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At least 1,531 records · Page 85

Fluorescent amplification for next generation sequencing (FA-NGS) library preparation

BACKGROUND: Next generation sequencing (NGS) has become a universal practice in modern molecular biology. As the throughput of sequencing experiments increases, the preparation of conventional multiplexed libraries becomes more labor intensive. Conventional library preparation typically requires quality control (QC) testing for individual libraries such as amplification success evaluation and quantification, none of which occur until the end of the library preparation process. RESULTS: In this study, we address the need for a more streamlined high-throughput NGS workflow by tethering real-time quantitative PCR (qPCR) to conventional workflows to save time and implement single tube and single reagent QC. We modified two distinct library preparation workflows by replacing PCR and quantification with qPCR using SYBR Green I. qPCR enabled individual library quantification for pooling in a single tube without the need for additional reagents. Additionally, a melting curve analysis was implemented as an intermediate QC test to confirm successful amplification. Sequencing analysis showed comparable percent reads for each indexed library, demonstrating that pooling calculations based on qPCR allow for an even representation of sequencing reads. To aid the modified workflow, a software toolkit was developed and used to generate pooling instructions and analyze qPCR and melting curve data. CONCLUSIONS: We successfully applied fluorescent amplification for next generation sequencing (FA-NGS) library preparation to both plasmids and bacterial genomes. As a result of using qPCR for quantification and proceeding directly to library pooling, the modified library preparation workflow has fewer overall steps. Therefore, we speculate that the FA-NGS workflow has less risk of user error. The melting curve analysis provides the necessary QC test to identify and troubleshoot library failures prior to sequencing. While this study demonstrates the value of FA-NGS for plasmid or gDNA libraries, we speculate that its versatility could lead to successful application across other library types.

59 BASIC BIOLOGICAL SCIENCES↗

Novel Modified Optical Fibers for High Temperature In-Situ Miniaturized Gas Sensors in Advanced Fossil Energy Systems

This report covers the technical progress on the program “Novel Modified Optical Fibers for High Temperature In-Situ Miniaturized Gas Sensors in Advanced Fossil Energy Systems”, funded by the National Energy Technology Laboratory of the U.S. Department of Energy, and performed by the Materials Science & Engineering and Electrical & Computer Engineering Departments at Virginia Tech, and summarizes technical progress from July 1st, 2005 –June 30th, 2014. The objective of this program was to develop novel fiber materials for high temperature gas sensors based on evanescent wave absorption in optical fibers. This project focused on two primary areas: the study of a sapphire photonic crystal fiber (SPCF) for operation at high temperature and long wavelengths, and a porous glass based fiber optic sensor for gas detection. The sapphire component of the project focused on the development of a sapphire photonic crystal fiber, modeling of the new structures, fabrication of the optimal structure, development of a long wavelength interrogation system, testing of the optical properties, and gas and temperature testing of the final sensor. The fabrication of the 6 rod SPCF gap bundle (diameter of 70μm) with a hollow core was successfully constructed with lead-in and lead-out 50μm diameter fiber along with transmission and gas detection testing. Testing of the sapphire photonic crystal fiber sensor capabilities with the developed long wavelength optical system showed the ability to detect CO 2 at or below 1000ppm at temperatures up to 1000°C. Work on the porous glass sensor focused on the development of a porous clad solid core optical fiber, a hollow core waveguide, gas detection capabilities at room and high temperature, simultaneous gas species detection, suitable joining technologies for the lead-in and lead-out fibers and the porous sensor, sensor system sensitivity improvement, signal processing improvement, relationship between pore structure and fiber geometry to optical properties, and the development of a sensor packaging prototype for laboratory testing. Analysis and experiments determined that a bonding technique using a CO 2 laser is the most suitable joining technique. Pore morphology alteration showed that transmission improved with increasing annealing temperature (producing smaller pores), while the sensor response time increased and the mechanical strength decreased with increasing annealing temperature. Software was developed for data acquisition and signal processing to collect and interpret spectral gas absorption data. Gas detection on porous glass sensors was completed and the detection limit was evaluated using acetylene and was found to be around 1- 200ppm. A complete materials package for porous glass sensors was manufactured for testing.

36 MATERIALS SCIENCE↗

Machine-Learning-aided Approach for Predicting the Thermal Expansion Behaviors in Advanced Test Reactor Capsules (NURETH-20 full paper)

Instrumented experiments at test reactors are essential to deploying new advanced reactor systems. Designing new experiments and generating data on specific conditions require both time and cost investment. A high-fidelity model of the experiment environment can be created using finite element analysis software to support the actual experiments, but computation time is still a concern in applying outcomes to real-time usage (e.g., a digital twin). This research proposes a machine-learning-aided approach to temperature and displacement predictions, based on the thickness of the outer gas gap on the experimental capsule used for the in-pile demonstration of a novel thermal conductivity probe in the Advanced Test Reactor. The capsule consisted of U10Zr fuel, a rodlet, sodium, and inner and outer capsules. There were gas gaps between the fuel and rodlet and between the inner and outer capsule. The learning data consisted of an experimental capsule’s radial distributions of temperature and displacement, as obtained from Abaqus and the physical features. For the first step, temperature was predicted using three positional parameters. Then the displacement was predicted using six different positional parameters. Each physical feature was normalized to be both nondimensional and standardized. The temperature and displacement predictions showed good agreement in all cases involving interpolation and extrapolation. Also, data similarity enhancement increased the similarity between training and target data increasing the predictive accuracy of machine-learning models. In some cases of extrapolation, the accuracy of the machine-learning model showed limited performance, but still data similarity enhancement improved the accuracy.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Comparative analysis of thermal management systems in electric vehicles at extreme weather conditions: Case study on Nissan Leaf 2019 Plus, Chevrolet Bolt 2020 and Tesla Model 3 2020

With the surge in electric vehicle (EV) adoption and the need for extended driving ranges, optimizing energy efficiency, particularly through thermal management, is critical, especially in extreme weather. Managing the substantial energy needed for cabin climate control and battery temperature regulation can increase energy demands by over 50 %, severely limiting range. This study conducts a comparative analysis of thermal management systems (TMS) in three popular EV vehicles, 2020 Chevrolet Bolt, 2019 Nissan Leaf Plus, and 2020 Tesla Model 3, evaluating their distinct TMS configurations and performance under varied weather conditions. Using both numerical simulations and experimental data collected on a controlled test bench at Argonne National Laboratory, we assess how TMS architecture and operational modes influence energy consumption and range. A comprehensive TMS model was developed, integrating cabin and battery thermal sub-models in the Autonomie software platform, to simulate temperature fluctuations and range impacts. Cabin climate was modeled using a mono-zonal approach, while battery cell temperature distribution was estimated through a 2D nodal structure. Each vehicle's distinct TMS setup was evaluated: the Chevrolet Bolt and Tesla Model 3 use a dual evaporator vapor compression cycle with a PTC heater for the cabin and a coolant loop for battery thermal management; the Nissan Leaf Plus employs a heat pump with a PTC heater for the cabin and air-cooling for the battery. Tests conducted at ambient temperatures of 35°C, 22°C, -7°C, and -18°C reveal significant differences in energy use and range reduction across both configurations and conditions. At 35°C, the Tesla Model 3, Chevrolet Bolt, and Nissan Leaf Plus have a range reduction of 8%, 9%, and 13%, respectively, due to air conditioning. In winter, heating technology is paramount; at -7°C, the Nissan Leaf's heat pump configuration achieves a lower range reduction (19.3%) compared to the Tesla and Chevrolet Bolt PTC heaters, which reduce range by 28.3% and 31%, respectively. Further, this study provides valuable insights for automotive engineers, EV technology researchers, and thermal management system designers aiming to enhance electric vehicle performance by understanding how different weather conditions and TMS architectures impact energy consumption and driving range.

33 ADVANCED PROPULSION SYSTEMS↗

Novel Low-Cost Approach for Acquiring High Resolution High-Speed Data

The Oak Ridge National Laboratory (ORNL) has developed and tested a novel system architecture for acquiring high fidelity high-speed data. The approach uses a low-cost consumer grade audio recording device coupled with computing technology running open-source software. The main advantage of this approach is perchannel cost; an instrument grade data acquisition system typically costs between $800 to $2,000 per channel compared to less than $50 per channel for these consumer grade components. Three systems, each featuring four channels, have been deployed for acquiring data from geophones and the electrical supply system that supports the High Flux Isotope Reactor (HFIR) and the Radiochemical Engineering Development Center (REDC) at ORNL. Each channel samples at 96 kHz at 24-bit resolution. The deployed systems operate continuously 24/7 and produce about 4 terabytes of data per month per system. This paper provides a technical overview of this approach, its implementation, and some preliminary results from qualification testing. This work was conducted in support of the Multi-Informatics for Nuclear Operations Scenarios (MINOS).

Wetherington Jr, G↗

SU-E-J-04: Integration of Interstitial High Intensity Therapeutic Ultrasound Applicators On a Clinical MRI-Guided High Intensity Focused Ultrasound Treatment Planning Software Platform

Purpose: Interstitial high intensity therapeutic ultrasound (HITU) applicators can be used to ablate tissue percutaneously, allowing for minimally-invasive treatment without ionizing radiation [1,2]. The purpose of this study was to evaluate the feasibility and usability of combining multielement interstitial HITU applicators with a clinical magnetic resonance imaging (MRI)-guided focused ultrasound software platform. Methods: The Sonalleve software platform (Philips Healthcare, Vantaa, Finland) combines anatomical MRI for target selection and multi-planar MRI thermometry to provide real-time temperature information. The MRI-compatible interstitial US applicators (Acoustic MedSystems, Savoy, IL, USA) had 1–4 cylindrical US elements, each 1 cm long with either 180° or 360° of active surface. Each applicator (4 Fr diameter, enclosed within a 13 Fr flexible catheter) was inserted into a tissue-mimicking agar-silica phantom. Degassed water was circulated around the transducers for cooling and coupling. Based on the location of the applicator, a virtual transducer overlay was added to the software to assist targeting and to allow automatic thermometry slice placement. The phantom was sonicated at 7 MHz for 5 minutes with 6–8 W of acoustic power for each element. MR thermometry data were collected during and after sonication. Results: Preliminary testing indicated that the applicator location could be identified in the planning images and the transducer locations predicted within 1 mm accuracy using the overlay. Ablation zones (thermal dose ≥ 240 CEM43) for 2 active, adjacent US elements ranged from 18 mm × 24 mm (width × length) to 25 mm × 25 mm for the 6 W and 8 W sonications, respectively. Conclusion: The combination of interstitial HITU applicators and this software platform holds promise for novel approaches in minimally-invasive MRI-guided therapy, especially when bony structures or air-filled cavities may preclude extracorporeal HIFU.[1] Diederich et al. IEEE UFFFC 46.5 (1999): 1218.[2] Chopra et al. PMB 50.21 (2005): 4957. Funding support was provided by Philips Healthcare and in-kind support from Acoustic MedSystems Inc. Ari Partanen is a paid employee of Philips Healthcare. Goutam Ghoshal and Everette Clif Burdette are paid employees of Acoustic MedSystems Inc.

60 APPLIED LIFE SCIENCES↗

Modeling fission product diffusion in TRISO fuel particles with BISON

Diffusion of fission products in intact TRISO particles depends on particle geometry, fission product source rates, time, temperature, and temperature-dependent diffusion coefficients. Simulating this diffusion process requires models for source rates and diffusion coefficients, plus computation of the temperature field if not prescribed. In addition, simulation quality depends on discretization of the geometry, appropriate time stepping, and the accuracy of the solution method. In this paper, we explore the simulation of fission product diffusion in TRISO fuel particles using the finite element method via the fuel performance code Bison. Recent material model development has occurred in Bison for each material present in tri-structural isotropic (TRISO) fuel particles: the buffer, inner pyrolytic carbon, silicon carbide, and outer pyrolytic carbon layers, as well as the fuel kernel. Also, new mesh generation and fission product release fraction capabilities have been added. Diffusion capabilities are shown to converge to the correct solution via formal verification tests. A large number of code benchmarking problems are also given, with good results, showing that Bison’s computed release fractions closely match those of other software tools. Finally, a significant validation effort is detailed in which fission product release, measured as part of the AGR-1 capsule experiments, is compared to Bison outputs. Bison outputs compare very well to the experimental data and to PARFUME results.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Harmonic Analysis of Electric Vehicle Loadings on Distribution System

With the increasing number of Electric Vehicles (EV) in this age, the power system is facing huge challenges of the high penetration rates of EVs charging stations. Therefore, a technical study of the impact of EVs charging on the distribution system is required. This paper is applied with PSCAD software and aimed to analyzing the Total Harmonic Distortion (THD) brought by Electric Vehicles charging stations in power systems. The paper starts with choosing IEEE34 node test feeder as the distribution system, building electric vehicle level two charging battery model and other four different testing scenarios: overhead transmission line and underground cable, industrial area, transformer and photovoltaic (PV) system. Then the statistic method is used to analyze different characteristics of THD in the plug-in transient, plug-out transient and steady-state charging conditions associated with these four scenarios are taken into the analysis. Finally, the factors influencing the THD in different scenarios are found. The analyzing results lead the conclusion of this paper to have constructive suggestions for both Electric Vehicle charging station construction and customers' charging habits.

Xu, Yijun A↗

MO-F-16A-05: Spot-Scanning Proton Therapy Patient-Specific Quality Assurance: Our Methodology and Results From 295 Treatment Plans

Purpose: To report on the patient-specific quality assurance (PSQA) results for 295 spot-scanning proton therapy treatment plans from the MD Anderson PTC-Houston. We show how the results differed by treatment site and how they were affected by the treatment plan optimization method and by a range shifter in the treatment field. We also discuss some causes of PSQA problems. Methods: The PSQA procedure, which is designed to verify both the accuracy of the treatment planning system's (Eclipse™ v8.9) dose calculations and the dose delivery of the Hitachi PROBEAT synchrotron, consists of (1) an end-to-end test in which the beam is delivered and measured at the prescribed gantry angle, and (2) additional dose plane measurements made from gantry angle 270°. HPlusQA™ software automatically performs the gamma analysis with criteria 3% (dose tolerance), 3 mm (distance-to-agreement, DTA) and 2%, 2 mm. Passing is defined as at least 90% of the pixels having a gamma score less than 1. Results: The PSQA gamma passing rate was 96.2% for 3%, 3 mm, and 85.3% for 2%, 2 mm. The rate depended on the treatment site. For example, the 3%, 3 mm passing rate was 95% for head and neck plans, vs 100% for prostate plans. The passing rates of multi- vs. single-field optimization plans did not significantly differ. However, the rate for fields with range shifters was 94.8±0.6%, vs 99.0±0.6% for those without (p = 0.002). Longitudinal dose gradients caused most of the low scores. Overestimation of the calculated dose proximal to the spread-out Bragg peak (SOBP) caused many of the others. Conclusion: The planned and delivered doses consistently agreed within tolerance levels. Minor dose modeling deficiencies remain proximal to the SOBP. The 3% dose tolerance, 3 mm DTA, with 90% pixel passing rate is a reasonable action level for 2D gamma comparisons.

60 APPLIED LIFE SCIENCES↗

SU-E-J-127: Implementation of An Online Replanning Tool for VMAT Using Flattening Filter-Free Beams

Purpose: This is to report the implementation of an online replanning tool based on segment aperture morphing (SAM) for VMAT with flattening filter free (FFF) beams. Methods: Previously reported SAM algorithm modified to accommodate VMAT with FFF beams was implemented in a tool that was interfaced with a treatment planning system (Monaco, Elekta). The tool allows (1) to output the beam parameters of the original VMAT plan from Monaco, and (2) to input the apertures generated from the SAM algorithm into Monaco for the dose calculation on daily CT/CBCT/MRI in the following steps:(1) Quickly generating target contour based on the image of the day, using an auto-segmentation tool (ADMIRE, Elekta) with manual editing if necessary; (2) Morphing apertures based on the SAM in the original VMAT plan to account for the interfractional change of the target from the planning to the daily images; (3) Calculating dose distribution for new apertures with the same numbers of MU as in the original plan; (4) Transferring the new plan into a record & verify system (MOSAIQ, Elekta); (5) Performing a pre-delivery QA based on software; (6) Delivering the adaptive plan for the fraction.This workflow was implemented on a 16-CPU (2.6 GHz dual-core) hardware with GPU and was tested for sample cases of prostate, pancreas and lung tumors. Results: The online replanning process can be completed within 10 minutes. The adaptive plans generally have improved the plan quality when compared to the IGRT repositioning plans. The adaptive plans with FFF beams have better normal tissue sparing as compared with those of FF beams. Conclusion: The online replanning tool based on SAM can quickly generate adaptive VMAT plans using FFF beams with improved plan quality than those from the IGRT repositioning plans based on daily CT/CBCT/MRI and can be used clinically. This research was supported by Elekta Inc. (Crawley, UK)

60 APPLIED LIFE SCIENCES↗

The Monte Carlo estimation of an effect of uncertainties in initial data on solving the transport equation by means of the MCU code

A new version of the tally module of the MCU software package is developed in which the approach for taking directly into account the uncertainty in initial data is implemented that is recommended by the international standard on estimating the uncertainty in results of measuring (ISO 13005). The new module makes it possible to evaluate the effect of uncertainty in initial data (caused by technological tolerances in fabrication of structural members of the core) on neutronic characteristics of the reactor. The developed software is adapted to parallel computing with the use of multiprocessor computers, which significantly reduces the computation time: the parallelization coefficient is almost equal to 1. Testing is performed by examples of solving the problem on criticality for the Godiva benchmark experiment and also for the infinite lattice of fuel assemblies of the VVER-440, VVER-1000, and VVER-1200. The results of calculations of the uncertainty in neutronic characteristics (effective multiplication factor, fission reaction rate), which is caused by uncertainties in initial data due to technological tolerances, are compared (in the first case) to the published results obtained using the precision MCNP5 code and (in the second case) to those obtained by means of the RADAR engineering program. A good agreement of results is achieved for all cases.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Quantified fracture (joint) clustering in Archean basement, Wyoming: application of the normalized correlation count method

We demonstrate statistically significant self-organized clustering over a length scale range from 10 -2 to 10 1 m for north-striking opening-mode fractures (joints) in Late Archean Mount Owen Quartz Monzonite. Spatial arrangement is a critical fracture network attribute that until recently has only been assessed qualitatively. We use normalized fracture intensity plots and the normalized correlation count (NCC) method of Marrett et al. to discriminate clustered from randomly placed or evenly spaced patterns quantitatively over a wide range of length scales and to test the statistical significance of the resulting patterns. We propose a procedure for interpreting cluster patterns on NCC diagrams generated by the freely available spatial analysis software CorrCount. Results illustrate the efficacy of NCC to measure fracture clustering patterns in texturally homogeneous Archean granitic rock in a setting distant (>2 km) from folds or faults. In their current geological setting, these regional fractures are conduits for water flow and their patterns – and the NCC approach to defining clusters – may be useful guides to the spatial arrangement style and clustering magnitude of conductive fractures in other, less accessible fractured basement rocks.

02 PETROLEUM↗

Oak Ridge Institutional Cluster Autotune Test Drive Report

The Oak Ridge Institutional Cluster (OIC) provides general purpose computational resources for the ORNL staff to run computation heavy jobs that are larger than desktop applications but do not quite require the scale and power of the Oak Ridge Leadership Computing Facility (OLCF). This report details the efforts made and conclusions derived in performing a short test drive of the cluster resources on Phase 5 of the OIC. EnergyPlus was used in the analysis as a candidate user program and the overall software environment was evaluated against anticipated challenges experienced with resources such as the shared memory-Nautilus (JICS) and Titan (OLCF). The OIC performed within reason and was found to be acceptable in the context of running EnergyPlus simulations. The number of cores per node and the availability of scratch space per node allow non-traditional desktop focused applications to leverage parallel ensemble execution. Although only individual runs of EnergyPlus were executed, the software environment on the OIC appeared suitable to run ensemble simulations with some modifications to the Autotune workflow. From a standpoint of general usability, the system supports common Linux libraries, compilers, standard job scheduling software (Torque/Moab), and the OpenMPI library (the only MPI library) for MPI communications. The file system is a Panasas file system which literature indicates to be an efficient file system.

99 GENERAL AND MISCELLANEOUS↗

Applying computationally efficient schemes for biogeochemical cycles (ACES4BGC)

NCAR contributed to the ACES4BGC project through software engineering work on aerosol model implementation, build system and script changes, coupler enhancements for biogeochemical tracers, improvements to the Community Land Model (CLM) code and testing infrastructure, and coordinating and integrating code changes from the various project participants.

54 ENVIRONMENTAL SCIENCES↗

Utility of Big Area Additive Manufacturing for Part Production for Low-Head Hydropower (CRADA NFE-18-07280 Final Report)

ORNL worked with Cadens, LLC, to explore the use of additive manufacturing (AM) to produce low-cost parts for low-head hydropower systems. Cadens develops design optimization software that leverages the flexible, low-cost, high-strength benefits of AM and composite materials. Cadens also operates a micro-hydro lab to test AM components in controlled environments. Until now, Cadens’ tests have been limited to components of a size that they can cost-effectively manufacture using local commercial systems. This project provided an opportunity for Cadens to scale up their modular AM hydropower parts using the capabilities of Big Area Additive Manufacturing (BAAM). This project was a success and resulted in the design and fabrication of several end-use parts of a hydropower system, using a Big Area Additive Manufacturing (BAAM) system. The fabricated parts include a draft tube, thimble, runner housing mold, PVC end fitting and two PVC pipe supports. In addition, a runner system was fabricated using fused deposition modeling on a 3D Platform Workbench 400 Series System.

13 HYDRO ENERGY↗

Hydrodynamic Analysis and Optimization of Aquantis Marine Turbine: Cooperative Research and Development (Final Report)

The primary aim of this proposal is to improve the accurate prediction of hydrodynamic performance and dynamic load responses of the AQ10 floating axial-flow tidal turbine with a tri-cat mooring configuration. The validation of reduced-order modeling approaches with high-fidelity model will be implemented. Additionally, the frequency response domain, Response Amplitude Floating Wind (RAFT) toolbox plus an optimizer expanded for marine hydrokinetic turbines under the Submarine Hydrokinetic And Riverine Kilo-megawatt. Systems (SHARKS) program will be used for designing and exploring different key design parameters (platform dimension, mooring layout and its parameters) of next marine hydrokinetic (MHK) turbine generation.

16 TIDAL AND WAVE POWER↗

Large Load Impacts to Distribution System Hosting Capacity

This work examined the impact of large loads on utility distribution system models using the Sandia-developed open-source software DREAMS. It was shown that hosting capacity varies with location and changes after any asset is added to, or removed from, a system. Despite the tested models having similar rated voltages and other characteristics, their thermal and voltage constrained hosting capacity varied over 2 MW. The addition of a 3-phase balanced constant power large load with power factor of 1.0 exhibited non-linear reductions to all voltage constrained hosting capacities. The reductions to thermal constrained hosting capacity from a load with similar characteristics was more linear, related to the size of the added load, and did not impact all model buses. Co-located capacitors were shown to accommodate demand that was beyond the baseline voltage constrained hosting capacity limits, however, the costs and benefits from this approach were found to not be 1:1 and required additional available thermal capacity.

24 POWER TRANSMISSION AND DISTRIBUTION↗