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All sources NASA NTRS DOE OSTI

DOE OSTI2014

F3D Image Processing and Analysis for Many - and Multi-core Platforms

F3D is written in OpenCL, so it achieve[sic] platform-portable parallelism on modern mutli-core CPUs and many-core GPUs. The interface and mechanims to access F3D core are written in Java as a plugin for Fiji/ImageJ to deliver several key image-processing algorithms necessary to remove artifacts from micro-tomography data. The algorithms consist of data parallel aware filters that can efficiently utilizes[sic] resources and can work on out of core datasets and scale efficiently across multiple accelerators. Optimizing for data parallel filters, streaming out of core datasets, and efficient resource and memory and data managements over complex execution sequence of filters greatly expedites any scientific workflow with image processing requirements. F3D performs several different types of 3D image processing operations, such as non-linear filtering using bilateral filtering and/or median filtering and/or morphological operators (MM). F3D gray-level MM operators are one-pass constant time methods that can perform morphological transformations with a line-structuring element oriented in discrete directions. Additionally, MM operators can be applied to gray-scale images, and consist of two parts: (a) a reference shape or structuring element, which is translated over the image, and (b) a mechanism, or operation, that defines the comparisons to be performed between the image and the structuring element. This tool provides a critical component within many complex pipelines such as those for performing automated segmentation of image stacks. F3D is also called a "descendent" of Quant-CT, another software we developed in the past. These two modules are to be integrated in a next version. Further details were reported in: D.M. Ushizima, T. Perciano, H. Krishnan, B. Loring, H. Bale, D. Parkinson, and J. Sethian. Structure recognition from high-resolution images of ceramic composites. IEEE International Conference on Big Data, October 2014.

Source record↗

DOE OSTI2014

F3D Image Processing and Analysis for Many - and Multi-core Platforms

Source record↗

NASA NTRS2020

A Computer Program to Generate Tri-Truss Structures for On- and Off-Axis Telescope Dishes

The size of traditional space telescopes has been limited by the size of the launch vehicle shroud size. Designs of space telescopes with larger apertures and greater resolving power can be achieved with multiple launches incorporating modular elements and in-space assembly techniques. The modular elements of an in-space assembled telescope include segmented reflectors supported on an assembled truss structure. The modular truss structures are most commonly based on a tessellation of triangles across a reflector’s surface, and in some cases utilize deployable trusses to simplify in-space assembly. One design effort, the in-Space Assembled Telescope (iSAT), proposes the use of deployable “tri-truss” modules to form an off-set parabolic reflector. In support of the iSAT, a computer program was developed to tesselate tri-truss modules over a parabolic surface. Based on several user-defined variables, the program renders a tri-truss structure and generates a stereolithography file of the generated truss structure for three dimensional (3D) printing. In addition, due to the importance of packing efficiency for space launch, the program attempts to minimize unnecessary differences in strut lengths using a grade parameter based on previous work.

Structures↗

DOE OSTI2019

Ducting arrangement with injector assemblies arranged in an expanding cross-sectional area of a downstream combustion stage in a gas turbine engine

A ducting arrangement (10) in a combustion stage downstream of a main combustion stage of a gas turbine engine is provided. A duct (18) is fluidly coupled to receive a cross-flow of combustion gases from the main combustion stage. Duct (18) includes a duct segment (23) with an expanding cross-sectional area (24) where one or more injector assemblies (26) are disposed. Injector assembly (26) includes one or more reactant-guiding structures (27) arranged to deliver a flow of reactants into the downstream combustion stage to be mixed with the cross-flow of combustion gases. Disclosed injector assemblies are arranged in expanding cross-sectional area (24) to reduce total pressure loss while providing an effective level of mixing of the injected reactants with the passing cross-flow. Respective duct components or the entire ducting arrangement may be formed as a unitized structure, such as a single piece using a rapid manufacturing technology, such as 3D Printing/Additive Manufacturing (AM) technologies.

33 ADVANCED PROPULSION SYSTEMS↗

DOE OSTI2016

Multiscale Dynamics of Polymers in Particle-Rich Nanocomposites

In this paper we report on the dynamics of entangled polymers in polymer–nanoparticle composites (PNCs) with moderate and high particle loadings. Using composites comprised of poly(ethylene glycol) (PEG)-tethered silica (SiO 2 ) nanoparticles and poly(methyl methacrylate) (PMMA), we show by means of small-angle X-ray scattering (SAXS) analysis that the nanoparticles are uniformly dispersed over a range of particle concentrations. From oscillatory shear rheology measurements, we find that the time–temperature superposition (TTS) principle holds for these SiO 2 -PEG/PMMA PNCs up to a particle concentration Φ G ≈ 11% where the materials begin to exhibit soft glassy rheological properties. At particle concentrations below Φ G , we take advantage of TTS to create dynamic maps for PNCs that span time scales ranging from fast segmental motions to slow terminal relaxation of polymer chains. These maps reveal that at low Φ and depending on the host polymer (PMMA) molecular weight ( M w ), hairy nanoparticles may either speed up or slow down terminal relaxation of the host. In contrast, at high Φ, nanoparticles slow down polymer dynamics on intermediate and long time scales, irrespective of the host polymer M w . The slowdown coincides with particle concentrations at which the mean interparticle spacing lies below the equilibrium tube diameter of the entangled PMMA host and is thought to reflect the onset of confinement dynamics of polymer chains in PNCs. Studies of PNCs in the confinement regime reveal important analogies between glassy attributes of 3D-confined polymer chains in nanocomposites with those of polymer thin films supported on attractive substrates.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2015

Circuit model of the ITER-like antenna for JET and simulation of its control algorithms

The ITER-like Antenna (ILA) for JET [1] is a 2 toroidal by 2 poloidal array of Resonant Double Loops (RDL) featuring in-vessel matching capacitors feeding RF current straps in conjugate-T manner, a low impedance quarter-wave impedance transformer, a service stub allowing hydraulic actuator and water cooling services to reach the aforementioned capacitors and a 2nd stage phase-shifter-stub matching circuit allowing to correct/choose the conjugate-T working impedance. Toroidally adjacent RDLs are fed from a 3dB hybrid splitter. It has been operated at 33, 42 and 47MHz on plasma (2008-2009) while it presently estimated frequency range is from 29 to 49MHz. At the time of the design (2001-2004) as well as the experiments the circuit models of the ILA were quite basic. The ILA front face and strap array Topica model was relatively crude and failed to correctly represent the poloidal central septum, Faraday Screen attachment as well as the segmented antenna central septum limiter. The ILA matching capacitors, T-junction, Vacuum Transmission Line (VTL) and Service Stubs were represented by lumped circuit elements and simple transmission line models. The assessment of the ILA results carried out to decide on the repair of the ILA identified that achieving routine full array operation requires a better understanding of the RF circuit, a feedback control algorithm for the 2nd stage matching as well as tighter calibrations of RF measurements. The paper presents the progress in modelling of the ILA comprising a more detailed Topica model of the front face for various plasma Scrape Off Layer profiles, a comprehensive HFSS model of the matching capacitors including internal bellows and electrode cylinders, 3D-EM models of the VTL including vacuum ceramic window, Service stub, a transmission line model of the 2nd stage matching circuit and main transmission lines including the 3dB hybrid splitters. A time evolving simulation using the improved circuit model allowed to design and simulate the effectiveness of a feedback control algorithm for the 2nd stage matching and demonstrates the simultaneous matching and control of the 4 RDLs: 11 feedback loops control 21 actuators (8 capacitors, 4 phase shifters and 4 stubs for the 2nd stage matching, 4 main phase shifters controlling of the toroidal phasing and the electronically controlled phase between RF sources feeding top and bottom parts of the array and determines the poloidal phasing of the array which is solved explicitly at each time step) on (simulated) ELMy plasmas.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2025

SiC Receiver/Reactor by Additive Manufacturing for Concentrated Solar Thermocatalysis with Thermal Energy Storage (Final Technical Report - Public)

The direct use of solar thermal energy provides opportunities for low-cost heating sources for a variety of applications. Ultra-high temperatures around 1000°C are high value and highly useful for energy-demanding industries. Many materials cannot withstand these conditions. In the area of Sustainable Chemicals, further limitations on material stability exist. Combining state-of-the-art materials with new designs provides a promising pathway for harvesting solar thermal energy and performing high temperature chemical processes. However, conventional manufacturing limits the potential for design flexibility. In this project, Additive Manufacturing was combined with advanced materials and new chemical reactor designs. In addition, 24/7 energy is necessary for chemical processing, and designs for ultra-high temperature thermal storage were devised. Specifically, preliminary design of a novel solar thermal receiver was developed in this project and designed to work with thermocatalytic reactors for producing sustainable chemicals and fuels. An ultra-high temperature particle storage system and heat exchangers were proposed to transport ultra-hot air as thermal fluid for the system. On a broader scale, this system could be used to tap solar thermal energy for a centralized facility with capability of transferring that heat to various segments at a full range of temperatures to 1000°C. The project pushed the temperature boundaries past those in current use, and Additive Manufacturing was envisaged for fabricating the receiver to meet requirements of extreme environments. An extensive analysis of silicon carbide additive manufacturing was performed to compare the thermal and mechanical properties of complex geometries compared to conventional material and those manufactured via other methods. The Additive Manufacturing via Binder-Jet printing was optimized and characterized to provide high quality and reproducible components capable of withstanding the proposed extreme environments. The designs for the concentrating solar thermal cavity with ultra-hot air thermal fluid showed high performance in simulations, attributable to the complex optimized geometries of the 3D printed systems. The bright future of Additive Manufacturing with advanced materials developments should provide more options and even higher quality as the technology further develops. Current costs for Additive Manufacturing of advanced ceramics is relatively low, however post-processing of the materials for extreme environments is currently high. There is little industrial-scale infrastructure for these, but it is growing as niche applications become more mainstream. The results of the project can be translated into similar extreme environments for concentrating solar thermal energy as well as its integration with ultra-hot air thermal fluids. A number of industries that require ultra-high temperatures need to electrify or otherwise decarbonize for climate goals, and this project showed that theoretically there is a pathway to do so with direct concentrated solar thermal power.

10 SYNTHETIC FUELS↗

NASA NTRS2010

Software Development to Assist in the Processing and Analysis of Data Obtained Using Fiber Bragg Grating Interrogation Systems

A fiber Bragg grating is a portion of a core of a fiber optic stand that has been treated to affect the way light travels through the strand. Light within a certain narrow range of wavelengths will be reflected along the fiber by the grating, while light outside that range will pass through the grating mostly undisturbed. Since the range of wavelengths that can penetrate the grating depends on the grating itself as well as temperature and mechanical strain, fiber Bragg gratings can be used as temperature and strain sensors. This capability, along with the light-weight nature of the fiber optic strands in which the gratings reside, make fiber optic sensors an ideal candidate for flight testing and monitoring in which temperature and wing strain are factors. A team of NASA Dryden engineers has been working to advance the fiber optic sensor technology since the mid 1990 s. The team has been able to improve the dependability and sample rate of fiber optic sensor systems, making them more suitable for real-time wing shape and strain monitoring and capable of rivaling traditional strain gauge sensors in accuracy. The sensor system was recently tested on the Ikhana unmanned aircraft and will be used on the Global Observer unmanned aircraft. Since a fiber Bragg grating sensor can be placed every halfinch on each optic fiber, and since fibers of approximately 40 feet in length each are to be used on the Global Observer, each of these fibers will have approximately 1,000 sensors. A total of 32 fibers are to be placed on the Global Observer aircraft, to be sampled at a rate of about 50 Hz, meaning about 1.6 million data points will be taken every second. The fiber optic sensors system is capable of producing massive amounts of potentially useful data; however, methods to capture, record, and analyze all of this data in a way that makes the information useful to flight test engineers are currently limited. The purpose of this project is to research the availability of software capable of processing massive amounts of data in both real-time and post-flight settings, and to produce software segments that can be integrated to assist in the task as well. The selected software must be able to: (1) process massive amounts of data (up to 4GB) at a speed useful in a real-time settings (small fractions of a second); (2) process data in post-flight settings to allow test reproduction or further data analysis, inclusive; (3) produce, or make easier to produce, three-dimensional plots/graphs to make the data accessible to flight test engineers; and (4) be customized to allow users to use their own processing formulas or functions and display the data in formats they prefer. Several software programs were evaluated to determine their utility in completing the research objectives. These programs include: OriginLab, Graphis, 3D Grapher, Visualization Sciences Group (VSG) Avizo Wind, Interactive Analysis and Display System (IADS), SigmaPlot, and MATLAB.

Hicks, Rebecca↗

DOE OSTI2023

Multilevel atomic structural model for interstratified opal materials

The structure of opal has long fascinated scientists. It occurs in a number of structural states, ranging from amorphous to exhibiting features of stacking disorder. Opal-CT, where C and T signify cristobalite- and tridymite-like interstratification, represents an important link in the length scales between amorphous and crystalline states. However, details about local atomic (dis)order and arrangements extending to long-range stacking faults in opal polymorphs remain incompletely understood. Here, a multilevel modeling approach is reported that considers stacking states in correlation with the abundance of C and T segments as a high-level structural parameter (i.e. not each atom). Optimization accounting for inter-tetrahedral bond lengths and angles and the regularity of the silicate tetrahedra is included as lower levels of structural parameters. Together, a set of parameters with both coarse-grained and atomistic features for different levels of structural details is refined. Structural disorder at the ~10–100 Å distance scale is evaluated using experimental pair distribution function and diffraction datasets, comparing peak intensities, widths and asymmetry. Here this work presents a complete multilevel structural description of natural opal-CT and explains many of the unusual features observed in X-ray powder diffraction patterns. This modeling approach can be adopted generally for analyzing layered materials and their assembly into 3D structures.

36 MATERIALS SCIENCE↗

DOE OSTI2014

MO-G-BRE-04: Automatic Verification of Daily Treatment Deliveries and Generation of Daily Treatment Reports for a MR Image-Guided Treatment Machine

Purpose: Two aims of this work were to develop a method to automatically verify treatment delivery accuracy immediately after patient treatment and to develop a comprehensive daily treatment report to provide all required information for daily MR-IGRT review. Methods: After systematically analyzing the requirements for treatment delivery verification and understanding the available information from a novel MR-IGRT treatment machine, we designed a method to use 1) treatment plan files, 2) delivery log files, and 3) dosimetric calibration information to verify the accuracy and completeness of daily treatment deliveries. The method verifies the correctness of delivered treatment plans and beams, beam segments, and for each segment, the beam-on time and MLC leaf positions. Composite primary fluence maps are calculated from the MLC leaf positions and the beam-on time. Error statistics are calculated on the fluence difference maps between the plan and the delivery. We also designed the daily treatment delivery report by including all required information for MR-IGRT and physics weekly review - the plan and treatment fraction information, dose verification information, daily patient setup screen captures, and the treatment delivery verification results. Results: The parameters in the log files (e.g. MLC positions) were independently verified and deemed accurate and trustable. A computer program was developed to implement the automatic delivery verification and daily report generation. The program was tested and clinically commissioned with sufficient IMRT and 3D treatment delivery data. The final version has been integrated into a commercial MR-IGRT treatment delivery system. Conclusion: A method was developed to automatically verify MR-IGRT treatment deliveries and generate daily treatment reports. Already in clinical use since December 2013, the system is able to facilitate delivery error detection, and expedite physician daily IGRT review and physicist weekly chart review.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2026

Web-based Preprocessing and Visualization of 3D FIB Tomography Data for Nuclear Fuel Characterization

Three-dimensional (3D) focused ion beam (FIB) tomography enables reconstruction of internal nuclear fuel features that can't be fully evaluated through surface imaging alone. This capability supports characterization of fuel constituents and defects under thermal and irradiation conditions relevant to microreactor development. However, large tomography datasets can create data-handling, loading, and visualization challenges, especially when image-stack preparation and file conversion must be completed with separate tools. The Computational Ultraspatial Tomography Toolkit for High-Resolution Object Analysis Tools (CUTTRHOAT) is an open-source web application being developed to display FIB tomography datasets available through the Nuclear Research Data System (NRDS). The current alpha version requires prepared HDF5 datasets and has limited integrated data-preparation capabilities. This project improves CUTTHROAT by adding dataset-folder selection, automatic input detection, dataset scanning, missing-slice identification, blank-slice insertion, and image-stack-to-HDF5 conversion. Two applications will be compared: the baseline CUTTHROAT alpha workflow and the updated application containing the integrated data-handling and preprocessing functions. Evaluation will consider dataset detection accuracy, conversion success, loading time, rendering responsiveness, application stability, and user interaction. Preliminary results demonstrate successful loading of existing HDF5 files and converted image stacks, while testing also identified performance reductions caused by excessive blank-slice generation. The updated workflow reduces reliance on external preparation tools and supports more direct movement from image stacks to color-code 3D visualization. Future work includes refining missing-slice handling, integrating additional preprocessing functions, like a denoising feature, parsing TIFF metadata for automatic voxel scaling, and adding manual X, Y, and Z voxel-spacing inputs for PNG and JPEG.

36 - MATERIALS SCIENCE↗

NASA NTRS2005

NASA Tech Briefs, April 2005

Gas-Tolerant Device Senses Electrical Conductivity of Liquid Nanoactuators Based on Electrostatic Forces on Dielectrics Replaceable Microfluidic Cartridges for a PCR Biosensor CdZnTe Image Detectors for Hard-X-Ray Telescopes High-Aperture-Efficiency Horn Antenna Full-Circle Resolver-to-Linear-Analog Converter Continuous, Full-Circle Arctangent Circuit Advanced Three-Dimensional Display System Automatic Focus Adjustment of a Microscope Topics covered include: FastScript3D - A Companion to Java 3D; Generating Mosaics of Astronomical Images; Simulating Descent and Landing of a Spacecraft; Simulating Vibrations in a Complex Loaded Structure; Rover Sequencing and Visualization Program; Software Template for Instruction in Mathematics; Support for User Interfaces for Distributed Systems; Nanostructured MnO2-Based Cathodes for Li-Ion/Polymer Cells; Multi-Layer Laminated Thin Films for Inflatable Structures; Two-Step Laser Ranging for Precise Tracking of a Spacecraft; Growing Aligned Carbon Nanotubes for Interconnections in ICs; Multilayer Composite Pressure Vessels; Texturing Blood-Glucose-Monitoring Optics Using Oxygen Beams; Fault-Tolerant Heat Exchanger; Atomic Clock Based on Opto-Electronic Oscillator; Microfocus/Polycapillary-Optic Crystallographic X-Ray Sys; Depth-Penetrating Luminescence Thermography of Thermal- Barrier Coatings; One-Dimensional Photonic Crystal Superprisms; Measuring Low-Order Aberrations in a Segmented Telescope; Mapping From an Instrumented Glove to a Robot Hand; Application of the Hilbert-Huang Transform to Financial Data; Optimizing Parameters for Deep-Space Optical Communication; and Low-Shear Microencapsulation and Electrostatic Coating.

Source record↗

DOE OSTI2014

Motion as perturbation. II. Development of the method for dosimetric analysis of motion effects with fixed-gantry IMRT

Purpose: In this work, the feasibility of implementing a motion-perturbation approach to accurately estimate volumetric dose in the presence of organ motion—previously demonstrated for VMAT-–is studied for static gantry IMRT. The method's accuracy is improved for the voxels that have very low planned dose but acquire appreciable dose due to motion. The study describes the modified algorithm and its experimental validation and provides an example of a clinical application. Methods: A contoured region-of-interest is propagated according to the predefined motion kernel throughout time-resolved 4D phantom dose grids. This timed series of 3D dose grids is produced by the measurement-guided dose reconstruction algorithm, based on an irradiation of a staticARCCHECK (AC) helical dosimeter array (Sun Nuclear Corp., Melbourne, FL). Each moving voxel collects dose over the dynamic simulation. The difference in dose-to-moving voxel vs dose-to-static voxel in-phantom forms the basis of a motion perturbation correction that is applied to the corresponding voxel in the patient dataset. A new method to synchronize the accelerator and dosimeter clocks, applicable to fixed-gantry IMRT, was developed. Refinements to the algorithm account for the excursion of low dose voxels into high dose regions, causing appreciable dose increase due to motion (LDVE correction). For experimental validation, four plans using TG-119 structure sets and objectives were produced using segmented IMRT direct machine parameters optimization in Pinnacle treatment planning system (v. 9.6, Philips Radiation Oncology Systems, Fitchburg, WI). All beams were delivered with the gantry angle of 0°. Each beam was delivered three times: (1) to the static AC centered on the room lasers; (2) to a static phantom containing a MAPCHECK2 (MC2) planar diode array dosimeter (Sun Nuclear); and (3) to the moving MC2 phantom. The motion trajectory was an ellipse in the IEC XY plane, with 3 and 1.5 cm axes. The period was 5 s, with the resulting average motion speed of 1.45 cm/s. The motion-perturbed high resolution (2 mm voxel) volumetric dose grids on the MC2 phantom were generated for each beam. From each grid, a coronal dose plane at the detector level was extracted and compared to the corresponding moving MC2 measurement, using gamma analysis with both global (G) and local (L) dose-error normalization. Results: Using the TG-119 criteria of (3%G/3 mm), per beam average gamma analysis passing rates exceeded 95% in all cases. No individual beam had a passing rate below 91%. LDVE correction eliminated systematic disagreement patterns at the beams’ aperture edges. In a representative example, application of LDVE correction improved (2%L/2 mm) gamma analysis passing rate for an IMRT beam from 74% to 98%. Conclusions: The effect of motion on the moving region-of-interest IMRT dose can be estimated with a standard, static phantom QA measurement, provided the motion characteristics are independently known from 4D CT or otherwise. The motion-perturbed absolute dose estimates were validated by the direct planar diode array measurements, and were found to reliably agree with them in a homogeneous phantom.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

DOE OSTI2026

Particle trajectory representation learning with masked point modeling

Liquid argon time projection chambers (LArTPCs) offer millimeter-scale 3D images of particle trajectories, enabling precision studies of neutrino oscillation, detection of supernova and solar neutrinos, searches for exotic dark matter, and proton decay. Current approaches utilize supervised machine learning models, requiring extensive simulations of particle physics and detector response that can introduce bias. Self-supervised learning (SSL), a machine learning approach that learns useful representations of unlabeled data from the data itself, has significantly advanced how large datasets are utilized for representation learning; however, its potential for applications to sensory data in high precision particle physics experiments remains largely unexplored. We introduce the Point-based liquid argon masked autoencoder (PoLAr-MAE), a self-supervised framework that learns physically meaningful representations directly from unlabeled LArTPC images. PoLAr-MAE achieves remarkable data efficiency for a point-level segmentation task, outperforming fully supervised methods in low data regimes. Linear classifiers on model outputs demonstrate robust performance across multiple downstream tasks. Our results position sensor-level SSL as a practical foundation model strategy for LArTPCs.

Young, Samuel [Stanford Univ., CA (United States)]↗

DOE OSTI2013

Development and clinical evaluation of automatic fiducial detection for tumor tracking in cine megavoltage images during volumetric modulated arc therapy

Purpose: Real-time tracking of implanted fiducials in cine megavoltage (MV) imaging during volumetric modulated arc therapy (VMAT) delivery is complicated due to the inherent low contrast of MV images and potential blockage of dynamic leaves configurations. The purpose of this work is to develop a clinically practical autodetection algorithm for motion management during VMAT. Methods: The expected field-specific segments and the planned fiducial position from the Eclipse (Varian Medical Systems, Palo Alto, CA) treatment planning system were projected onto the MV images. The fiducials were enhanced by applying a Laplacian of Gaussian filter in the spatial domain for each image, with a blob-shaped object as the impulse response. The search of implanted fiducials was then performed on a region of interest centered on the projection of the fiducial when it was within an open field including the case when it was close to the field edge or partially occluded by the leaves. A universal template formula was proposed for template matching and normalized cross correlation was employed for its simplicity and computational efficiency. The search region for every image was adaptively updated through a prediction model that employed the 3D position of the fiducial estimated from the localized positions in previous images. This prediction model allowed the actual fiducial position to be tracked dynamically and was used to initialize the search region. The artifacts caused by electronic interference during the acquisition were effectively removed. A score map was computed by combining both morphological information and image intensity. The pixel location with the highest score was selected as the detected fiducial position. The sets of cine MV images taken during treatment were analyzed with in-house developed software written in MATLAB (The Mathworks, Inc., Natick, MA). Five prostate patients were analyzed to assess the algorithm performance by measuring their positioning accuracy during treatment. Results: The algorithm was able to accurately localize the fiducial position on MV images with success rates of more than 90% per case. The percentage of images in which each fiducial was localized in the studied cases varied between 23% and 65%, with at least one fiducial having been localized between 40% and 95% of the images. This depended mainly on the modulation of the plan and fiducial blockage. The prostate movement in the presented cases varied between 0.8 and 3.5 mm (mean values). The maximum displacement detected among all patients was of 5.7 mm. Conclusions: An algorithm for automatic detection of fiducial markers in cine MV images has been developed and tested with five clinical cases. Despite the challenges posed by complex beam aperture shapes, fiducial localization close to the field edge, partial occlusion of fiducials, fast leaf and gantry movement, and inherently low MV image quality, good localization results were achieved in patient images. This work provides a technique for enabling real-time accurate fiducial detection and tumor tracking during VMAT treatments without the use of extra imaging dose.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2016

3D Monte Carlo simulation of backscattered electron signal variation across pore-solid boundaries in cement-based materials

Three-dimensional (3D) Monte Carlo simulation was used to study the variation of backscattered electron (BSE) signal across pore-solid boundaries in cement-based materials in order to enhance quantitative analysis of pore structure. The effects of pore size, depth and boundary inclination angle were investigated. It is found that pores down to 1 nm can generate sufficient contrast to be detected. Visibility improves with larger pore size, smaller beam probe size and lower acceleration voltage. However, pixels in shallow pores or near pore boundaries display higher grey values (brightness) than expected due to sampling sub-surface or neighbouring solid material. Thus, cement-based materials may appear less porous or the pores appear smaller than they actually are in BSE images. Simulated BSE images were used to test the accuracy of the Overflow pore segmentation method. Results show the method is generally valid and gives low errors for pores that are 1 μm and greater.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Analysis of the molecular determinants for furin cleavage of the spike protein S1/S2 site in defined strains of the prototype coronavirus murine hepatitis virus (MHV)

We analyzed the spike protein S1/S2 cleavage of selected strains of a prototype coronavirus, mouse hepatitis virus (MHV) by the cellular protease furin, in order to understand the structural requirements underlying the sequence selectivity of the scissile segment. The probability of cleavage of selected MHV strains was first evaluated from furin cleavage scores predicted by the ProP computer software, and then cleavage was measured experimentally with a fluorogenic peptide cleavage assay consisting of S1/S2 peptide mimics and purified furin. We found that in vitro cleavability varied across MHV strains in line with predicted results—but with the notable exception of MHV-A59, which was not cleaved despite a high score predicted for its sequence. Using the known X-Ray structure of furin in complex with a substrate-like inhibitor as an initial structural reference, we carried out molecular dynamics (MD) simulations to learn the modes of binding of the peptides in the furin active site, and the suitability of the complex for initiation of the enzymatic cleavage. We identified the 3D structural requirements of the furin active site configuration that enable bound peptides to undergo cleavage, and the way in which the various strains tested experimentally are fulfilling these requirements. We find that despite some flexibility in the organization of the peptide bound to the active site of the enzyme, the presence of a histidine at P2 of MHV-A59 fails to properly orient the sidechain of His194 of the furin catalytic triad and therefore produces a distortion that renders the peptide/complex structural configuration in the active site incompatible with requirements for cleavage initiation. The Ser/Thr in P1 of MHV-2 and MHV-S has a similar effect of distorting the conformation of the furin active site residues produced by the elimination of the canonical salt-bridge formed by arginine in P1 position. This work informs a study of coronavirus infection and pathogenesis with respect to the function of the viral spike protein, and suggests an important process of viral adaptation and evolution within the spike S1/S2 structural loop.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2013

Generation of a suite of 3D computer-generated breast phantoms from a limited set of human subject data

Purpose: The authors previously reported on a three-dimensional computer-generated breast phantom, based on empirical human image data, including a realistic finite-element based compression model that was capable of simulating multimodality imaging data. The computerized breast phantoms are a hybrid of two phantom generation techniques, combining empirical breast CT (bCT) data with flexible computer graphics techniques. However, to date, these phantoms have been based on single human subjects. In this paper, the authors report on a new method to generate multiple phantoms, simulating additional subjects from the limited set of original dedicated breast CT data. The authors developed an image morphing technique to construct new phantoms by gradually transitioning between two human subject datasets, with the potential to generate hundreds of additional pseudoindependent phantoms from the limited bCT cases. The authors conducted a preliminary subjective assessment with a limited number of observers (n= 4) to illustrate how realistic the simulated images generated with the pseudoindependent phantoms appeared. Methods: Several mesh-based geometric transformations were developed to generate distorted breast datasets from the original human subject data. Segmented bCT data from two different human subjects were used as the 'base' and 'target' for morphing. Several combinations of transformations were applied to morph between the 'base' and 'target' datasets such as changing the breast shape, rotating the glandular data, and changing the distribution of the glandular tissue. Following the morphing, regions of skin and fat were assigned to the morphed dataset in order to appropriately assign mechanical properties during the compression simulation. The resulting morphed breast was compressed using a finite element algorithm and simulated mammograms were generated using techniques described previously. Sixty-two simulated mammograms, generated from morphing three human subject datasets, were used in a preliminary observer evaluation where four board certified breast radiologists with varying amounts of experience ranked the level of realism (from 1 ='fake' to 10 ='real') of the simulated images. Results: The morphing technique was able to successfully generate new and unique morphed datasets from the original human subject data. The radiologists evaluated the realism of simulated mammograms generated from the morphed and unmorphed human subject datasets and scored the realism with an average ranking of 5.87 {+-} 1.99, confirming that overall the phantom image datasets appeared more 'real' than 'fake.' Moreover, there was not a significant difference (p > 0.1) between the realism of the unmorphed datasets (6.0 {+-} 1.95) compared to the morphed datasets (5.86 {+-} 1.99). Three of the four observers had overall average rankings of 6.89 {+-} 0.89, 6.9 {+-} 1.24, 6.76 {+-} 1.22, whereas the fourth observer ranked them noticeably lower at 2.94 {+-} 0.7. Conclusions: This work presents a technique that can be used to generate a suite of realistic computerized breast phantoms from a limited number of human subjects. This suite of flexible breast phantoms can be used for multimodality imaging research to provide a known truth while concurrently producing realistic simulated imaging data.

60 APPLIED LIFE SCIENCES↗