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At least 1,027 records · Page 57

MO-G-304-02: Knowledge Based DVH Prediction Using a Geometric Dose Transform

Purpose: To demonstrate a novel method for predicting patient dose-volume histograms (DVHs) using a prior database of optimized radiotherapy treatment plans. Such predicted DVHs could be useful for automating treatment planning. Methods: Our initial demonstration utilized a database of 100 prostate intensity-modulated radiotherapy (IMRT) data-sets. Each data-set contained a CT image with contours of the planning target volume (PTV), rectum, and bladder, the parameters of a clinically approved IMRT plan, and a corresponding simulated dose distribution. We applied a novel geometric transformation to remove the influence of the PTV size, shape, and location on the dose distribution. We termed the transformed distribution the geometrically normalized dose distribution (GNDD). This normalization transform was applied to 80 data-sets randomly selected from the database, and a population GNDD was computed as the average. Next, the population GNDD was mapped onto each of the remaining 20 patient datasets using the reverse of the geometric normalization transform, and predicted DVHs were calculated from the reverse transformed dose distributions (GNDD-DVHs). In addition, a state of the art machine learning based method from the literature was tested for comparison. Results: DVH prediction accuracy was quantified by calculating the relative root mean squared error (rRMSE) on predicted DVHs for the 20 test patients using their known DVHs. For bladder, rectum, and PTV average rRMSEs for the GNDD method were 9.7 ± 4.2%, 13.9 ± 6.0%, and 2.3 ± 0.5% respectively. Prediction results using GNDD were roughly equivalent to that from the machine learning method. Conclusion: We developed a new method for predicting DVH curves from a database of prior patient plans. We demonstrated that our simple approach achieves accuracy comparable to a method using a complicated machine learning based approach.

60 APPLIED LIFE SCIENCES↗

Lean Miller Cycle System Development for Light-Duty Vehicles (Final Report)

This report summarizes activities conducted in support of the project “Lean Miller Cycle System Development for Light-Duty Vehicles” under Cooperative Agreement Number DE-EE0006853. In order to accomplish the government objective of achieving breakthrough thermal efficiencies while meeting U.S. EPA emission standards, this project focused on combining two enabling technologies in a gasoline engine: lean combustion and “Miller Cycle.” Lean combustion is thermodynamically more efficient than stoichiometric combustion but requires a more complex exhaust aftertreatment system compared to a traditional three-way catalyst system. The “Miller Cycle” concept increases expansion of combustion gases to extract additional work, reduces pumping losses, and increases efficiency. The objective of the project was to research, develop, and demonstrate the new Lean Miller Cycle (LMC) combustion concept to achieve a 35% improvement in fuel economy over a 2010 production baseline vehicle. The baseline vehicle chosen was a Chevrolet Impala equipped with a 3.5L V6 port-fuel injected naturally-aspirated engine, a four-speed automatic transmission with a peak-power and -torque of 157 kW and 290 N-m respectively. The enabling technologies were developed and demonstrated on a single cylinder engine and then integrated into a multicylinder engine and aftertreatment system. Along with achieving the efficiency targets, the downsized boosted LMC engine system was projected to achieve a peak-power and –torque of 172 kW at 354 Nm respectively exceeding the baseline engine performance. The multicylinder engine was optimized and calibrated over a set of steady-state operating points on an engine dynamometer. The target of the project was a 35% improvement in combined city/highway fuel economy at SULEV30 tailpipe emissions over the baseline vehicle. The project achieved a projected 42.4% from the vehicle drive cycle analysis assuming no penalty for management of the lean-aftertreatment system. This penalty was projected to fall within the fuel economy margin achieved and include control and calibration compromises for catalyst heating, NH3 formation for lean-NOx SCR and drive quality. A final vehicle demonstration was planned where emissions, drivability and performance were to be confirmed. Four decision gates were set up annually with deliverables to assess progress and determine whether status to deliverables warranted project continuation through the final vehicle demonstration. The project was closed in June 2019 at the end of budget period three after not passing the third decision gate due to projected system costs prohibiting economic feasibility in the light-duty vehicle industry landscape. However, the project’s efficiency targets were achieved by validation through steady-state dynamometer testing of the multicylinder engine.

33 ADVANCED PROPULSION SYSTEMS↗

The development of a multi-target compiler-writing system for flight software development

A wide variety of systems designed to assist the user in the task of writing compilers has been developed. A survey of these systems reveals that none is entirely appropriate to the purposes of the MUST project, which involves the compilation of one or at most a small set of higher-order languages to a wide variety of target machines offering little or no software support. This requirement dictates that any compiler writing system employed must provide maximal support in the areas of semantics specification and code generation, the areas in which existing compiler writing systems as well as theoretical underpinnings are weakest. This paper describes an ongoing research and development effort to create a compiler writing system which will overcome these difficulties, thus providing a software system which makes possible the fast, trouble-free creation of reliable compilers for a wide variety of target computers.

Feyock, S.↗

Transforming New Multifamily Construction to Zero: Strategies for Implementing Energy Targets and Design Pathways: Preprint

Creating zero energy (ZE) mid- to high-rise multifamily buildings represent significant challenges in the design world. Tenants often take responsibility for some of the utilities and are responsible for consumption of some of the largest end uses: hot water and plug loads. Furthermore, designers can experience risk in creating new sets of details and recommending new strategies to reach aggressive EUI targets. To assist in a more streamlined and successful design approach to ZE multifamily buildings, five major professional societies and experts from the multifamily space created a Zero Energy Advanced Energy Design Guide (AEDG) for multifamily buildings based on data driven results coupled with actual design experiences and case studies. Pathways to achieve ZE design were established including whole building energy use intensity targets coupled with details on how to achieve success in implementing individual efficiency measures. The guidance strives to overcome design barriers and this paper provides an overview of the recommended process to achieve ZE or ZE-ready status, along with details on selecting energy targets, and strategy pathways to achieve the targets.

advanced energy design guide↗

SU-E-J-231: Comparison of 3D Angiogram and MRI in Delineating the AVM Target for Frameless Stereotactic Radiosurgery

Purpose: Stereotactic radiation therapy (SRT) provides an excellent alternative to embolization and surgical excision for the management of appropriately selected cerebral arteriovenous malformations (AVMs). The currently accepted standard for delineating AVMs is planar digital subtraction angiography (DSA). DSA can be used to acquire a 3D data set that preserves osseous structures (3D-DA) at the time of the angiography for SRT planning. Magnetic resonance imaging (MRI) provides an alternative noninvasive method of visualizing the AVM nidus with comparable spatial resolution. We utilized 3D-DA and T1 post-contrast MRI data to evaluate the differences in SRT target volumes. Methods: Four patients underwent 3D-DA and high-resolution MRI. 3D T1 post-contrast images were obtained in all three reconstruction planes. A planning CT was fused with MRI and 3D-DA data sets. The AVMs were contoured utilizing one of the image sets at a time. Target volume, centroid, and maximum and minimum dimensions were analyzed for each patient. Results: Targets delineated using post-contrast MRI demonstrated a larger mean volume. AVMs >2 cc were found to have a larger difference between MRI and 3D-DA volumes. Larger AVMs also demonstrated a smaller relative uncertainty in contour centroid position (1 mm). AVM targets <2 cc had smaller absolute differences in volume, but larger differences in contour centroid position (2.5 mm). MRI targets demonstrated a more irregular shape compared to 3D-DA targets. Conclusions: Our preliminary data supports the use of MRI alone to delineate AVM targets >2 cc. The greater centroid stability for AVMs >2 cc ensures accurate target localization during image fusion. The larger MRI target volumes did not result in prohibitively greater volumes of normal brain tissue receiving the prescription dose. The larger centroid instability for AVMs <2 cc precludes the use of MRI alone for target delineation. We recommend incorporating a 3D-DA for these patients.

60 APPLIED LIFE SCIENCES↗

Fluctuation localization imaging-based fluorescence in situ hybridization (fliFISH) for accurate detection and counting of RNA copies in single cells

Here, quantitative gene expression analysis in intact single cells can be achieved using single molecule-based fluorescence in situ hybridization (smFISH). This approach relies on fluorescence intensity to distinguish between true signals, emitted from an RNA copy hybridized with multiple oligonucleotide probes, and background noise. Thus, the precision in smFISH is often compromised by partial or nonspecific probe binding and tissue autofluorescence, especially when only a small number of probes can be fitted to the target transcript. Here we provide an accurate approach for setting quantitative thresholds between true and false signals, which relies on on-off duty cycles of photoswitchable dyes. This fluctuation localization imaging-based FISH (fliFISH) uses on-time fractions (measured over a series of exposures) collected from transcripts bound to as low as 8 probes, which are distinct from on-time fractions collected from nonspecifically bound probes or autofluorescence. Using multicolor fliFISH, we identified radial gene expression patterns in mouse pancreatic islets for insulin, the transcription factor, NKX2-2 and their ratio ( Nkx2 - 2/Ins2 ). These radial patterns, showing higher values in β cells at the islet core and lower values in peripheral cells, were lost in diabetic mouse islets. In summary, fliFISH provides an accurate, quantitative approach for detecting and counting true RNA copies and rejecting false signals by their distinct on-time fractions, laying the foundation for reliable single-cell transcriptomics.

59 BASIC BIOLOGICAL SCIENCES↗

Global seismic attenuation imaging using full-waveform inversion: a comparative assessment of different choices of misfit functionals

We present the results of synthetic tests that aim at evaluating the relative performance of three different definitions of misfit functionals in the context of 3-D imaging of shear wave attenuation in the earth’s upper mantle at the global scale, using long-period full-waveform data. The synthetic tests are conducted with simple hypothetical upper-mantle models that contain Q μ anomalies centred at different depths and locations, with or without additional seismic velocity anomalies. To build synthetic waveform data sets, we performed simulations of 50 events in the hypothetical (target) models, using the spectral element method, filtered in the period range 60–400 s. The selected events are chosen among 273 events used in the development of radially anisotropic model SEMUCB-WM1 and recorded at 495 stations worldwide. The synthetic Z-component waveforms correspond to paths and time intervals (fundamental mode and overtone Rayleigh waves) that exist in the real waveform data set. The inversions for shear attenuation structure are carried out using a Gauss–Newton optimization scheme in which the gradient and Hessian are computed using normal mode perturbation theory. The three different misfit functionals considered are based on time domain waveform (WF) and waveform envelope (E-WF) differences, as well as spectral amplitude ratios (SA), between observed and predicted waveforms. We evaluate the performance of the three misfit functional definitions in the presence of seismic noise and unresolved S-wave velocity heterogeneity and discuss the relative importance of physical dispersion effects due to 3-D Q μ structure. We observed that the performance of WF is poorer than the other two misfit functionals in recovering attenuation structure, unless anelastic dispersion effects are taken into account in the calculation of partial derivatives. WF also turns out to be more sensitive to seismic noise than E-WF and SA. Overall, SA performs best for attenuation imaging. Our tests show that it is important to account for 3-D elastic effects (focusing) before inverting for Q μ . Additionally, we show that including high signal-to-noise ratio overtone wave packets is necessary to resolve Q μ structure at depths greater than 250 km.

58 GEOSCIENCES↗

CDTI target selection criteria

A Cockpit Display of Traffic Information (CDTI) is a cockpit instrument which provides information to the aircrew on the relative location of aircraft traffic in the vicinity of their aircraft (township). In addition, the CDTI may provide information to assist in navigation and in aircraft control. It is usually anticipated that the CDTI will be integrated with a horizontal situation indicator used for navigational purposes and/or with a weather radar display. In this study, several sets of aircraft traffic data are analyzed to determine statistics on the number of targets that will be displayed on a CDTI using various target selection criteria. Traffic data were obtained from an Atlanta Terminal Area Simulation and from radar tapes recorded at the Atlanta and Miami terminal areas. Results are given in the form of plots showing the average percentage of time (or probability) that an aircraft equipped with a CDTI would observe from 0 to 10 other aircraft on the display for range settings on the CDTI up to 30 n. mi. and using various target discrimination techniques.

Britt, C. L.↗

Numerical and Experimental Study of an Aircraft Igniter Plasma Jet Discharge

The spark discharge of an aircraft plasma jet igniter is studied using high-fidelity numerical simulations and X-ray radiography measurements. The target problem here features the thermal expansion of hot gas introduced by the electric spark within a confined igniter cavity, which eventually evolves into a pulsed jet of a high-temperature kernel. A comprehensive set of models adapted from existing strategies for internal combustion engine spark plug discharge is extended to the target problem, including the modeling of energy deposition, plasma reactions, thermodynamic properties, and heat losses. A series of validation and parameter studies are performed and presented. The kernel size is found to be sensitive to heat losses arising from radiation and hot gas remained within the discharge cavity, rather than heat conduction to the wall in the discharge cavity. Depending on the enforced shape of the post-breakdown electric arc, the spark kernel can be off-centered, tilted, and considerably asymmetric. These features have been previously not considered when studying such igniter configurations and may have a first-order impact on the ignition process. Provided a proper setup of the heat loss models and electric arc shape, the numerical results are quantitatively comparable to the experimental results in terms of the kernel size, shape, and velocity throughout different stages after the spark discharge.

Tang, Yihao↗

Effect of Acuros XB algorithm on monitor units for stereotactic body radiotherapy planning of lung cancer

Stereotactic body radiotherapy (SBRT) is a curative regimen that uses hypofractionated radiation-absorbed dose to achieve a high degree of local control in early stage non–small cell lung cancer (NSCLC). In the presence of heterogeneities, the dose calculation for the lungs becomes challenging. We have evaluated the dosimetric effect of the recently introduced advanced dose-calculation algorithm, Acuros XB (AXB), for SBRT of NSCLC. A total of 97 patients with early-stage lung cancer who underwent SBRT at our cancer center during last 4 years were included. Initial clinical plans were created in Aria Eclipse version 8.9 or prior, using 6 to 10 fields with 6-MV beams, and dose was calculated using the anisotropic analytic algorithm (AAA) as implemented in Eclipse treatment planning system. The clinical plans were recalculated in Aria Eclipse 11.0.21 using both AAA and AXB algorithms. Both sets of plans were normalized to the same prescription point at the center of mass of the target. A secondary monitor unit (MU) calculation was performed using commercial program RadCalc for all of the fields. For the planning target volumes ranging from 19 to 375 cm{sup 3}, a comparison of MUs was performed for both set of algorithms on field and plan basis. In total, variation of MUs for 677 treatment fields was investigated in terms of equivalent depth and the equivalent square of the field. Overall, MUs required by AXB to deliver the prescribed dose are on an average 2% higher than AAA. Using a 2-tailed paired t-test, the MUs from the 2 algorithms were found to be significantly different (p < 0.001). The secondary independent MU calculator RadCalc underestimates the required MUs (on an average by 4% to 5%) in the lung relative to either of the 2 dose algorithms.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Physics of the thermal quench in MST tokamak plasmas (Final Technical Report)

This project at the University of Wisconsin-Madison targeted measurements in tokamak plasmas in the Madison Symmetric Torus (MST) to help elucidate the physics of the tokamak disruption. We intended to focus on the thermal quench, during which energy is lost from the plasma in a very short time. Understanding and ultimately mitigating the thermal quench are among the highest priority research thrusts for ITER, a large international fusion experiment presently under construction. The measurements in MST exploited an advanced set of diagnostics for internal measurements with high time resolution, targeting linear and nonlinear magnetohydrodynamic (MHD) activity as well as the electron temperature and density profiles. We also exploited other features of the MST device, including very flexible power supplies for the toroidal magnetic field and toroidal plasma current that are capable of producing almost arbitrary waveforms. While the work funded by this project was purely experimental, we continued and expanded an existing collaboration with UW-Madison experts in nonlinear MHD computational modeling of tokamak plasmas. That modeling incorporated realistic, experimentally measured parameters. The results of the modeling were anticipated to deepen considerably our understanding of the experimental measurements, and in turn, the experimental measurements were anticipated to help validate the modeling results. The science of transients such as disruptions is one of the highest priority research areas in the U.S. and international fusion programs. The work carried out in this project was targeted to help advance the science of tokamak disruptions which will in turn contribute to the success of ITER.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Optimal conditions for shock ignition of scaled cryogenic deuterium-tritium targets

Within the framework of the shock-ignition (SI) scheme, ignition conditions are reached following the separation of the compression and heating phases. First, the shell is compressed at a sub-ignition implosion velocity; then an intense laser spike is launched at the end of the main drive, leading to the propagation of a strong shock through the precompressed fuel. The minimal laser energy required for ignition of scaled deuterium-tritium (DT) targets is assessed by calculations. A semi-empiric model describing the ignitor shock generation and propagation in the fuel assembly is defined. The minimal power needed in the laser spike pulse to achieve ignition is derived from the hydrodynamic model. Optimal conditions for ignition of scaled targets are explored in terms of laser intensity, shell-implosion velocity, and target scale range for the SI process. Curves of minimal laser requirements for ignition are plotted in the energy-power diagram. The most economic and reliable conditions for ignition of a millimeter DT target are observed in the 240- to 320-km/s implosion velocity range and for the peak laser intensity ranging from {approx}2 Multiplication-Sign 10{sup 15} W/cm{sup 2} up to 5 Multiplication-Sign 10{sup 15} W/cm{sup 2}. These optimal conditions correspond to shock-ignited targets for a laser energy of {approx}250 kJ and a laser power of 100 to 200 TW. Large, self-ignited targets are particularly attractive by offering ignition at a lower implosion velocity and a reduced laser intensity than for conventional ignition. The SI scheme allows for the compression and heating phases of the high power laser energy research facility target to be performed at a peak laser intensity below 10{sup 16} W/cm{sup 2}. A better control of parametric and hydrodynamic instabilities within the SI scheme sets it as an optimal and reliable approach to attain ignition of large targets.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Nuclear Structure Studies in the 132 Sn Region: Safe Coulex with Carbon Targets

The collective and single-particle structure of nuclei in the 132 Sn region was recently studied by Coulomb excitation and heavy-ion induced transfer reactions using carbon, beryllium, and titanium targets. In particular, Coulomb excitation was used determine a complete set of electromagnetic moments for the first 2 + states and one-neutron transfer was used to probe the purity and evolution of single-neutron states. These recent experiments were conducted at the Holifield Radioactive Ion Beam Facility at ORNL using a CsI-HPGe detector array (BareBall- CLARION) to detect scattered particles and emitted gamma rays from the in-beam reactions. A Bragg-curve detector was used to measure the energy loss of the various beams through the targets and to measure the radioactive beam compositions. A sample of the Coulomb excitation results is presented here with an emphasis placed on 116 Sn. In particular, the safe Coulex criterion for carbon targets will be analyzed and discussed.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

SBbadger: biochemical reaction networks with definable degree distributions

Abstract Motivation An essential step in developing computational tools for the inference, optimization and simulation of biochemical reaction networks is gauging tool performance against earlier efforts using an appropriate set of benchmarks. General strategies for the assembly of benchmark models include collection from the literature, creation via subnetwork extraction and de novo generation. However, with respect to biochemical reaction networks, these approaches and their associated tools are either poorly suited to generate models that reflect the wide range of properties found in natural biochemical networks or to do so in numbers that enable rigorous statistical analysis. Results In this work, we present SBbadger, a python-based software tool for the generation of synthetic biochemical reaction or metabolic networks with user-defined degree distributions, multiple available kinetic formalisms and a host of other definable properties. SBbadger thus enables the creation of benchmark model sets that reflect properties of biological systems and generate the kinetics and model structures typically targeted by computational analysis and inference software. Here, we detail the computational and algorithmic workflow of SBbadger, demonstrate its performance under various settings, provide sample outputs and compare it to currently available biochemical reaction network generation software. Availability and implementation SBbadger is implemented in Python and is freely available at https://github.com/sys-bio/SBbadger and via PyPI at https://pypi.org/project/SBbadger/. Documentation can be found at https://SBbadger.readthedocs.io. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗

Hardware-Conscious Optimization of the Quantum Toffoli Gate

While quantum computing holds great potential in combinatorial optimization, electronic structure calculation, and number theory, the current era of quantum computing is limited by noisy hardware. Many quantum compilation approaches can mitigate the effects of imperfect hardware by optimizing quantum circuits for objectives such as critical path length. Few approaches consider quantum circuits in terms of the set of vendor-calibrated operations (i.e., native gates) available on target hardware. This manuscript expands the analytical and numerical approaches for optimizing quantum circuits at this abstraction level. We present a procedure for combining the strengths of analytical native gate-level optimization with numerical optimization. Although we focus on optimizing Toffoli gates on the IBMQ native gate set, the methods presented are generalizable to any gate and superconducting qubit architecture. Our optimized Toffoli gate implementation demonstrates an 18% reduction in infidelity compared with the canonical implementation as benchmarked on IBM Jakarta with quantum process tomography. Assuming the inclusion of multi-qubit cross-resonance (MCR) gates in the IBMQ native gate set, we produce Toffoli implementations with only six multi-qubit gates, a 25% reduction from the canonical eight multi-qubit implementations for linearly connected qubits.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Impact of primer dimers and self-amplifying hairpins on reverse transcription loop-mediated isothermal amplification detection of viral RNA

Loop-mediated isothermal amplification (LAMP), coupled with reverse transcription (RT), has become a popular technique for detection of viral RNA due to several desirable characteristics for use in point-of-care or low-resource settings. The large number of primers in LAMP (six per target) leads to an increased likelihood of primer-dimer interactions, and the inner primers in particular are prone to formation of stable hairpin structures due to their length (typically 40-45 bases). Although primer-dimers and hairpin structures are known features to avoid in nucleic acid amplification techniques, there is little quantitative information in literature regarding the impact of these structures on LAMP or RT-LAMP assays. In this study, we examine the impact of primer-dimers and hairpins on previously-published primer sets for dengue virus and yellow fever virus. We demonstrate that minor changes to the primers to eliminate amplifiable primer dimers and hairpins improves the performance of the assays when monitored in real time with intercalating dyes, and when monitoring a fluorescent endpoint using the QUASR technique. We also discuss the thermodynamic implications of these minor changes on the overall stability of amplifiable secondary structures, and we present a single thermodynamic parameter to predict the probability of non-specific amplification associated with LAMP primers.

59 BASIC BIOLOGICAL SCIENCES↗

Coupling of an atmospheric pressure microplasma ionization source with an Orbitrap Fusion Lumos Tribrid 1M mass analyzer for ultra-high resolution isotopic analysis of uranium

The coupling of a combined atomic and molecular (CAM) ionization source, the liquid sampling-atmospheric pressure glow discharge (LS-APGD) microplasma to an Orbitrap Fusion Lumos Tribrid 1M mass spectrometer is described as a significant step towards the elimination of isobaric interferences in elemental/isotopic mass spectrometry. The developed setup permits broadband, elemental mass spectra to be easily acquired at a mass resolution (m/Δm) of 500 000. A new ion source housing and integrated control system provide enhanced stability and sensitivity of the microplasma ion source in comparison to the previous designs. Detailed evaluation of the ion sampling parameters provided insight into differences with other Orbitrap platforms leading to a 5-fold increase in resolution in elemental/isotopic analysis. The roles of data acquisition/ion processing parameters were evaluated with regards to the precision and accuracy of 235 U/ 238 U isotope ratios. Significantly, the precision of those measurements improves as a function of pre-set mass resolution up to a value of 1 000 000, where a precision of 0.086% RSD is obtained for uranium concentrations of 100 ng mL− 1 . Analytical response curves (log–log), acquired for the two uranium isotopes at a resolution of 120 000 were linear (R 2 = 0.9969) over more than 5 orders of magnitude, with limits of detection of 1 pg mL −1 for U. Based on 60 μL injection volumes, this represents a mass of 70 fg 235 U. These figures of merit satisfy International Target Values (ITVs) for Measurement Uncertainties in Safeguarding Nuclear Materials set by the International Atomic Energy Agency (IAEA). Ultimately, and totally unique from beam-type instruments, the move to the higher-resolution Orbitrap platform provides all of the benefits of high mass resolution, with no penalties in sensitivity, precision, or dynamic range for uranium analysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗