonies grew and altered the fluid dynamics of their microenvironment.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Extraction and Analysis of Time Series Data from Building Automation Systems Using Large Language Models

Semantic schemas like Haystack 4, Brick and ASHRAE standard 223 enable the structured, standardized, and machine-readable representation of building data, facilitating interoperability, data integration, and advanced analytics. However, extracting information from these models requires specialized expertise in SPARQL and other programming languages, skills that are not commonly found among building professionals. Recent advancements in Large Language Models (LLMs), such as ChatGPT, enable the construction of queries using natural language, making it easier for individuals to interact with these systems in a manner that resembles everyday speech. However, these methods have not yet been tested on building semantic ontologies. This paper introduces a novel workflow and tool for enabling users to ask questions about a specific building's data, using natural language and receive answers automatically generated by GPT-4o. Our approach integrates semantic ontologies with advanced LLM capabilities to automate three critical steps: (1) generating SPARQL queries to retrieve time series references from ontological models, (2) extracting the corresponding time series data from the Building Automation System, and (3) performing computations and visualizations tailored to the user's query. The proposed method simplifies access to BAS data, allowing both domain experts and non-specialists to conduct sophisticated analyses without needing extensive technical knowledge of semantic web technologies. By demonstrating this pipeline, we facilitate more accessible and scalable data-driven decision-making in building operations and management.

Mulayim, Ozan Baris↗

DOE OSTI2019

An Overview of the Database Framework for GEM Detector under CMS Experiment at CERN

In this paper, we give an overview of the database framework which we have developed for the Gas Electron Multiplier (GEM) Detector at CERN. The GEM constitutes a powerful addition to the family of fast radiation detectors; originally developed for particle physics experiments, and has spawned a large number of developments and applications. The GEM database framework comprises four components. The first component is the database itself. There are three instances of the database which have been deployed. One is for the development purpose which contains test data, other one is for the integration purposes while the last one is for the production purpose which contains real data. The database further comprises various schemas and each schema consists of different tables in it. We use separate schemas for various types of tables. The second component of the database framework is called DB Loader. The DB Loader is used to load data into database. The data is prepared in the predefined format which is in the XML form. Then the xml file is copied into a spool area of the server in which DB loader is running. Once the file is copied, the DB Loader loads the file into the database. The loader returns appropriate status codes after performing database insertion/update operation. The status of the database operations is checked against the status code which is returned by the loader. The third component of the database framework comprises graphical user interface (GUI). This is a web-based interface which can be accessed from the internet. This interface is basically used for the detector construction and to perform various quality control tests on the detector and its components. The last component of the database framework is called online monitoring system (OMS). The OMS is data visualization framework for the various detectors of the CMS experiment at CERN. It is also used to display data for the GEM. It enables users to view and retrieve database contents without having to learn database specifics.

Imran, Muhammad↗

DOE OSTI2017

Structural Characterization of Mannan Cell Wall Polysaccharides in Plants Using PACE

Plant cell wall polysaccharides are notoriously difficult to analyze, and most methods require expensive equipment, skilled operators, and large amounts of purified material. Here, we describe a simple method for gaining detailed polysaccharide structural information, including resolution of structural isomers. For polysaccharide analysis by gel electrophoresis (PACE), plant cell wall material is hydrolyzed with glycosyl hydrolases specific to the polysaccharide of interest (e.g., mannanases for mannan). Large format polyacrylamide gels are then used to separate the released oligosaccharides, which have been fluorescently labeled. Gels can be visualized with a modified gel imaging system (see Table of Materials). The resulting oligosaccharide fingerprint can either be compared qualitatively or, with replication, quantitatively. Linkage and branching information can be established using additional glycosyl hydrolases (e.g., mannosidases and galactosidases). Whilst this protocol describes a method for analyzing glucomannan structure, it can be applied to any polysaccharide for which characterized glycosyl hydrolases exist. Alternatively, it can be used to characterize novel glycosyl hydrolases using defined polysaccharide substrates.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2017

V773 Cas, QS Aql, AND BR Ind: ECLIPSING BINARIES AS PARTS OF MULTIPLE SYSTEMS

Eclipsing binaries remain crucial objects for our understanding of the universe. In particular, those that are components of multiple systems can help us solve the problem of the formation of these systems. Analysis of the radial velocities together with the light curve produced for the first time precise physical parameters of the components of the multiple systems V773 Cas, QS Aql, and BR Ind. Their visual orbits were also analyzed, which resulted in slightly improved orbital elements. What is typical for all these systems is that their most dominant source is the third distant component. The system V773 Cas consists of two similar G1-2V stars revolving in a circular orbit and a more distant component of the A3V type. Additionally, the improved value of parallax was calculated to be 17.6 mas. Analysis of QS Aql resulted in the following: the inner eclipsing pair is composed of B6V and F1V stars, and the third component is of about the B6 spectral type. The outer orbit has high eccentricity of about 0.95, and observations near its upcoming periastron passage between the years 2038 and 2040 are of high importance. Also, the parallax of the system was derived to be about 2.89 mas, moving the star much closer to the Sun than originally assumed. The system BR Ind was found to be a quadruple star consisting of two eclipsing K dwarfs orbiting each other with a period of 1.786 days; the distant component is a single-lined spectroscopic binary with an orbital period of about 6 days. Both pairs are moving around each other on their 148 year orbit.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2025

Extraction and Analysis of Time Series Data from Building Automation Systems Using Large Language Models

Mulayim, Ozan Baris↗

DOE OSTI2021

Spectroscopy imaging and analysis of live cells

Disclosed herein are systems, methods, systems and devices for measurement and visualization of chemical dynamics in living cells or tissues for diagnostic pathology. Devices can be open- or closed-channel microfluidic membrane devices for long-term IR spectroscopy of live adherent cells and ultimately for rapidly identifying time-dependent spectral features indicative of chemical abnormality in individual cells.

Holman, Hoi-Ying N.↗

DOE OSTI2018

Testing and Deployment of Remote Systems to Remove Highly Radioactive Soil at Hanford's 324 Building - 18043

U.S. Department of Energy (DOE) contractor CH2M HILL Plateau Remediation Company (CHPRC) is in the process of procuring, testing and deploying remotely operated tools to safely remove highly contaminated soil from beneath the 324 Building on the Hanford Site in southeastern Washington State. The 324 Building operated for more than 40 years, completing a variety of high-dose engineering development and demonstration activities inside six hot cells that shielded the workers from the highly radioactive materials. Activities to decommission, decontaminate and demolish the facility began in 2008. In 2010, soil contamination was found in the soil under one of the hot cells, and building deactivation was paused to evaluate the soil contamination. Sampling efforts, using borehole technology, revealed significant under-building contamination with dose rates measuring has high as 130 Sv/hr (13,000 R/hr). The highly-contaminated soil has to be removed before traditional open air deactivation activities can continue. CHPRC completed proof of concept testing and built a full-scale test facility to demonstrate the effectiveness of three primary tools that will accomplish the floor and soil removal. The tools include a commercially available concrete saw, and a commercially available excavator arm that have been modified to operate remotely in the high-radiation environment within the hot-cell. In order to reduce the wear on the hot-cell overhead cranes, a remote operated rail and cart system has been designed to transport soil and debris out of the hot-cell to an airlock area where the waste will be separated, according to its level of radioactivity. A camera and light system has been designed to provide visual and audio coverage of the hot-cell area that will allow the operations to proceed from remote control stations. This paper will describe the primary remote operated equipment designed for the project and the challenges and processes for developing, testing and deploying the equipment necessary to excavate the soil from below the 324 Building. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2026

Advanced Research on Integrated Energy Systems Cyber Range

As digital technologies expand to meet the needs of a more autonomous, interconnected, and advanced power system, new cybersecurity complexities and vulnerabilities arise. The ARIES Cyber Range enables the energy sector to evaluate these evolutions and validate cybersecurity solutions without impacting live systems. Combining power grid-scale hardware with emulation and simulation approaches, the ARIES Cyber Range can faithfully replicate modern energy systems - from grid physics to communication networks, and everything in between - with real-world fidelity. At NLR, researchers and partners are answering complex power system cybersecurity questions, examining emerging threats to the electric sector, and de risking new security technologies, all at a mission-relevant speed that keeps pace with rapidly evolving systems and hazards.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

DOE OSTI2023

Turbine-based Power System Tool

Advanced research tools are essential to illustrate the effects of turbine-based power system operations on the electric grid network. This paper presents the development of an open-source tool to visualize the operation of turbine-based electricity generation. The tool exposes power system models, control parameters, and corresponding values of the turbine model and its electrical system, allowing them to customize the simulation according to their needs. The developed tool enables users to simulate power profiles for different turbinebased energy generation such as wind, tidal, and gas turbines. It allows users to investigate the details of the generated profiles of various types of turbine systems at various scales. It can provide valuable insights into model development and facilitate the analysis of integrated power systems. By enabling access to turbine-based operations visualization, the tool aims to bridge the gap between advanced research tools and users, facilitating broader adoption of renewable energy technologies and aiding in developing sustainable power systems.

Kini, Roshan L.↗

DOE OSTI2018

Scalable Data Management of the Uintah Simulation Framework for Next-Generation Engineering Problems with Radiation

The need to scale next-generation industrial engineering problems to the largest computational platforms presents unique challenges. This paper focuses on data management related problems faced by the Uintah simulation framework at a production scale of 260K processes. Uintah provides a highly scalable asynchronous many-task runtime system, which in this work is used for the modeling of a 1000 megawatt electric (MWe) ultra-supercritical (USC) coal boiler. At 260K processes, we faced both parallel I/O and visualization related challenges, e.g., the default file-per-process I/O approach of Uintah did not scale on Mira. In this paper we present a simple to implement, restructuring based parallel I/O technique. We impose a restructuring step that alters the distribution of data among processes. The goal is to distribute the dataset such that each process holds a larger chunk of data, which is then written to a file independently. This approach finds a middle ground between two of the most common parallel I/O schemes–file per process I/O and shared file I/O–in terms of both the total number of generated files, and the extent of communication involved during the data aggregation phase. To address scalability issues when visualizing the simulation data, we developed a lightweight renderer using OSPRay, which allows scientists to visualize the data interactively at high quality and make production movies. Finally, this work presents a highly efficient and scalable radiation model based on the sweeping method, which significantly outperforms previous approaches in Uintah, like discrete ordinates. The integrated approach allowed the USC boiler problem to run on 260K CPU cores on Mira.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2018

Information Guided Exploration of Scalar Values and Isocontours in Ensemble Datasets

Uncertainty of scalar values in an ensemble dataset is often represented by the collection of their corresponding isocontours. Various techniques such as contour-boxplot, contour variability plot, glyphs and probabilistic marching-cubes have been proposed to analyze and visualize ensemble isocontours. All these techniques assume that a scalar value of interest is already known to the user. Not much work has been done in guiding users to select the scalar values for such uncertainty analysis. Moreover, analyzing and visualizing a large collection of ensemble isocontours for a selected scalar value has its own challenges. Interpreting the visualizations of such large collections of isocontours is also a difficult task. In this work, we propose a new information-theoretic approach towards addressing these issues. Using specific information measures that estimate the predictability and surprise of specific scalar values, we evaluate the overall uncertainty associated with all the scalar values in an ensemble system. This helps the scientist to understand the effects of uncertainty on different data features. To understand in finer details the contribution of individual members towards the uncertainty of the ensemble isocontours of a selected scalar value, we propose a conditional entropy based algorithm to quantify the individual contributions. This can help simplify analysis and visualization for systems with more members by identifying the members contributing the most towards overall uncertainty. We demonstrate the efficacy of our method by applying it on real-world datasets from material sciences, weather forecasting and ocean simulation experiments.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2016

CyberPetri at CDX 2016: Real-time Network Situation Awareness

CyberPetri is a novel visualization technique that provides a flexible map of the network based on available characteristics, such as IP address, operating system, or service. Previous work introduced CyberPetri as a visualization feature in Ocelot, a network defense tool that helped security analysts understand and respond to an active defense scenario. In this paper we present a case study in which we use the CyberPetri visualization technique to support real-time situation awareness during the 2016 Cyber Defense Exercise.

Cybersecurity↗

DOE OSTI2022

US Department of Energy, Office of Science High Performance Computing Facility Operational Assessment 2021: Oak Ridge Leadership Computing Facility

Oak Ridge National Laboratory’s (ORNL’s) Leadership Computing Facility (OLCF) continues to surpass its operational target goals of supporting users; delivering fast, reliable computational ecosystems; creating innovative solutions for high-performance computing (HPC) needs; contributing to the community to build the next generation HPC workforce, and managing risks, safety, and security associated with operating some of the most powerful computers in the world. The results can be seen in the cutting-edge science conducted by users and the praise from the research community. Calendar year (CY) 2021 saw continued excellence in research supported by the OLCF’s leadership-class computing resources, including Summit (the nation’s most powerful supercomputer), the global scratch file system Alpine, the Scalable Protected Infrastructure (SPI), the Exploratory Visualization Environment for Research in Science and Technology (EVEREST), and the archival mass-storage resource High-Performance Storage System (HPSS). While maintaining access and exceptional user support for Summit, the OLCF continued to make progress on the installation and deployment of Frontier, which will be the nation’s first exascale system when it comes online at the start of CY 2023. Users have already begun running and optimizing scientific codes on Crusher, the OLCF test and development system equipped with Frontier’s architecture. Throughout the year, the OLCF maintained a strong culture of operational excellence, including risk management, workplace safety, and cybersecurity. The OLCF’s rigorous risk management strategy anticipated and mitigated risks, and at this time there are no high-priority operational risks. Similarly, ORNL and the OLCF were committed to operating under the US Department of Energy’s (DOE’s) safety regulations that ensure a safe workplace. Technical staff tracked and monitored existing threats and vulnerabilities within the OLCF while continually developing tools and practices to enhance operations without increasing the facility’s risk. CY 2021 was filled with outstanding results and accomplishments, including a very high rating from users on overall satisfaction for the eighth consecutive year; a tremendous number of node hours delivered to 1,671 researchers on Summit; and the successful delivery of the allocation split of roughly 60%, 20%, and 20% of core-hours offered for the Innovative and Novel Computational Impact on Theory and Experiment (INCITE), Advanced Scientific Computing Research Leadership Computing Challenge (ALCC), and Director’s Discretionary (DD) programs, respectively (Section 2). COVID-19 research remained a focus in 2021, and the ALCC and DD programs allocated over 1 million Summit hours to the COVID-19 High Performance Computing Consortium. These accomplishments, coupled with the high utilization rates (i.e., overall and capability usage), represent the fulfillment of the promise of leadership class machines: efficient facilitation of leadership-class computational applications.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2019

Three-dimensional radiograph security system

A method and apparatus for displaying a three-dimensional radiograph in a security scanner. A first X-ray image of an object is generated by the security scanner from a first viewpoint. A second X-ray image of the object is generated by the security scanner from a second viewpoint. The first X-ray image and the second X-ray image form a stereogram. The stereogram is displayed by the security scanner on a display system for the security scanner such that a first eye of a viewer sees the first X-ray image in the stereogram and a second eye of the viewer sees the second X-ray image in the stereogram. A parallax between the first viewpoint and the second viewpoint in the stereogram results in a three-dimensional visualization of the object on the display system for the security scanner.

Jimenez, Jr., Edward Steven↗

DOE OSTI2023

Advanced Grid Operational Technology Edge-Level Threat Detection

This report presents a deployable solution to improve the cybersecurity situational awareness of the legacy SCADA system infrastructure in power grids. The main goal of this project is to provide system owners and operators a highly trusted, intelligent alarm system and comprehensive situational awareness of ongoing or potential cybersecurity threats on the grid network. The key contributions of this project include: (1) the development of software, the Intrusion Detection Visualizer for the Operational Technology Network (IViz-OT), to visualize and locate intrusions on the grid network; (2) testing the signature-based Hybrid Intrusion Detection for Energy Systems (HIDES) for different types of intrusions; (3) the integration of HIDES and IViz-OT into the visualization dashboard; and (4) real-time testing using a hardware-in-the-loop test bed.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2016

Continuous whole-system monitoring toward rapid understanding of production HPC applications and systems

A detailed understanding of HPC applications’ resource needs and their complex interactions with each other and HPC platform resources are critical to achieving scalability and performance. Such understanding has been difficult to achieve because typical application profiling tools do not capture the behaviors of codes under the potentially wide spectrum of actual production conditions and because typical monitoring tools do not capture system resource usage information with high enough fidelity to gain sufficient insight into application performance and demands. In this paper we present both system and application profiling results based on data obtained through synchronized system wide monitoring on a production HPC cluster at Sandia National Laboratories (SNL). We demonstrate analytic and visualization techniques that we are using to characterize application and system resource usage under production conditions for better understanding of application resource needs. Furthermore, our goals are to improve application performance (through understanding application-to-resource mapping and system throughput) and to ensure that future system capabilities match their intended workloads.

97 MATHEMATICS AND COMPUTING↗