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At least 307 records · Page 17

A public website for the automated assessment and validation of SARS-CoV-2 diagnostic PCR assays

Abstract Summary Polymerase chain reaction-based assays are the current gold standard for detecting and diagnosing SARS-CoV-2. However, as SARS-CoV-2 mutates, we need to constantly assess whether existing PCR-based assays will continue to detect all known viral strains. To enable the continuous monitoring of SARS-CoV-2 assays, we have developed a web-based assay validation algorithm that checks existing PCR-based assays against the ever-expanding genome databases for SARS-CoV-2 using both thermodynamic and edit-distance metrics. The assay-screening results are displayed as a heatmap, showing the number of mismatches between each detection and each SARS-CoV-2 genome sequence. Using a mismatch threshold to define detection failure, assay performance is summarized with the true-positive rate (recall) to simplify assay comparisons. Availability and implementation The assay evaluation website and supporting software are Open Source and freely available at https://covid19.edgebioinformatics.org/#/assayValidation, https://github.com/jgans/thermonucleotide BLAST and https://github.com/LANL-Bioinformatics/assay_validation. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗

Energy Management Information Systems Technical Resources Report

Guide supports federal facility staff in understanding, designing, procuring, and implementing Energy Management Information Systems (EMIS) as a valuable component of their portfolio-level energy and water planning and management strategies. As a broad and rapidly evolving family of tools that monitor, analyze, and control building energy use and system performance, EMIS tools present significant opportunities for federal sector energy savings and improved operational performance. EMIS are at the forefront of transforming energy management best practices by providing building owners and operators with well-organized building performance and energy consumption data, enabling a host of analytic capabilities. These capabilities include portfolio-wide energy benchmarking, data visualization, and key performance indicator tracking; automated fault detection and diagnostics (AFDD); artificial intelligence for predictive analytics and control; automated measurement and verification of energy conservation measures; and supervisory control enabling automated system optimization and demand management.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Artificial intelligence-based predictive modeling for imaging neutral particle analyzers on the DIII-D tokamak

The Imaging Neutral Particle Analyzer (INPA) at DIII-D is a diagnostic system used to accurately resolve the energy and spatial distributions of fast ions in fusion plasmas. A novel artificial intelligence (AI) technique named INPA-net is based on Reservoir Computing Networks and developed here to predict active and passive signals produced by charge-exchange reactions from injected and edge-cold neutrals, respectively, in magnetically confined fusion plasmas. This model is trained using a set of 21 time domain signals between 0 s to 3.35 s that includes injected beam and thermal plasma information, and 6444 real 2D experimental images of the INPA in 12 plasma discharges at DIII-D. The trained neural network is able to forecast experimental images in real-time. The model achieves an R-squared value of 0.91, which is higher than the 0.83 value achieved by a simple linear regression model. This improvement highlights the model's enhanced predictive accuracy for measured images from the validation set. This AI approach is valuable due to its rapid response times and potential for integration into real-time plasma control systems. A version of this model capable of generating syntehic images would be useful for the real-time monitoring of fast-ion transport. A comprehensive sensitivity study reveals that INPA-net maintains high performance even with variations in the input parameters, indicating the model's robustness and reliability. While developed for the INPA, the underlying architecture is adaptable and may be applied to various 2D imaging diagnostics in fusion research.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Measurement of Beam Energy in the Fermilab's Linac taken at the Transfer Line

Linac is the first machine in the accelerator chain at Fermilab where H$^{-}$ ions are accelerated from 35 keV to 401.5\,MeV and then injected into a synchronton known as Booster where they are stripped of their electrons to become protons. One of the tools used during tuning of the Linac extraction energy is two beam pickups known as Griffin Detectors. Our goal is to control the output energy using machine learning techniques to increase the reliability and quality of the beam delivered from Linac. The first step is to understand the data from the diagnostics to develop reliable and accurate energy measurement, and control methods before implementing machine learning techniques. Two methods of energy measurement were studied, and their results are compared. The first method was the time of flight measurement using Beam Position Monitors that provide beam phase measurement. The second method used the relation between beam transverse positions and dispersion values to calculate momentum variation. The results of these two measurement methods are found to be consistent.

43 PARTICLE ACCELERATORS↗

Representing Complex Systems as Graphs for Debugging and Predictive Maintenance-Preliminary Thoughts

Representing complex systems as graphs enables use of mathematical tools to identify faults or predict failures. Graph nodes correspond to individual modules or subsystems, and edges link coupled system parts. ‘Probes’ measure the node outputs, monitoring the system health for unexpected behavior. Assuming one cannot probe every point, within a system, the fault correlates to a region—not necessarily the specific location. Bayesian networks trained to understand fault patterns can accurately identify the source. The diagnostic tool described aides debugging by pinpointing system failure causes. For predictive maintenance, probe data develop probability distribution functions describing subsystem mean time to failure. Unit lifetime can be estimated through these probability distributions. Two approaches include using Bayesian classifiers to infer the system failure source and developing maintenance schedules by treating systems as collections of random variables. When failure behavior does not follow a closed form function, use of similarity models is proposed.

97 MATHEMATICS AND COMPUTING↗

AI-Ready Control System for the Fermilab Accelerator Complex

Reliable, high-intensity operation of the Fermilab Accelerator Complex is critical to the success of the Long-Baseline Neutrino Facility and Deep Underground Neutrino Experiment. We describe the requirements and infrastructure necessary to support routine use of artificial intelligence and machine learning (AI/ML) in the accelerator control system. Three capabilities are identified: a machine learning operations (MLOps) framework standardizing the lifecycle of AI/ML automation from data management through deployment and monitoring; a data quality framework defining and enforcing standards required to build trustworthy AI/ML applications; and workflow integration with large language models to assist physicists, engineers, and operators with information retrieval, code development, and routine analysis. Use cases spanning beam diagnostics, beam control, and support system automation illustrate the technical requirements across the complex.

43 PARTICLE ACCELERATORS↗

NO x Control and Measurement Technology for Heavy-Duty Diesel Engines (CRADA Final Report)

The Catalyst CRADA focused on lean-NO x trap (LNT) and selective catalytic reduction (SCR) automotive emission control catalyst technology. It particularly had the goal of developing and applying advanced diagnostics capable of elucidating the network and sequence of catalyst reactions, as well as how they are affected by real-world operation and aging. Another overarching goal and action of this CRADA section was to develop methods to quantify and monitor catalyst states and support the development of full and reduced models for design and in-use control applications. William Partridge was the ORNL principal investigator (PI) throughout the Catalyst CRADA; Neal Currier was the Cummins PI through circa 2017, and Saurabh Joshi was the subsequent Cummins PI.

33 ADVANCED PROPULSION SYSTEMS↗

Online Bayesian State Estimation for Real-Time Monitoring of Growth Kinetics in Thin Film Synthesis

Rapid validation of newly predicted materials through autonomous synthesis requires real-time adaptive control methods that exploit physics knowledge, a capability that is lacking in most systems. Here, in this study, we demonstrate an approach to enable real-time control of thin film synthesis by combining in situ optical diagnostics with a Bayesian state estimation method. We developed a physical model for film growth and applied the direct filter (DF) method for real-time estimation of nucleation and growth rates during pulsed laser deposition (PLD). We validated the approach using simulated and experimental reflectivity data for WSe 2 growth and ultimately deployed the algorithm on an autonomous PLD system during the growth of 1T'-MoTe 2 . The DF robustly estimates growth parameters in real time at early stages of growth, down to 15% monolayer area coverage. This fusion of in situ diagnostics, data assimilation, and physical modeling opens new opportunities in adaptive control of synthesis trajectories toward desired material states.

36 MATERIALS SCIENCE↗

Key Learnings from Hydraulic Fracturing Test Site - 2 (HFTS-2), Delaware Basin

Hydraulic fractures (HF) play a dominant role in oil and gas production from unconventional reservoirs, fracture characteristics, geometry, and extent are generally not well known and are typically inferred from various monitoring methods or subsurface models. The Hydraulic Fracturing Test Site-2 (HFTS-2) is a field-based research experiment performed in the Wolfcamp formation of the Permian (Delaware) Basin. HFTS-2, a unique joint industry program (JIP) that brings together government, academia, and industry, focused on field data acquisition and interpretation. The project has built a comprehensive HF research dataset that includes microseismic (MS), 1,500 ft of core, diagnostic formation injection tests (DFIT), fluid characterization, advanced logs, geochemistry, downhole gauges, varying completions, and permanent fiber optic (FO) cable in vertical and horizontal wells. These data were integrated and used to characterize HF geometry/dimensions and resulting depletion profiles, gain insights for completion design, and achieve a better understanding of parent well depletion effects on child well performance. The analysis and integration of the comprehensive HFTS-2 diagnostics dataset provide insights for optimal well placement and completions and improves understanding about the effects of parent well depletion. Furthermore, this dataset can be used to blind test and develop subsurface workflows for unconventional resources. Key learnings from HFTS-2 and the new technologies tested can easily be transferred to other unconventional plays.

58 GEOSCIENCES↗

Overview of the New Beam Physics Research at the IOTA/FAST Facility

The Fermilab Accelerator Science and Technology (FAST) facility is dedicated to the exploration of novel concepts in accelerator and beam physics, and the development of a robust workforce, in order to enable and enhance next-generation particle accelerators. FAST comprises a high-brightness superconducting electron linac, and a storage ring, the Integrable Optics Test Accelerator (IOTA). Experiments in the most recent operational run include studies of nonlinear integrable lattices; tracking of single electrons; precise characterization of undulator radiation; studies with low-momentum-compaction lattices; and ultra-wide range beam diagnostics based on Photomultiplier tubes. In the linac, experiments on noise in intense electron bunches were conducted. The IOTA proton injector, currently being commissioned, will enable a diverse program on space-charge-dominated beams. Research areas include non-invasive beam profile monitoring for proton beams; beam dynamics with electron lenses; halo suppression, feedback systems, and electron cooling. In this presentation, we provide an overview of the recent results and highlight future plans together with opportunities for collaboration.

43 PARTICLE ACCELERATORS↗

High-resolution in-beam video rate imaging with the ClearXCam for synchrotron beamlines

The ClearXCam detector is a new video rate imaging in-beam monitor based on a diamond sensor. Imaging with 2304 effective pixels is achieved by sequentially biasing one of 48 metal stripes on one side of a diamond sensor, while reading out the current from 48 stripes on the other side of the sensor. This system was characterized for real-time X-ray beam diagnostics at synchrotron beam­line 17-BM at the National Synchrotron Light Source II. Significant results include: detection of in-beam structure via the imaging mode, beam focusing in one minute with real-time imaging feedback during a focusing event, linearity over five orders of magnitude, validation of a fast mode operating at 100 Hz, and sub-micron beam-positioning resolution. The system is now available commercially.

36 MATERIALS SCIENCE↗

Preliminary Development of Heat Transfer Model-Based Control Algorithms of Liquid Sodium Purification System: Advanced Sensors and Instrumentation Advanced Controls

Monitoring the operation of sodium purification system is essential for efficient operation of sodium fast reactors. In this work, a heat transfer model has been developed for monitoring the plugging meter and cold trap systems at the Mechanisms Engineering Test Loop (METL) liquid sodium facility at Argonne National Laboratory. The model of the purification system was developed by treating the respective aspects of the cold trap purification loop and plugging meter diagnostic loop as two separate control volumes using information from the METL piping and instrumentation diagram (P&ID). A model predictive controller was designed using first order differential equations with the specified boundary conditions. The system behavior was studied with a tuned optimized procedure using the internal cold trap temperature and plugging meter outlet temperature as control variables, and the air blower temperature as an independent variable respectively. Results of computer simulations obtained in this study compared favorably with experimental data showing very good reference tracking response with negligible overshoot as both plugging meter and cold trap physical models approach the setpoint.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Innovative Biomonitoring and Remediation of Heavy Metals Using Phytotechnologies at the Savannah River Site (SRS) Coal Combustion Product (CCP) Impoundment Sites

The Savannah River Site (SRS) contains legacy coal combustion product (CCP) impoundments that are impacted by elevated concentrations of heavy metals and radionuclides, posing long-term risks to soil health, ecosystem functioning, and environmental sustainability. Traditional environmental monitoring approaches rely primarily on chemical analyses to quantify contaminant concentrations but often provide limited information regarding biological responses or ecosystem recovery. This project addressed these limitations by integrating environmental chemistry, microbial ecology, artificial intelligence (AI), and bioremediation into a comprehensive framework for environmental diagnostics and restoration of contaminated soils. The overarching goal of this collaborative project between Florida A&M University (FAMU) and the University of Georgia's Savannah River Ecology Laboratory (SREL) was to develop innovative biomonitoring and remediation strategies for heavy metal-contaminated CCP impoundment sites at the Savannah River Site. Specifically, the project sought to (i) characterize heavy metal contamination, (ii) determine microbial responses to contamination, (iii) isolate indigenous heavy metal-resistant microorganisms for remediation applications, (iv) develop a microbial ecological health index using machine learning, and (v) optimize fungal-mediated bioremediation using artificial intelligence.

01 COAL, LIGNITE, AND PEAT↗

Radiation Hardened Beam Instrumentations for Multi-mega-watt Beam Facilities

A beam instrumentation is an essential element for the successful operate particle accelerators in which various diagnostics and beam control systems are integrated into beam optics. However, the performance of beam instrumentation is often subject to constraints such as prompt radiation dose, integrated radiation dose, operation (ambient) temperature and humidity, available space, and strength of embedded electromagnetic fields at the monitoring point. These constraints will limit the dynamic range of operational beam parameters, like the maximum achievable beam power. A seamless R\&D effort to develop the radiation hardened beam instrumentation should be made for future multi-MW beam facilities. In this paper, we describes about a radiation hardened beam instrumentation based on the operational experience of the NuMI beam line.

43 PARTICLE ACCELERATORS↗

Online Monitoring of Medium Voltage Cable Systems with Spread Spectrum Time Domain and Frequency Domain Reflectometry

In-service failures of wave energy convertor (WEC) cable systems can have a significant cost and power availability impact. Close parallel research 2019 data showed > 1B£ and 9 Terra-Watt-Hours associated with global off-shore wind (OSW) cable failures (Strang-Moran 2020). OSW is a closely related technology but currently is significantly cheaper than WEC technology. For wave energy to compete, the problem of reliable cable transmission must be mitigated. This project develops isolation technology to allow online high frequency reflectometry testing of medium voltage cables (1 to 10 kV and higher) without arcing or damage to the test instrument. Online spread spectrum time domain reflectometry (SSTDR) testing has been established for low voltage cable systems in the aircraft and rail industry and the ability to detect and locate cable flaws of interest is well understood. Extending reflectometry testing to medium voltage systems could enable detection of cable damage before failures occur thereby allowing repair and replacement of damaged cable segments to be scheduled and managed. The seedling project succeeded to pass and receive high frequency SSTDR signals onto a cable up to 1 kV using a parallel trace isolation circuit board that can be connected onto the test cable. The approach used a novel circuit design for which an invention disclosure has been filed. A proposed sapling project would extend the technology toward the higher operating voltages used by WEC systems, thereby enabling online SSTDR cable monitoring. The goal of the seedling project was to extend the capability of the ARENA cable/motor test bed to address medium voltages and to develop a high pass filter isolation architecture to protect the reflectometry instrument from the low frequency (DC – 60 Hz) line voltage while allowing the high frequency diagnostic signal to pass to and from the test instrument to the live line. Initial efforts focused on passive LCR filter circuits to reduce 60 Hz levels below 10 volts from a 10 kV line while allowing the MHz high frequency chirps to pass onto the cables and for mV signals to be detected. We discovered that the parasitic loss behavior of real high voltage components precluded this approach from working. An alternate approach was adapted for the electric field to couple between two parallel traces on a printed circuit board much like a radio-frequency coupler. The challenge here was and is to have the parallel traces close enough to each other to effectively pass the high frequency chirp onto the live line and receive any reflected signal from any encountered impedance change along the cable. This reflected signal will be in the mV range. The traces however must be far enough apart to not allow arcing on the board. A design with 3 mm spacing was determined to allow the high frequency signal to pass onto the live line and receive the mV signal back into the instrument while reducing the 60 Hz voltage amplitude by >80 dB (more than a factor of 10,000) without allowing arcing from across the parallel traces. This was confirmed by simulation and test.

16 TIDAL AND WAVE POWER↗

Adaptive model tuning studies for non-invasive diagnostics and feedback control of plasma wakefield acceleration at FACET-II

Beam-driven plasma wakefield acceleration (PWFA) achieves the same energy gain in a single meter, for which conventional accelerators require several kilometers, however much work is still required to match the beam quality of conventional accelerators. The PWFA processes to be studied at the FACET-II facility will utilize extremely short (down to a few fs) high energy (10 GeV), high charge (few nC) electron and eventually positron bunches. The PWFA process is extremely sensitive to the detailed longitudinal current profiles of these bunches and it would be of great benefit to have precise measurement and control of these profiles. We present an adaptive model tuning technique for FACET-II to adaptively tune online models based on real time accelerator and beam data to continuously provide a non-invasive diagnostic which predicts the longitudinal phase space (LPS) of extremely short and highly compressed electron beams, which otherwise require destructive X-band transverse deflecting cavity (XTCAV)-based measurements. Based on simulation studies, our method has the potential for: (1). The development of a non-invasive longitudinal phase space diagnostic by adaptively tuning models based on non-invasive measurements such as energy spread spectra which could be recorded at all of the bunch compressors in the facility. (2). Utilize these diagnostic to perform model-independent feedback-based to achieve desired longitudinal phase space distributions. (3). Utilize the model-independent feedback approach to maximize energy gain while minimizing emittance growth and energy gain variance of the PWFA process by tuning accelerator parameters, while monitoring what longitudinal phase space the algorithm has found, information that will be useful for further analytical and simulation studies.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Moisture availability mediates the relationship between terrestrial gross primary production and solar-induced chlorophyll fluorescence: Insights from global-scale variations

Effective use of solar-induced chlorophyll fluorescence (SIF) to estimate and monitor gross primary production (GPP) in terrestrial ecosystems requires a comprehensive understanding and quantification of the relationship between SIF and GPP. To date, this understanding is incomplete and somewhat controversial in the literature. Here we derived the GPP/SIF ratio from multiple data sources as a diagnostic metric to explore its global-scale patterns of spatial variation and potential climatic dependence. We found that the growing season GPP/SIF ratio varied substantially across global land surfaces, with the highest ratios consistently found in boreal regions. Spatial variation in GPP/SIF was strongly modulated by climate variables. The most striking pattern was a consistent decrease in GPP/SIF from cold-and-wet climates to hot-and-dry climates. We propose that the reduction in GPP/SIF with decreasing moisture availability may be related to stomatal responses to aridity. Furthermore, we show that GPP/SIF can be empirically modeled from climate variables using a machine learning (random forest) framework, which can improve the modeling of ecosystem production and quantify its uncertainty in global terrestrial biosphere models. Finally, our results point to the need for targeted field and experimental studies to better understand the patterns observed and to improve the modeling of the relationship between SIF and GPP over broad scales.

59 BASIC BIOLOGICAL SCIENCES↗