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SU-F-I-03: Correction of Intra-Fractional Set-Up Errors and Target Coverage Based On Cone-Beam Computed Tomography for Cervical Cancer Patients

Purpose: The purpose of this study is to investigate the patient set-up error and interfraction target coverage in cervical cancer using image-guided adaptive radiotherapy (IGART) with cone-beam computed tomography (CBCT). Methods: Twenty cervical cancer patients undergoing intensity modulated radiotherapy (IMRT) were randomly selected. All patients were matched to the isocenter using laser with the skin markers. Three dimensional CBCT projections were acquired by the Varian Truebeam treatment system. Set-up errors were evaluated by radiation oncologists, after CBCT correction. The clinical target volume (CTV) was delineated on each CBCT, and the planning target volume (PTV) coverage of each CBCT-CTVs was analyzed. Results: A total of 152 CBCT scans were acquired from twenty cervical cancer patients, the mean set-up errors in the longitudinal, vertical, and lateral direction were 3.57, 2.74 and 2.5mm respectively, without CBCT corrections. After corrections, these were decreased to 1.83, 1.44 and 0.97mm. For the target coverage, CBCT-CTV coverage without CBCT correction was 94% (143/152), and 98% (149/152) with correction. Conclusion: Use of CBCT verfication to measure patient setup errors could be applied to improve the treatment accuracy. In addition, the set-up error corrections significantly improve the CTV coverage for cervical cancer patients.

60 APPLIED LIFE SCIENCES↗

Code Coverage Status of the ARC code GAMSRC

The Argonne Reactor Code (ARC) software system supports users in their fast reactor design goals by providing neutronic, thermal-hydraulic, and structural analysis capabilities. GAMSOR serves as procedure to obtain the neutron and gamma power distribution information in the ARC code system. GAMSOR is a specially modified version of DIF3D (dif3d.x becomes dif3d_gamsor.x). After some work, it was determined that carrying out software on GAMSOR was impractical and would not fit well with commercial grade dedication. GAMSRC was written in the last decade to replace GAMSOR such that the user can rely soley upon the verified DIF3D (dif3d.x) code and GAMSRC to obtain the neutron and gamma power distribution information. GAMSRC is also fully verified and ready for commercial grade dedication. In the coming years, GAMSOR will be deprecated and GAMSRC will fully take over in the ARC code system. This document identifies the set of test problems used to assess the code coverage for GAMSRC. The goal is to document what parts of the existing GAMSRC code are touched by the set of test problems and which are not. The code coverage analysis of GAMSRC was performed with the Code Coverage Tool of the Intel Fortran compiler which requires modifications to the compilation of GAMSRC. The code coverage tables are given for each submodule of GAMSRC. Because GAMSRC links to modules in DIF3D, some details on coverage changes to the DIF3D lined files is provided. As will be seen, most of the uncovered parts/files can be ignored because they are either for error message and debugging output or obviously not needed by GAMSRC today.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Code Coverage Status of the ARC Code DASSH-F

The Argonne Reactor Code (ARC) software system supports users in their fast reactor design goals by providing neutronic, thermal-hydraulic, and structural analysis capabilities. DASSH-F serves as a steady state thermal hydraulic capability within the ARC system and replaces the SE2-ANL software that preceded it. This document identifies the set of test problems used to assess the code coverage for DASSH-F. The goal is to document what parts of the existing DASSH-F code are touched by the set of test problems and which are not. Because the verification work remains to be done on DASSH-F, one can assume that most of these issues will be resolved as part of that work. The code coverage analysis of DASSH-F was performed with the Code Coverage Tool of the Intel Fortran compiler which requires modifications to the compilation of DASSH-F. The code coverage tables are given for each submodule of DASSH-F. Because DASSH-F links to modules in DIF3D, some details on coverage changes to the DIF3D linked files is provided. As will be seen, most of the uncovered parts/files can be ignored because they are either for error message and debugging output or obviously not needed by DASSH-F today. Seven features of the DASSH-F code were identified to not be covered by the existing testing suite and thus additional verification test problems are suggested to fully cover these sections.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Impact of coverage on the reliability of a fault tolerant computer

A mathematical reliability model is established for a reconfigurable fault tolerant avionic computer system utilizing state-of-the-art computers. System reliability is studied in light of the coverage probabilities associated with the first and second independent hardware failures. Coverage models are presented as a function of detection, isolation, and recovery probabilities. Upper and lower bonds are established for the coverage probabilities and the method for computing values for the coverage probabilities is investigated. Further, an architectural variation is proposed which is shown to enhance coverage.

Bavuso, S. J.↗

The conservativeness of reliability estimates based on instantaneous coverage

Reliability modeling must take into account two different types of phenomena, including the fault-occurrence behavior and the fault/error-handling behavior of a system. The effectiveness of the fault/error-handling behavior can be captured by instantaneous coverage probabilities. This paper has the objective to show that the assumption of instantaneous coverage leads to conservative predictions of system reliability for systems characterized by relatively long interevent times for fault occurrences and relatively short interevent times for fault/error-handling actions. The importance of this result is related to the fact that it can now be shown that model predictions based on instantaneous coverage are lower bounds on the true system reliability. Attention is given to a semi-Markov reliability model, instantaneous coverage approximations, the proof of conservative prediction, and the computation of coverage probabilities.

Mcgough, J.↗

Analysis of cloud top height and cloud coverage from satellites using the O2 A and B bands

Cloud height and cloud coverage detection are important for total ozone retrieval using ultraviolet and visible scattered light. Use of the O2 A and B bands, around 761 and 687 nm, by a satellite-borne instrument of moderately high spectral resolution viewing in the nadir makes it possible to detect cloud top height and related parameters, including fractional coverage. The measured values of a satellite-borne spectrometer are convolutions of the instrument slit function and the atmospheric transmittance between cloud top and satellite. Studies here determine the optical depth between a satellite orbit and the Earth or cloud top height to high accuracy using FASCODE 3. Cloud top height and a cloud coverage parameter are determined by least squares fitting to calculated radiance ratios in the oxygen bands. A grid search method is used to search the parameter space of cloud top height and the coverage parameter to minimize an appropriate sum of squares of deviations. For this search, nonlinearity of the atmospheric transmittance (i.e., leverage based on varying amounts of saturation in the absorption spectrum) is important for distinguishing between cloud top height and fractional coverage. Using the above-mentioned method, an operational cloud detection algorithm which uses minimal computation time can be implemented.

Kuze, Akihiko↗

High Coverages of Hydrogen on a (10,0) Carbon Nanotube

The binding energy of H to a (10,0) carbon nanotube is calculated at 24, 50, and 100% coverage. Several different bonding configurations are considered for the 50% coverage case. Using the ONIOM (our own n-layered integrated molecular orbital and molecular mechanics) approach, the average C-H bond energy for the most stable 50% coverage and for the 100% coverage are 57.3 and 38.6 kcal/mol, respectively. Considering the size of the bond energy of H2, these values suggest that it will be difficult to achieve 100% atomic H coverage on a (10,0) nanotube.

Bauschlicher, Charles W., Jr.↗

Assessing Requirements Quality through Requirements Coverage

In model-based development, the development effort is centered around a formal description of the proposed software system the model. This model is derived from some high-level requirements describing the expected behavior of the software. For validation and verification purposes, this model can then be subjected to various types of analysis, for example, completeness and consistency analysis [6], model checking [3], theorem proving [1], and test-case generation [4, 7]. This development paradigm is making rapid inroads in certain industries, e.g., automotive, avionics, space applications, and medical technology. This shift towards model-based development naturally leads to changes in the verification and validation (V&V) process. The model validation problem determining that the model accurately captures the customer's high-level requirements has received little attention and the sufficiency of the validation activities has been largely determined through ad-hoc methods. Since the model serves as the central artifact, its correctness with respect to the users needs is absolutely crucial. In our investigation, we attempt to answer the following two questions with respect to validation (1) Are the requirements sufficiently defined for the system? and (2) How well does the model implement the behaviors specified by the requirements? The second question can be addressed using formal verification. Nevertheless, the size and complexity of many industrial systems make formal verification infeasible even if we have a formal model and formalized requirements. Thus, presently, there is no objective way of answering these two questions. To this end, we propose an approach based on testing that, when given a set of formal requirements, explores the relationship between requirements-based structural test-adequacy coverage and model-based structural test-adequacy coverage. The proposed technique uses requirements coverage metrics defined in [9] on formal high-level software requirements and existing model coverage metrics such as the Modified Condition and Decision Coverage (MC/DC) used when testing highly critical software in the avionics industry [8]. Our work is related to Chockler et al. [2], but we base our work on traditional testing techniques as opposed to verification techniques.

Rajan, Ajitha↗

Architecture Study on Telemetry Coverage for Immediate Post-Separation Phase

This document is the viewgraphs that accompanies a paper that presents the preliminary results of an architecture study that provides continuous telemetry coverage for NASA missions for immediate post-separation phase. After launch when the spacecraft separated from the upper stage, the spacecraft typically executes a number of mission-critical operations prior to the deployment of solar panels and the activation of the primary communication subsystem. JPL, GSFC, and APL have similar design principle statements that require continuous coverage of mission-critical telemetry during the immediate post-separation phase. To conform to these design principles, an architecture that consists of a separate spacecraft transmitter and a robust communication network capable of tracking the spacecraft signals is needed. The main results of this study are as follows: 1) At low altitude (< 10000 km) when most post-separation critical operations are executed, Earth-based network (e.g. Deep Space Network (DSN)) can only provide limited coverage, whereas space-based network (e.g. Space Network (SN)) can provide continuous coverage. 2) Commercial-off-the-shelf SN compatible transmitters are available for small satellite applications. In this paper we present the detailed coverage analysis of Earth-based and Space-based networks. We identify the key functional and performance requirements of the architecture, and describe the proposed selection criteria of the spacecraft transmitter. We conclude the paper with a proposed forward plan.

architecture↗

Statistical analysis of HAADF-STEM images to determine the surface coverage and distribution of immobilized molecular complexes

The surface immobilization of molecular catalysts is attractive because it combines the benefits of homogeneous and heterogeneous catalysis. However, determining the surface coverage and distribution of a molecular catalyst on a solid support is often challenging, inhibiting our ability to design improved catalytic systems. Here, in this work, we demonstrate that the combination of scanning transmission electron microscopy (STEM) and image analysis of the individual positions of heavy atoms in transition metal complexes via a convolutional neural network (CNN) allows statistically robust determination of the surface coverage and distribution of immobilized molecular catalysts. These observations provide information about how changes in the functionalization conditions, attachment group, and structure of the molecular catalyst affect the surface coverage and distribution, providing insight into the chemical mechanism of surface immobilization. The method could be generally valuable for correlating the surface coverage and distribution to the activity, selectivity, and stability of a catalytic system.

HAADF-STEM↗

Capturing Surface Coverage Effects in Heterogeneous Catalysis

Adsorbate–adsorbate lateral interactions at relevant surface coverages have a significant effect on chemical kinetics, thereby influencing the activity of a heterogeneous catalyst. Coverage-dependent kinetic and thermodynamic parameters therefore must be included in studies of such complex systems to properly predict the turnover frequencies and kinetic trends. Thus, it becomes extremely important to accurately capture the strength of lateral interactions between neighboring species under realistic reaction conditions. In this Perspective, we discuss the various existing computational and experimental methods for determining adspecies coverage and configurational effects. The choice of the tools and methods employed in such studies depends on factors such as time, length scales, computational cost, the presence of solvents, and reaction conditions. The applications of each method and the respective challenges are also discussed here. As a result, we discuss the recent developments and future of the state-of-the-art for inclusion of surface coverage and configuration into a holistic picture for accurate predictions of catalytic behavior.

09 BIOMASS FUELS↗

A Coverage Self-Consistent Microkinetic Model for Vapor-Phase Formic Acid Decomposition over Pd/C Catalysts

An iterative approach utilizing density functional theory (DFT, PW91-GGA)-informed mean-field microkinetic models and reaction kinetics experiments is used to determine the reaction mechanism and the active site for formic acid (HCOOH, FA) decomposition over a Pd/C catalyst. Models parametrized using DFT energetics on clean Pd(100) and Pd(111) required large corrections to the DFT energetics for capturing our experimental data. Further, both Pd(111) and Pd(100) models predicted a high coverage of adsorbed CO (CO*), inconsistent with the assumption of a clean surface at which the rate parameters for these models were calculated. To better represent the active site under reaction conditions and explicitly account for the presence of CO*, subsequent microkinetic models were formulated using DFT energetics that were calculated on partially (5/9 ML) CO*-covered Pd (111) and (100) facets. Upon parameter adjustment, the resultant 5/9 ML CO*-covered Pd(100) model, although consistent in terms of CO* coverage, was unable to capture the dehydration path measured in the experiments and was, therefore, deemed not to offer an accurate representation of the active site for FA decomposition over Pd/C. In contrast, a partially CO*-covered Pd(111) model was better at representing the catalytic active site, as in addition to being consistent in terms of CO* coverages, it required small adjustments of the DFT parameters to accurately capture the experimental data set (both dehydrogenation and dehydration). Our results suggest that the reaction occurs via the spectroscopically elusive carboxyl (COOH*) intermediate and that spectator CO*-assisted decomposition pathways play an important role under typical experimental conditions. In addition, our study highlights the importance of striving for coverage self-consistent microkinetic models and for including spectator-assisted mechanisms in order to develop an improved picture of the active site under reaction conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Incorporating Coverage-Dependent Reaction Barriers into First-Principles-Based Microkinetic Models: Approaches and Challenges

Mean-field microkinetic models (MKMs) are appealing for their relatively facile construction, computational tractability, and high-throughput catalyst screening capabilities. As such, they will continue to be a valuable tool for materials design in heterogeneous catalysis even as the field aims to describe more complex systems. Numerous prior reports have provided the groundwork for constructing first-principles-based MKMs, including the analysis of strategies for incorporating lateral interactions into thermodynamic parameters (e.g., adsorption energies). Yet, there remains a need for concerted dialogue on methods for calculating and incorporating coverage-dependent kinetic parameters into MKMs. In this Perspective, we assess strategies for doing so, including the corresponding key physical implications and computational challenges. Here, we emphasize that decoupling thermodynamic and kinetic parameters within MKMs can violate thermodynamic consistency and risk unphysical solutions. For some reactions and catalyst materials, scaling relationships can predict coverage-dependent activation energies, but there are several exceptions evident in the literature, indicating that this approach is not universally applicable and that the field could benefit from research aimed at elucidating the limitations. Conducting high-coverage transition state searches is a rigorous but computationally costly strategy, and the effects of various methods for mitigating this cost on resulting energetics have yet to be broadly explored and validated. The goal of this Perspective is to generate discussion on and inspire focused research into the physical relevance of approaches for describing coverage-dependent reaction barriers in MKMs, including the development of computationally tractable methodologies, to advance the applicability of MKMs across diverse reaction chemistries and conditions.

36 MATERIALS SCIENCE↗

Nonpareil 3: Fast Estimation of Metagenomic Coverage and Sequence Diversity

Estimations of microbial community diversity based on metagenomic data sets are affected, often to an unknown degree, by biases derived from insufficient coverage and reference database-dependent estimations of diversity. For instance, the completeness of reference databases cannot be generally estimated since it depends on the extant diversity sampled to date, which, with the exception of a few habitats such as the human gut, remains severely undersampled. Further, estimation of the degree of coverage of a microbial community by a metagenomic data set is prohibitively time-consuming for large data sets, and coverage values may not be directly comparable between data sets obtained with different sequencing technologies. Here, we extend Nonpareil, a database-independent tool for the estimation of coverage in metagenomic data sets, to a high-performance computing implementation that scales up to hundreds of cores and includes, in addition, a k -mer-based estimation as sensitive as the original alignment-based version but about three hundred times as fast. Further, we propose a metric of sequence diversity ( N d ) derived directly from Nonpareil curves that correlates well with alpha diversity assessed by traditional metrics. We use this metric in different experiments demonstrating the correlation with the Shannon index estimated on 16S rRNA gene profiles and show that N d additionally reveals seasonal patterns in marine samples that are not captured by the Shannon index and more precise rankings of the magnitude of diversity of microbial communities in different habitats. Therefore, the new version of Nonpareil, called Nonpareil 3, advances the toolbox for metagenomic analyses of microbiomes.

59 BASIC BIOLOGICAL SCIENCES↗

Number of sites-based solver for determining coverages from steady-state mean-field micro-kinetic models

Kinetic models parameterized by ab-initio calculations have led to significant improvements in understanding chemical reactions in heterogeneous catalysis. These studies have been facilitated by implementations which determine steady-state coverages and rates of mean-field micro-kinetic models. As implemented in the open-source kinetic modeling program, CatMAP, the conventional solution strategy is to use a root-finding algorithm to determine the coverage of all intermediates through the steady-state expressions, constraining all coverages to be non-negative and to properly sum to unity. Though intuitive, this root-finding strategy causes issues with convergence to solution due to these imposed constraints. In this work, we avoid explicitly imposing these constraints, solving the mean-field steady-state micro-kinetic model in the space of number of sites instead of solving it in the space of coverages. Here, we transform the constrained root-finding problem to an unconstrained least-squares minimization problem, leading to significantly improved convergence in solving micro-kinetic models and thus enabling the efficient study of more complex catalytic reactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A Comparison of the Fatigue Life of Shot-Peened 4340M Steel with 100, 200, and 300% Coverage

Shot peening has been widely used for improving the fatigue performance of structural components. The objectives of this study are to increase the fatigue life of 4340M steel by shot peening and to compare performance at three different shot-peening coverages (100, 200, and 300%). The results show that the optimum coverage for 4340M steel is 200% in this experiment. Scanning electron microscopy (SEM) was used to evaluate the microstructural properties and estimate the depth and length of the resulting cracks. A proposed innovative technique, which still needs further verification, was applied to enable SEM to differentiate between the appearances of the three coverages. Residual stresses measured using x-ray diffraction showed that 200% coverage had comparatively the highest residual compressive stresses.

36 MATERIALS SCIENCE↗

Mean field model parameterization to recover coverage-dependent kinetics

Lateral interactions between adsorbates introduce coverage dependence into adsorption energies and activation barriers of surface reactions. Lattice-based kinetic Monte Carlo (kMC) simulations can capture these interactions quantitatively but are laborious to parameterize and solve. Mean field models are more tractable, but protocols to construct and parameterize them are unclear. Here we explore the ability of a coverage-aware mean-field model to map to a lattice-kMC model of a generic two-step reaction network, including quasi-equilibrated adsorption and rate-limiting dissociation steps. We derive expressions for mean-field and coverage-dependent adsorption energies and dissociation barriers and parameterize against lattice-kMC predictions. We show that the parameterized mean-field rates correlate with ground truth lattice-kMC results across a wide range of reaction conditions and identify regions where the mean field fails. The mean field model similarly captures kMC-derived rate-order, Arrhenius and Sabatier plots at a greatly reduced computational cost. Further, the results provide guidance for parameterizing mean-field models, benchmarked against explicit lattice-based approaches for incorporating the influence of coverage effects.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Combined photon-electron beams in the treatment of the supraclavicular lymph nodes in breast cancer: A novel technique that achieves adequate coverage while reducing lung dose

Radiation pneumonitis is a well-documented side effect of radiation therapy for breast cancer. The purpose of this study was to compare combined photon-electron, photon-only, and electron-only plans in the radiation treatment of the supraclavicular lymph nodes. In total, 13 patients requiring chest wall and supraclavicular nodal irradiation were planned retrospectively using combined photon-electron, photon-only, and electron-only supraclavicular beams. A dose of 50 Gy over 25 fractions was prescribed. Chest wall irradiation parameters were fixed for all plans. The goal of this planning effort was to cover 95% of the supraclavicular clinical target volume (CTV) with 95% of the prescribed dose and to minimize the volume receiving ≥ 105% of the dose. Comparative end points were supraclavicular CTV coverage (volume covered by the 95% isodose line), hotspot volume, maximum radiation dose, contralateral breast dose, mean total lung dose, total lung volume percentage receiving at least 20 Gy (V{sub 20} {sub Gy}), heart volume percentage receiving at least 25 Gy (V{sub 25} {sub Gy}). Electron and photon energies ranged from 8 to 18 MeV and 4 to 6 MV, respectively. The ratio of photon-to-electron fractions in combined beams ranged from 5:20 to 15:10. Supraclavicular nodal coverage was highest in photon-only (mean = 96.2 ± 3.5%) followed closely by combined photon-electron (mean = 94.2 ± 2.5%) and lowest in electron-only plans (mean = 81.7 ± 14.8%, p < 0.001). The volume of tissue receiving ≥ 105% of the prescription dose was higher in the electron-only (mean = 69.7 ± 56.1 cm{sup 3}) as opposed to combined photon-electron (mean = 50.8 ± 40.9 cm{sup 3}) and photon-only beams (mean = 32.2 ± 28.1 cm{sup 3}, p = 0.114). Heart V{sub 25} {sub Gy} was not statistically different among the plans (p = 0.999). Total lung V{sub 20} {sub Gy} was lowest in electron-only (mean = 10.9 ± 2.3%) followed by combined photon-electron (mean = 13.8 ± 2.3%) and highest in photon-only plans (mean = 16.2 ± 3%, p < 0.001). As expected, photon-only plans demonstrated the highest target coverage and total lung V{sub 20} {sub Gy}. The superiority of electron-only beams, in terms of decreasing lung dose, is set back by the dosimetric hotspots associated with such plans. Combined photon-electron treatment is a feasible technique for supraclavicular nodal irradiation and results in adequate target coverage, acceptable dosimetric hotspot volume, and slightly reduced lung dose.

61 RADIATION PROTECTION AND DOSIMETRY↗