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DOE OSTI2025

PyTUQ: Python Toolkit for Uncertainty Quantification

SAND2025-03661O PyTUQ is a user-friendly software toolkit designed to help researchers and professionals understand and manage uncertainty in several scientific fields. By providing tools for analyzing how uncertainties affect outcomes, PyTUQ can be applied in areas such as energy production, and biology. Its unique approach allows users to make more informed decisions by assessing risks and improving predictions. Whether you're studying combustion processes or exploring complex biological systems, PyTUQ empowers you to gain deeper insights and enhance the reliability of your results. 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.

SciDAC↗

DOE OSTI2014

Using Micro-Synchrophasor Data for Advanced Distribution Grid Planning and Operations Analysis

This report reviews the potential for distribution-grid phase-angle data that will be available from new micro-synchrophasors (µPMUs) to be utilized in existing distribution-grid planning and operations analysis. This data could augment the current diagnostic capabilities of grid analysis software, used in both planning and operations for applications such as fault location, and provide data for more accurate modeling of the distribution system. µPMUs are new distribution-grid sensors that will advance measurement and diagnostic capabilities and provide improved visibility of the distribution grid, enabling analysis of the grid’s increasingly complex loads that include features such as large volumes of distributed generation. Large volumes of DG leads to concerns on continued reliable operation of the grid, due to changing power flow characteristics and active generation, with its own protection and control capabilities. Using µPMU data on change in voltage phase angle between two points in conjunction with new and existing distribution-grid planning and operational tools is expected to enable model validation, state estimation, fault location, and renewable resource/load characterization. Our findings include: data measurement is outstripping the processing capabilities of planning and operational tools; not every tool can visualize a voltage phase-angle measurement to the degree of accuracy measured by advanced sensors, and the degree of accuracy in measurement required for the distribution grid is not defined; solving methods cannot handle the high volumes of data generated by modern sensors, so new models and solving methods (such as graph trace analysis) are needed; standardization of sensor-data communications platforms in planning and applications tools would allow integration of different vendors’ sensors and advanced measurement devices. In addition, data from advanced sources such as µPMUs could be used to validate models to improve/ensure accuracy, providing information on normally estimated values such as underground conductor impedance, and characterization of complex loads. Although the input of high-fidelity data to existing tools will be challenging, µPMU data on phase angle (as well as other data from advanced sensors) will be useful for basic operational decisions that are based on a trend of changing data.

25 ENERGY STORAGE↗

DOE OSTI2019

Achieving Verifiable and High Integrity Instrumentation and Control Systems through Complexity Awareness and Constrained Design. Final Report

While most process control industries have been able to embrace digital Instrumentation and Control (I&C) technology to improve performance, reliability, maintainability, and efficiency of production, the nuclear industry has been relatively slow to adopt digital I&C for safety critical plant functions. There are a variety of reasons for this, but in general the nuclear industry takes a conservative stance that new technologies must mature before adoption. A deeper underlying reason for not fully realizing digital I&C and automation in nuclear power is associated with the complexity that can manifest in software-based systems that is different in nature from the complexity of their analog predecessors. Accordingly, this research pursued the development of innovative architectures and methods to “constrain complexity” to enhance verifiability of digital I&C devices. These constraints can positively impact the reduction of Software Common Cause Failures (SCCF) and other systematic errors. The architectural concept developed in this research effort is called SymPLe. SymPLe is specifically aimed at safety critical functions within Nuclear Power Plants and other critical infrastructure where constraining device complexity to support verifiability and safety case arguments is important. The SymPLe architecture is designed to promote “accessible verification” between OEM/utility engineers and the regulatory agencies who review and license nuclear power plant I&C systems. The major contributions of this work to the nuclear industry are: Demonstration of SymPLe as a viable approach to “complexity aware” I&C systems and Embedded Digital Devices.Comprehensive use of model-based design and engineering to produce verifiable I&C systems for the nuclear industry with clear findings on the usability of model-based engineering. Employ comprehensive use of model-based engineering, testing, and verification in an IEC 61508 workflow in support of design assurance. Gathered evidence of “difficult to find” design flaws found using model-based design and testing methods. Detailed the nature of these SCCFs including where they were introduced, the triggers, and how they were found. Gathered evidence on the synergistic use of practical formal methods and testing and how these methods can be used to significantly increase assurance of reduction and avoidance of design flaws.

Testing↗

DOE OSTI2015

Evaluation of the radiation doses in newborn patients submitted to CT examinations

The number of computed tomography (CT) scans available to the population is increasing, as well as the complexity of such exams. As a result, the radiation doses are increasing as well. Considering the population exposed to CT exams, pediatric patients are considerably more sensitive to radiation than adults. They have a longer life expectancy than adults, and may receive a higher radiation dose than necessary if the CT scan settings are not adjusted for their smaller body size. As a result of these considerations, the risk of developing cancer is of great concern when newborn patients are involved. The objective of this work was to study the radiation doses on radiosensitive organs of newborn patients undergoing a whole body CT examination, utilizing Monte Carlo simulations. The novelty of this work is the use of pediatric virtual anthropomorphic phantoms, developed at the Department of Nuclear Energy at the Federal University of Pernambuco (DEN/UFPE). The CT equipment utilized during the simulations was a Discovery VCT GE PET/CT system, with a tube voltage of 140 kVp. The X-ray spectrum of this CT scanner was generated by the SRS-78 software, which takes into account the X-ray beam energy used in PET/CT procedures. The absorbed organ doses were computed employing the F6 tally (MeV/g). The results were converted to dose coefficients (mGy/100 mA) for all the structures, considering all employed beams. The highest dose coefficients values were obtained for the brain and the thyroid. This work provides useful information regarding the risks involving ionizing radiation in newborn patients, employing a new and reliable technique. (authors)

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2017

Microgrid Design Toolkit (MDT) User Guide Software v1.2.

The Microgrid Design Toolkit (MDT) supports decision analysis for new ("greenfield") microgrid designs as well as microgrids with existing infrastructure. The current version of MDT includes two main capabilities. The first capability, the Microgrid Sizing Capability (MSC), is used to determine the size and composition of a new, grid connected microgrid in the early stages of the design process. MSC is focused on developing a microgrid that is economically viable when connected to the grid. The second capability is focused on designing a microgrid for operation in islanded mode. This second capability relies on two models: the Technology Management Optimization (TMO) model and Performance Reliability Model (PRM).

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

Microgrid Design Toolkit (MDT) User Guide. Software v1.3.

42 ENGINEERING↗

DOE OSTI2017

Demand Response Resource Quantification with Detailed Building Energy Models

Demand response is a broad suite of technologies that enables changes in electrical load operations in support of power system reliability and efficiency. Although demand response is not a new concept, there is new appetite for comprehensively evaluating its technical potential in the context of renewable energy integration. The complexity of demand response makes this task difficult -- we present new methods for capturing the heterogeneity of potential responses from buildings, their time-varying nature, and metrics such as thermal comfort that help quantify likely acceptability of specific demand response actions. Computed with an automated software framework, the methods are scalable.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2015

The experiment filtering tool in the MACSENS workbench - 14341

The MACSENS (outils Moret d'Aide a la Caracterisation et aux etudes de SENSibilite) workbench is dedicated to the advanced validation work for criticality studies. The aim of this kind of tool is to determine the experiments from a validation database being the 'closest' to an application case and, from there, to evaluate a calculation bias with a related uncertainty. To achieve this goal, the MACSENS workbench relies on different kind of information stored in various databases depending on the origin of the data. Two main kinds of data can be identified. The first one concerns the data used to describe the experiments of the validation database (e.g. the inputs needed to perform a calculation). These values characterize the chemical and geometrical models. They can be considered as constant, as they do not vary once evaluated, and some of them can be from a non-numerical nature (reflector material for example...). The second kind of data gathers the results obtained with the use of a simulation code, such as reaction rates, fluxes and leakages, sensitivities, k{sub eff}, etc. These values depend on the version of the code and are purely numerical. In the early 2000's, regarding the increasing number of experiments evaluated in the ICSBEP handbook, the OECD/NEA (Organization for Economic Co-operation and Development/Nuclear Energy Agency), under the ICSBEP (International Criticality Safety Benchmark Evaluation Project) working group direction, decided to store such information in a database and to provide a software, called DICE (Database for the International Criticality safety benchmark Evaluation project), allowing users to search easily criticality experiments of interest. Up to now, more than 4400 critical or subcritical configurations have been compiled by ICSBEP, described and stored in the DICE database. Over time, a validation work has been done on the data, with the participation of IRSN, and a quality assurance policy has been defined. For these reasons, the DICE database is highly reliable. These features were fundamental for the MACSENS developers, who were looking for a database containing descriptive data of the experiments included in the MORET code validation database. The paper describes the solution chosen by IRSN to take advantage of the DICE database content and to overcome the DICE limits. It also explains the quality assurance policy applied to guaranty the reliability of the stored data. It will also discuss the use of the experiment-filtering module of the MACSENS workbench to select a set of experiments and to examine numerical parameter trends for an application case. (authors)

42 ENGINEERING↗

DOE OSTI2025

Enhanced Boundary Layer Height Detection Using Ceilometer, Surface Meteorology, and Radiation Products With a Random Forest Ensemble Method

This study develops and evaluates a Random Forest (RF) model for estimating planetary boundary layer height (PBLH) using 9 years of data from the Atmospheric Radiation Measurement Southern Great Plains (ARM SGP) user facility, with potential application in the NOAA Surface Radiation (SURFRAD) Network. The model integrates ceilometer, surface meteorology, and radiation measurements, and is trained using thermodynamic PBLH estimates derived from radiosondes. This approach aims to bridge gaps between aerosol-based and thermodynamic-based PBLH estimates. The RF model outperformed traditional methods during daytime and better captured transition periods, demonstrating improved accuracy and robustness. At ARM SGP, it showed a substantial reduction in both bias and RMSE, with a bias near zero (−4.9 m) compared with traditional Haar Wavelet (HW) (70.9 m) and Vaisala BL-View software (124.1 m), and an RMSE of 303.2 m, lower than both BL-View (566.9 m) and HW (404.6 m). During daytime hours, RF consistently outperformed both alternatives, maintaining lower bias and RMSE across all periods. At a second evaluation site, RF achieved the lowest overall RMSE (323.7 m), similar to HW (326.4 m) and significantly better than BL-View (738.3 m). However, all models showed reduced accuracy under stable nighttime conditions, limiting the reliability of PBLH estimates. Key predictors for the model included the lifting condensation level height (LCLH), aerosol gradients, and month for seasonal variability. The study underscores the potential of integrating machine learning with multiple data sets such as surface energy and thermodynamic data to advance PBLH estimation.

boundary layer height↗

DOE OSTI2021

Instrument for spatially resolved, temperature-dependent electrochemical impedance spectroscopy of thin films under locally controlled atmosphere

We demonstrate an instrument for spatially resolved measurements (mapping) of electrochemical impedance under various temperatures and gas environments. Automated measurements are controlled by a custom LabVIEW program, which manages probe motion, sample motion, temperature ramps, and potentiostat functions. Sample and probe positioning is provided by stepper motors. Dry or hydrated atmospheres (air or nitrogen) are available. The configurable heater reaches temperatures up to 500 °C, although the temperature at the sample surface is moderated by the gas flow rate. The local gas environment is controlled by directing flow toward the sample via a glass enclosure that surrounds the gold wire probe. Software and hardware selection and design are discussed. Reproducibility and accuracy are quantified on a Ba(Zr,Y)O 3-δ proton-conducting electrolyte thin film synthesized by pulsed laser deposition. The mapping feature of the instrument is demonstrated on a compositionally graded array of electrocatalytically active Ba(Co,Fe,Zr,Y)O 3-δ thin film microelectrodes. The resulting data indicate that this method proficiently maps property trends in these materials, thus demonstrating the reliability and usefulness of this method for investigating electrochemically active thin films.

47 OTHER INSTRUMENTATION↗

DOE OSTI2021

Information Leakage Analysis using a Co-design-Based Fault Injection Technique on a RISC-V Microprocessor

The RISC-V instruction set architecture open licensing policy has spawned a hive of development activity, making a range of implementations publicly available. The environments in which RISC-V operates have expanded correspondingly, driving the need for a generalized approach to evaluating the reliability of RISC-V implementations under adverse operating conditions or after normal wear-out periods. Fault injection (FI) refers to the process of changing the state of registers or wires, either permanently or momentarily, and then observing execution behavior. The analysis provides insight into the development of countermeasures that protect against the leakage or corruption of sensitive information which might occur because of unexpected execution behavior. In this paper, we develop a hardware-software co-design architecture that enables fast, configurable fault emulation and utilize it for information leakage and data corruption analysis. Modern System-on-chip FPGAs enable building an evaluation platform where control elements run on a processor(s) (PS) simultaneously with the target design running in the programmable logic (PL). Software components of the FI system introduce faults and report execution behavior. A pair of RISC-V FI-instrumented implementations are created and configured to execute the Advanced Encryption Standard and Twister algorithms. Key and plaintext information leakage and degraded pseudo-random sequences are both observed in the output for a subset of the emulated faults.

42 ENGINEERING↗

DOE OSTI2022

National Ignition Facility. Facility and Infrastructure Systems Maintenance Plan

Ensuring the reliability of the NIF, including its support systems, laser systems, target diagnostic systems, and utilities, is essential to the availability of the NIF in its support of NNSA missions. NIF is a key capability in the DOE Stockpile Stewardship Program and supports high energy physics experiments for nuclear weapons, energy, and astrophysics applications. High system reliability provides opportunities for shots and scientific discoveries with opportunities to enhance and upgrade capabilities. This Maintenance Plan (MP) identifies the policies and procedures used to perform and support asset management of the NIF Facility and Infrastructure Systems (FInS), NIF Lasers & Alignment (LASE), NIF Target Experimental Operations (TOPS), NIF Target Area Science and Engineering (TASE), and NIF&PS Control Systems (NCS). The FInS systems include the facility, HVAC, contamination control, beampath, and Line Replaceable Units (LRUs) as well as utilities which create the beampath environments, such as vacuum, argon, or clean dry air. The LASE systems are Programmatic systems which include laser diagnostics, alignment, power conditioning, pulsed power, and input laser systems. The TOPS and TASE systems are also Programmatic systems which include target and diagnostic delivery systems and positioners, many different insertable and fixed target diagnostics, and cryogenic and target gas fill systems. Finally, the NCS systems include both software and hardware for industrial and shot operation control systems. Policies governing administrative and operational practices related to maintenance of FInS, LASE, TOPS, TASE, and NCS systems are described in this plan. In addition, the plan provides processes and procedures for managing, tracking, and documenting the work. This document, the NIF Operations Management Plan, NIF-5020544 (Ref. 1), and NIF Shot Operations Plan, NIF-5018506 (Ref. 2), together satisfy the requirements of the Conduct of Operations. Duties, responsibilities, and reporting requirements of the various positions associated with FInS, LASE, and TOPS maintenance are detailed in this plan. The FInS systems include both Real Property systems with asset management requirements specified in DOE Order 430.1C (Ref. 3) and Programmatic systems. In addition, for FInS, there is a list of the System Level Maintenance Plans (SLMPs) in NIF-1007419198 (Ref. 4) which provide the system descriptions and maintenance plan and schedule. In addition, the list includes the Reliability Centered Maintenance (RCM) and Experience Centered Maintenance (ECM) evaluations that have been performed for applicable FInS systems as well as reliability criticality per Section 3.5. The -AM version of the NIF Maintenance Plan focuses on the reliability program for FInS, LASE, TOPS, TASE, and NCS within the context of the overall NIF Reliability, Availability, and Maintainability (RAM) program and incorporates changes since the -AL version from August 2011 and has been updated to be fully consistent with the updates to Ref. 1. It also includes asset management considerations, updates to the Work Order (WO) process within the NIF Computerized Maintenance Management System (CMMS) which is EAM infor® System Maintenance and Reliability Tracking (SMaRT) (Ref. 5), and updates to metrics and key performance indicators (KPIs).

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

DOE OSTI2016

Dose-Dependent Cortical Thinning After Partial Brain Irradiation in High-Grade Glioma

Purpose: Radiation-induced cognitive deficits may be mediated by tissue damage to cortical regions. Volumetric changes in cortex can be reliably measured using high-resolution magnetic resonance imaging (MRI). We used these methods to study the association between radiation therapy (RT) dose and change in cortical thickness in high-grade glioma (HGG) patients. Methods and Materials: We performed a voxel-wise analysis of MRI from 15 HGG patients who underwent fractionated partial brain RT. Three-dimensional MRI was acquired pre- and 1 year post RT. Cortex was parceled with well-validated segmentation software. Surgical cavities were censored. Each cortical voxel was assigned a change in cortical thickness between time points, RT dose value, and neuroanatomic label by lobe. Effects of dose, neuroanatomic location, age, and chemotherapy on cortical thickness were tested using linear mixed effects (LME) modeling. Results: Cortical atrophy was seen after 1 year post RT with greater effects at higher doses. Estimates from LME modeling showed that cortical thickness decreased by −0.0033 mm (P<.001) for every 1-Gy increase in RT dose. Temporal and limbic cortex exhibited the largest changes in cortical thickness per Gy compared to that in other regions (P<.001). Age and chemotherapy were not significantly associated with change in cortical thickness. Conclusions: We found dose-dependent thinning of the cerebral cortex, with varying neuroanatomical regional sensitivity, 1 year after fractionated partial brain RT. The magnitude of thinning parallels 1-year atrophy rates seen in neurodegenerative diseases and may contribute to cognitive decline following high-dose RT.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

DOE OSTI2023

Deployment of Dynamic Neural Network Optimization to Minimize Heat Rate During Ramping for Coal Power Plants (Final Technical Report)

Much success was achieved throughout the course of this project. A successful implementation of Dynamic Neural Network Optimization (D-NNO) was coupled with Adaptive Predictive Controls (APC) and a novel hardware installation comprised of an advanced sensor network (ASN) measuring mass-weighted averages of flue gas constituents above the horizontal superheater of a coal-fired utility boiler. From 2019 through 2023 (including an extension due to COVID delays), the team was able to prototype, evaluate, deploy, iterate, and ultimately finalize an advanced closed-loop control D-NNO system which demonstrated the ability to: •improve unit efficiency ~2.0% relative to unoptimized operation (represented as total fuel fired per MWh generated) •improve unit NOx emission rates 10%+ beyond static optimization baselines •improve unit temperature stability as much as 58% and on average 12% •improve operating load stability as much as 35% The culmination of this project has generated an advanced methodology of deploying specially designed recurrent neural networks (long short-term memory, gated recurrent unit, encoder-decoder networks, transformers, etc.), customized trajectory planning and closed-loop optimization modules capable of adapting to live electric grid responses and demands, self-tuning and adaptive expert controls constantly adjusting prediction parameters to real-time unit behavior, and a hardware/software package able to reliably calculate net unit heat rate (NUHR) in real-time using flue gas constituents, machine learning, and known combustion relationships. Through this real-time NUHR value, immediate feedback on system adjustments relative to operating efficiency was available, allowing for rapid improvements to system performance. In addition to development and deployment of the advanced D-NNO system, the approach methodology has been readily commercialized through the project platform Griffin Open Systems, LLC, the D-NNO software platform host. Similar methodologies to those developed by this project have already been deployed at 5 other units across the United States, with another 6 implementations scheduled, and more expected. Over the course of the project, multiple academic papers were submitted and accepted for publication within esteemed academic journals, and PhD students were trained and graduated, as well as undergraduate students becoming involved and participating to project objectives.

01 COAL, LIGNITE, AND PEAT↗

DOE OSTI2025

Demonstrating Advanced Sensors for In-Situ Monitoring Towards Qualification of Nuclear Relevant Components

The U.S. Department of Energy’s Office of Nuclear Energy Advanced Materials and Manufacturing Technologies (AMMT) program is pursuing qualification of laser powder bed fusion (LPBF) components for nuclear applications. A major focus of this effort is the use of in situ process monitoring and machine learning–based tools to establish real-time quality assurance. The primary objective of this report is to identify and evaluate the most relevant in situ sensor systems for LPBF, and to document the deployment of these systems across platforms critical to the AMMT program. This work demonstrates how in situ monitoring can detect process anomalies, track geometry-dependent flaws, and identify limiting combinations of processing parameters—particularly those related to energy density and complex geometries (e.g., overhanging structures). To support this goal, a diverse suite of sensor modalities was evaluated across LPBF platforms, including visible and near-infrared (NIR) imaging, fringe projection profilometry, long-wavelength infrared (LWIR) thermography, and high-speed photodiode/pyrometry systems. These sensor streams were integrated with Peregrine, a machine-agnostic software platform that, among other capabilities, can generate real-time process anomaly classification. This report documents sensor deployments on multiple AMMT flagship platforms, including the Concept Laser M2 and Renishaw AM400/AM250 systems. Calibration builds with complex, flaw-prone geometries such as unsupported overhangs, stepped features, and thin walls, were used to evaluate how well Peregrine and its associated sensors could detect process anomalies and other instabilities under varied energy densities. It will be shown how Peregrine reliably identifies common process anomalies such as recoater streaking, superelevation, etc., and can be used in post-build analysis for anomaly spatial distributions throughout the build height to better understand the impact of geometry and processing parameter choice on the build. This work demonstrates measurable progress toward the vision that components can be born-qualified by establishing a real-time monitoring framework, identifying limiting process conditions, and laying the foundation for sensor fusion–enabled prediction pipelines that are scalable across platforms and applicable to nuclear-relevant components.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2017

Improving plant efficiency through the installation of TecSOLCEP online monitoring system - 362

In February 2016, Nuclear Energy Institute (NEI) launched its 'Delivering the Nuclear Promise (DNP)' strategic plan with the objective of reducing electric generating costs by 30% across the nuclear power industry by 2018. Improving efficiency has been addressed as one of the strategic focus areas in the plan. In nuclear power plants (NPPs) there is room for improvement in main components efficiency and TecSOLCEP is a software tool that has proved its value for that purpose. TecSOLCEP is a software tool for monitoring, diagnosing and quantifying performance deviations in Power Plants. It faithfully follows the methodology of ASME standards. Over 15 years of success stories in more than 50 electric power plants of different technologies worldwide, justify the benefits for the plants. The implicit concept in TecSOLCEP is 'Benefit based Maintenance' (BbM) as complementary to usual maintenance strategies like time-based, condition-based or predictive. These maintenance strategies are oriented to obtain the Safety and Reliability goals shared by all the electricity generation technologies. BbM is oriented to get the maximum economic benefit by Efficiency care, which historically has not been a priority, especially in nuclear plants. BbM applied with the help of performance monitoring tools like TecSOLCEP, is called to play an important role to improve efficiency which, in plants mainly operating at full power, is equivalent to increase the maximum power. Nuclear power plants that intend to extend their lives may also take advantage of identifying and quantifying inefficiencies in equipment to better address necessary investments. (authors)

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2021

Micromachined ceramic-based chipless LC resonator for high-temperature wireless sensing applications in harsh environments

The primary objective of this work was the fabrication and testing of a wireless LC resonator based on micro-patterned electroceramic materials for the monitoring of high-temperature systems. The twodimensional planar LC resonator sensors were designed and simulated using ANSYS Maxwell software, and these sensors were then fabricated from electrically conductive La 2 NiO 4 /Al 2 O 3 particulate inks. Initially, the phases of La 2 NiO 4 /Al 2 O 3 composite were evaluated by XRD. The patterning and deposition of the ink were completed using a novel micro-casting process onto Al 2 O 3 ceramic substrates, and the final pattern was bonded onto the substrate at 1200 °C for 2 h. The features and the reliability were analyzed by SEM microscopy. The frequency shift with respect to temperature was measured, which is directly related to changes in the sensor’s dielectric permittivity and pattern dimensions. The sensors were characterized at 500 °C–1000 °C in an ambient atmosphere with an RF signal ranging from 10–80 MHz at 175 kHz·s –1 sweep rate. The sensors showed a sensitivity of ~350 kHz °C –1 from 500 °C–1000 °C. Here, a new robust and adaptive signal processing approach was introduced to increase the degree of freedom for analyzing wireless sensors.

42 ENGINEERING↗

DOE OSTI2021

A Targeted Sequencing Assay for Serotyping Escherichia coli Using AgriSeq Technology

The gold standard method for serotyping Escherichia coli has relied on antisera-based typing of the O- and H-antigens, which is labor intensive and often unreliable. In the post-genomic era, sequence-based assays are potentially faster to provide results, could combine O-serogrouping and H-typing in a single test, and could simultaneously screen for the presence of other genetic markers of interest such as virulence factors. Whole genome sequencing is one approach; however, this method has limited multiplexing capabilities, and only a small fraction of the sequence is informative for subtyping or identifying virulence potential. A targeted, sequence-based assay and accompanying software for data analysis would be a great improvement over the currently available methods for serotyping. The purpose of this study was to develop a high-throughput, molecular method for serotyping E. coli by sequencing the genes that are required for production of O- and H-antigens, as well as to develop software for data analysis and serotype identification. To expand the utility of the assay, targets for the virulence factors, Shiga toxins ( stx 1 , and stx 2 ) and intimin ( eae ) were included. To validate the assay, genomic DNA was extracted from O-serogroup and H-type standard strains and from Shiga toxin-producing E. coli , the targeted regions were amplified, and then sequencing libraries were prepared from the amplified products followed by sequencing of the libraries on the Ion S5™ sequencer. The resulting sequence files were analyzed via the SeroType Caller™ software for identification of O-serogroup, H-type, and presence of stx 1 , stx 2 , and eae . We successfully identified 169 O-serogroups and 41 H-types. The assay also routinely detected the presence of stx 1a,c,d (3 of 3 strains), stx 2c−e,g (8 of 8 strains), stx 2f (1 strain), and eae (6 of 6 strains). Taken together, the high-throughput, sequence-based method presented here is a reliable alternative to antisera-based serotyping methods for E. coli .

Elder, Jacob R.↗