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All sourcesNASA NTRSDOE OSTI
DOE OSTI2014

TH-C-12A-12: Veritas: An Open Source Tool to Facilitate User Interaction with TrueBeam Developer Mode

Purpose: To address the challenges of creating delivery trajectories and imaging sequences with TrueBeam Developer Mode, a new open-source graphical XML builder, Veritas, has been developed, tested and made freely available. Veritas eliminates most of the need to understand the underlying schema and write XML scripts, by providing a graphical menu for each control point specifying the state of 30 mechanical/dose axes. All capabilities of Developer Mode are accessible in Veritas. Methods: Veritas was designed using QT Designer, a ‘what-you-is-what-you-get’ (WYSIWIG) tool for building graphical user interfaces (GUI). Different components of the GUI are integrated using QT's signals and slots mechanism. Functionalities are added using PySide, an open source, cross platform Python binding for the QT framework. The XML code generated is immediately visible, making it an interactive learning tool. A user starts from an anonymized DICOM file or XML example and introduces delivery modifications, or begins their experiment from scratch, then uses the GUI to modify control points as desired. The software automatically generates XML plans following the appropriate schema. Results: Veritas was tested by generating and delivering two XML plans at Brigham and Women's Hospital. The first example was created to irradiate the letter ‘B’ with a narrow MV beam using dynamic couch movements. The second was created to acquire 4D CBCT projections for four minutes. The delivery of the letter ‘B’ was observed using a 2D array of ionization chambers. Both deliveries were generated quickly in Veritas by non-expert Developer Mode users. Conclusion: We introduced a new open source tool Veritas for generating XML plans (delivery trajectories and imaging sequences). Veritas makes Developer Mode more accessible by reducing the learning curve for quick translation of research ideas into XML plans. Veritas is an open source initiative, creating the possibility for future developments and collaboration with other researchers. I am an employee of Varian Medical Systems.

07 ISOTOPE AND RADIATION SOURCES↗
DOE OSTI2014

Sci—Thur PM: Planning and Delivery — 02: Treatment planning workflow for very high-energy electron beam radiotherapy

Purpose: To develop treatment planning workflow for rapid radiotherapy delivered with very-high energy electron (VHEE) scanning beam. Methods: VHEE radiotherapy treatment planning was performed by linking Monte Carlo (MC) dose calculations with inverse optimization in a research version of RayStation. In order to study a number of treatment parameters, a Matlab graphical user interface (GUI) for calculation of VHEE beamlet dose was developed. Through the GUI, EGSnrc MC simulations were run for a number of beam energies, number of beams, beamlet spot and grid sizes, and machine bore sizes. VHEE plans for a pediatric patient with a 4.3 cm{sup 3} brain target optimized with spot-scanning algorithm in RayStation were compared to the clinically delivered 6 MV VMAT plan. Results and Discussion: VHEE beam energy had the largest effect on the quality of dose distributions. For the same target dose, the mean doses to critical organs decreased by 10–15% when planned with 100 MeV compared to 60 MeV. VHEE plans calculated with 36 beams outperformed plans calculated with 13 and 17 beams. While beamlet spacing and bore size had a small effect on VHEE dose distributions, 0.1-3mm beamlet sizes resulted in identical dose distributions. Critical organ doses were by up to 70% lower in the best VHEE plan compared to the clinical 6 MV VMAT plan. Conclusions: We have developed a GUI for MC beamlet generation for treatment planning of VHEE radiotherapy. We have demonstrated that pediatric VHEE plans resulted in significant critical organ dose sparing compared to the clinical VMAT plan.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2014

Automated characterization of perceptual quality of clinical chest radiographs: Validation and calibration to observer preference

Purpose: The authors previously proposed an image-based technique [Y. Lin et al. Med. Phys. 39, 7019–7031 (2012)] to assess the perceptual quality of clinical chest radiographs. In this study, an observer study was designed and conducted to validate the output of the program against rankings by expert radiologists and to establish the ranges of the output values that reflect the acceptable image appearance so the program output can be used for image quality optimization and tracking. Methods: Using an IRB-approved protocol, 2500 clinical chest radiographs (PA/AP) were collected from our clinical operation. The images were processed through our perceptual quality assessment program to measure their appearance in terms of ten metrics of perceptual image quality: lung gray level, lung detail, lung noise, rib–lung contrast, rib sharpness, mediastinum detail, mediastinum noise, mediastinum alignment, subdiaphragm–lung contrast, and subdiaphragm area. From the results, for each targeted appearance attribute/metric, 18 images were selected such that the images presented a relatively constant appearance with respect to all metrics except the targeted one. The images were then incorporated into a graphical user interface, which displayed them into three panels of six in a random order. Using a DICOM calibrated diagnostic display workstation and under low ambient lighting conditions, each of five participating attending chest radiologists was tasked to spatially order the images based only on the targeted appearance attribute regardless of the other qualities. Once ordered, the observer also indicated the range of image appearances that he/she considered clinically acceptable. The observer data were analyzed in terms of the correlations between the observer and algorithmic rankings and interobserver variability. An observer-averaged acceptable image appearance was also statistically derived for each quality attribute based on the collected individual acceptable ranges. Results: The observer study indicated that, for each image quality attribute, the averaged observer ranking strongly correlated with the algorithmic ranking (linear correlation coefficient R > 0.92), with highest correlation (R = 1) for lung gray level and the lowest (R = 0.92) for mediastinum noise. There was a strong concordance between the observers in terms of their rankings (i.e., Kendall’s tau agreement > 0.84). The observers also generally indicated similar tolerance and preference levels in terms of acceptable ranges, as 85% of the values were close to the overall tolerance or preference levels and the differences were smaller than 0.15. Conclusions: The observer study indicates that the previously proposed technique provides a robust reflection of the perceptual image quality in clinical images. The results established the range of algorithmic outputs for each metric that can be used to quantitatively assess and qualify the appearance quality of clinical chest radiographs.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2015

Computer aided detection of surgical retained foreign object for prevention

Purpose: Surgical retained foreign objects (RFOs) have significant morbidity and mortality. They are associated with approximately $1.5 × 10{sup 9} annually in preventable medical costs. The detection accuracy of radiographs for RFOs is a mediocre 59%. The authors address the RFO problem with two complementary technologies: a three-dimensional (3D) gossypiboma micro tag, the μTag that improves the visibility of RFOs on radiographs, and a computer aided detection (CAD) system that detects the μTag. It is desirable for the CAD system to operate in a high specificity mode in the operating room (OR) and function as a first reader for the surgeon. This allows for fast point of care results and seamless workflow integration. The CAD system can also operate in a high sensitivity mode as a second reader for the radiologist to ensure the highest possible detection accuracy. Methods: The 3D geometry of the μTag produces a similar two dimensional (2D) depiction on radiographs regardless of its orientation in the human body and ensures accurate detection by a radiologist and the CAD. The authors created a data set of 1800 cadaver images with the 3D μTag and other common man-made surgical objects positioned randomly. A total of 1061 cadaver images contained a single μTag and the remaining 739 were without μTag. A radiologist marked the location of the μTag using an in-house developed graphical user interface. The data set was partitioned into three independent subsets: a training set, a validation set, and a test set, consisting of 540, 560, and 700 images, respectively. A CAD system with modules that included preprocessing μTag enhancement, labeling, segmentation, feature analysis, classification, and detection was developed. The CAD system was developed using the training and the validation sets. Results: On the training set, the CAD achieved 81.5% sensitivity with 0.014 false positives (FPs) per image in a high specificity mode for the surgeons in the OR and 96.1% sensitivity with 0.81 FPs per image in a high sensitivity mode for the radiologists. On the independent test set, the CAD achieved 79.5% sensitivity with 0.003 FPs per image in a high specificity mode for the surgeons and 90.2% sensitivity with 0.23 FPs per image in a high sensitivity mode for the radiologists. Conclusions: To the best of the authors’ knowledge, this is the first time a 3D μTag is used to produce a recognizable, substantially similar 2D projection on radiographs regardless of orientation in space. It is the first time a CAD system is used to search for man-made objects over anatomic background. The CAD system for the μTags achieved reasonable performance in both the high specificity and the high sensitivity modes.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

Treatment planning for radiotherapy with very high-energy electron beams and comparison of VHEE and VMAT plans

Purpose: The aim of this work was to develop a treatment planning workflow for rapid radiotherapy delivered with very high-energy electron (VHEE) scanning pencil beams of 60–120 MeV and to study VHEE plans as a function of VHEE treatment parameters. Additionally, VHEE plans were compared to clinical state-of-the-art volumetric modulated arc therapy (VMAT) photon plans for three cases. Methods: VHEE radiotherapy treatment planning was performed by linking EGSnrc Monte Carlo (MC) dose calculations with inverse treatment planning in a research version of RayStation. In order to study the effect of VHEE treatment parameters on VHEE dose distributions, a MATLAB graphical user interface (GUI) for calculation of VHEE MC pencil beam doses was developed. Through the GUI, pediatric case MC simulations were run for a number of beam energies (60, 80, 100, and 120 MeV), number of beams (13, 17, and 36), pencil beam spot (0.1, 1.0, and 3.0 mm) and grid (2.0, 2.5, and 3.5 mm) sizes, and source-to-axis distance, SAD (40 and 50 cm). VHEE plans for the pediatric case calculated with the different treatment parameters were optimized and compared. Furthermore, 100 MeV VHEE plans for the pediatric case, a lung, and a prostate case were calculated and compared to the clinically delivered VMAT plans. All plans were normalized such that the 100% isodose line covered 95% of the target volume. Results: VHEE beam energy had the largest effect on the quality of dose distributions of the pediatric case. For the same target dose, the mean doses to organs at risk (OARs) decreased by 5%–16% when planned with 100 MeV compared to 60 MeV, but there was no further improvement in the 120 MeV plan. VHEE plans calculated with 36 beams outperformed plans calculated with 13 and 17 beams, but to a more modest degree (<8%). While pencil beam spacing and SAD had a small effect on VHEE dose distributions, 0.1–3 mm pencil beam sizes resulted in identical dose distributions. For the 100 MeV VHEE pediatric plan, OAR doses were up to 70% lower and the integral dose was 33% lower for VHEE compared to 6 MV VMAT. Additionally, VHEE conformity indices (CI{sub 100} = 1.09 and CI{sub 50} = 4.07) were better than VMAT conformity indices (CI{sub 100} = 1.30 and CI{sub 50} = 6.81). The 100 MeV VHEE lung plan resulted in mean dose decrease to all OARs by up to 27% for the same target coverage compared to the clinical 6 MV flattening filter-free (FFF) VMAT plan. The 100 MeV prostate plan resulted in 3% mean dose increase to the penile bulb and the urethra, but all other OAR mean doses were lower compared to the 15 MV VMAT plan. The lung case CI{sub 100} and CI{sub 50} conformity indices were 3% and 8% lower, respectively, in the VHEE plan compared to the VMAT plan. The prostate case CI{sub 100} and CI{sub 50} conformity indices were 1% higher and 8% lower, respectively, in the VHEE plan compared to the VMAT plan. Conclusions: The authors have developed a treatment planning workflow for MC dose calculation of pencil beams and optimization for treatment planning of VHEE radiotherapy. The authors have demonstrated that VHEE plans resulted in similar or superior dose distributions for pediatric, lung, and prostate cases compared to clinical VMAT plans.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

GMctdospp: Description and validation of a CT dose calculation system

Purpose: To develop a Monte Carlo (MC)-based computed tomography (CT) dose estimation method with a graphical user interface with options to define almost arbitrary simulation scenarios, to make calculations sufficiently fast for comfortable handling, and to make the software free of charge for general availability to the scientific community. Methods: A framework called GMctdospp was developed to calculate phantom and patient doses with the MC method based on the EGSnrc system. A CT scanner was modeled for testing and was adapted to half-value layer, beam-shaping filter, z-profile, and tube-current modulation (TCM). To validate the implemented variance reduction techniques, depth-dose and cross-profile calculations of a static beam were compared against DOSXYZnrc/EGSnrc. Measurements for beam energies of 80 and 120 kVp at several positions of a CT dose-index (CTDI) standard phantom were compared against calculations of the created CT model. Finally, the efficiency of the adapted code was benchmarked against EGSnrc defaults. Results: The CT scanner could be modeled accurately. The developed TCM scheme was confirmed by the dose measurement. A comparison of calculations to DOSXYZnrc showed no systematic differences. Measurements in a CTDI phantom could be reproduced within 2% average, with a maximal difference of about 6%. Efficiency improvements of about six orders of magnitude were observed for larger organ structures of a chest-examination protocol in a voxelized phantom. In these cases, simulations took 25 s to achieve a statistical uncertainty of ∼0.5%. Conclusions: A fast dose-calculation system for phantoms and patients in a CT examination was developed, successfully validated, and benchmarked. Influences of scan protocols, protection method, and other issues can be easily examined with the developed framework.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

SU-E-J-253: The Radiomics Toolbox in the Computational Environment for Radiological Research (CERR)

Purpose: To present an open source and free platform to facilitate radiomics research — The “Radiomics toolbox” in CERR. Method: There is scarcity of open source tools that support end-to-end modeling of image features to predict patient outcomes. The “Radiomics toolbox” strives to fill the need for such a software platform. The platform supports (1) import of various kinds of image modalities like CT, PET, MR, SPECT, US. (2) Contouring tools to delineate structures of interest. (3) Extraction and storage of image based features like 1st order statistics, gray-scale co-occurrence and zonesize matrix based texture features and shape features and (4) Statistical Analysis. Statistical analysis of the extracted features is supported with basic functionality that includes univariate correlations, Kaplan-Meir curves and advanced functionality that includes feature reduction and multivariate modeling. The graphical user interface and the data management are performed with Matlab for the ease of development and readability of code and features for wide audience. Open-source software developed with other programming languages is integrated to enhance various components of this toolbox. For example: Java-based DCM4CHE for import of DICOM, R for statistical analysis. Results: The Radiomics toolbox will be distributed as an open source, GNU copyrighted software. The toolbox was prototyped for modeling Oropharyngeal PET dataset at MSKCC. The analysis will be presented in a separate paper. Conclusion: The Radiomics Toolbox provides an extensible platform for extracting and modeling image features. To emphasize new uses of CERR for radiomics and image-based research, we have changed the name from the “Computational Environment for Radiotherapy Research” to the “Computational Environment for Radiological Research”.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

SU-E-T-258: Development of a New Patient Set-Up Monitoring System Using Force Sensing Resistor (FSR) Sensor for the Radiation Therapy

Purpose: The purpose of this work is to develop a new patient set-up monitoring system using force sensing resistor (FSR) sensors that can confirm pressure of contact surface and evaluate its feasibility. Methods: In this study, we focused on develop the patient set-up monitoring system to compensate for the limitation of existing optical based monitoring system, so the developed system can inform motion in the radiation therapy. The set-up monitoring system was designed consisting of sensor units (FSR sensor), signal conditioning devices (USB cable/interface electronics), a control PC, and a developed analysis software. The sensor unit was made by attaching FSR sensor and dispersing pressure sponge to prevent error which is caused by concentrating specific point. Measured signal from the FSR sensor was sampled to arduino mega 2560 microcontroller, transferred to control PC by using serial communication. The measured data went through normalization process. The normalized data was displayed through the developed graphic user interface (GUI) software. The software was designed to display a single sensor unit intensity (maximum 16 sensors) and display 2D pressure distribution (using 16 sensors) according to the purpose. Results: Changes of pressure value according to motion was confirmed by the developed set-up monitoring system. Very small movement such as little physical change in appearance can be confirmed using a single unit and using 2D pressure distribution. Also, the set-up monitoring system can observe in real time. Conclusion: In this study, we developed the new set-up monitoring system using FSR sensor. Especially, we expect that the new set-up monitoring system is suitable for motion monitoring of blind area that is hard to confirm existing optical system and compensate existing optical based monitoring system. As a further study, an integrated system will be constructed through correlation of existing optical monitoring system. This work was supported by the Industrial R&D program of MOTIE/KEIT. [10048997, Development of the core technology for integrated therapy devices based on real-time MRI guided tumor tracking] and the Mid-career Researcher Program (2014R1A2A1A10050270) through the National Research Foundation of Korea funded by the Ministry of Science, ICT&Future Planning.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

SU-E-T-262: Development of An In-House Forward Planning System for Conformal Arc Therapy

Purpose: Conformal radiotherapy with forward planning has many practical advantages (e.g., more uniform target dose) and has been used routinely for stereotactic body radiation therapy (SBRT) and other conventional treatment. This study investigates a forward-planning approach for conformal arc therapy and a dedicated treatment planning system (TPS) for a newly designed cobalt 60 machine with a ring type gantry and a multileaf collimator (MLC). Methods: Conformal arcs were modeled with continuous delivery of treatment fields conformal to the target cross-section. Treatment plans were further optimized by weighting or offsetting beams based on the target-critical structure relationship. CT and structure data of seven previous SBRT patients treated at our center were used for plan evaluation. An in-house forward planning tool was developed to aid the forward planning process. A graphical user interface (GUI) was designed with interactive and automatic adjustment between beam gantry angle and the beam weight. Dose distributions were calculated using our in-house Monte Carlo based TPS. Dose contributions from individual beam angles were summed together with different weight factors, which were continuously optimized until the pre-set dose conformity goal was met. Results: We were able to achieve target coverage and critical structure sparing to meet the required clinical criteria in all studied cases. It should be mentioned that those cases were selected having critical structures not proximal to the target. However, this was usually the case in the majority of SBRT cases especially those involving lung targets. The developed GUI tool was very useful in the forward treatment planning process. Conclusion: Conformal arcs can be used successfully on the new Cobalt 60 modality for the treatment of a sizeable fraction of cancer patients, which can be efficiently planned with our simple forward planning approach.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

MO-D-213-07: RadShield: Semi- Automated Calculation of Air Kerma Rate and Barrier Thickness

Purpose: To develop the first Java-based semi-automated calculation program intended to aid professional radiation shielding design. Air-kerma rate and barrier thickness calculations are performed by implementing NCRP Report 147 formalism into a Graphical User Interface (GUI). The ultimate aim of this newly created software package is to reduce errors and improve radiographic and fluoroscopic room designs over manual approaches. Methods: Floor plans are first imported as images into the RadShield software program. These plans serve as templates for drawing barriers, occupied regions and x-ray tube locations. We have implemented sub-GUIs that allow the specification in regions and equipment for occupancy factors, design goals, number of patients, primary beam directions, source-to-patient distances and workload distributions. Once the user enters the above parameters, the program automatically calculates air-kerma rate at sampled points beyond all barriers. For each sample point, a corresponding minimum barrier thickness is calculated to meet the design goal. RadShield allows control over preshielding, sample point location and material types. Results: A functional GUI package was developed and tested. Examination of sample walls and source distributions yields a maximum percent difference of less than 0.1% between hand-calculated air-kerma rates and RadShield. Conclusion: The initial results demonstrated that RadShield calculates air-kerma rates and required barrier thicknesses with reliable accuracy and can be used to make radiation shielding design more efficient and accurate. This newly developed approach differs from conventional calculation methods in that it finds air-kerma rates and thickness requirements for many points outside the barriers, stores the information and selects the largest value needed to comply with NCRP Report 147 design goals. Floor plans, parameters, designs and reports can be saved and accessed later for modification and recalculation. We have confirmed that this software accurately calculates air-kerma rates and required barrier thicknesses for diagnostic radiography and fluoroscopic rooms.

07 ISOTOPE AND RADIATION SOURCES↗
DOE OSTI2015

MO-FG-303-06: Evaluation of the Performance of Very High-Energy Electron (VHEE) Beams in Radiotherapy: Five Clinical Cases

Purpose: To evaluate the performance of 100–120 MeV very-high energy electron (VHEE) scanning pencil beams to radiotherapy by means of Monte Carlo (MC) simulations. Methods: We selected five clinical cases with target sizes of 1.2 cm{sup 3} to 990.4 cm{sup 3}. We calculated VHEE treatment plans using the MC EGSnrc code implemented in a MATLAB-based graphical user interface developed by our group. We generated phase space data for beam energies: 100 and 120 MeV and pencil beam spot sizes of 1, 3, and 5 mm at FWHM. The number of equidistant beams considered in this work was 16 or 32. Dose was calculated and then imported into a research version of RayStation where treatment plan optimization was performed. We compared the VHEE plans with the clinically delivered volumetric modulated arc therapy (VMAT) plan to evaluate VHEE plans performance. Results: VHEE plans provided the same PTV coverage and dose homogeneity than VMAT plans for all the cases. In average, the mean dose to organs at risk (OARs) was 24% lower for the VHEE plans. The structures that benefited the most from using VHEE were: large bowel for the esophagus case, chest wall for the liver case, brainstem for the acoustic case, carina for the lung case, and genitalia for the anal case, with 23.7–34.6% lower dose. VHEE dose distributions were more conformal than VMAT solution as confirmed by conformity indices CI100 and CI50. Integral dose to the body was in average 19.6% (9.2%–36.5%) lower for the VHEE plans. Conclusion: We have shown that VHEE plans resulted in similar or superior dose distributions compared to clinical VMAT plans for five different cases and a wide range of target volumes, including a case with a small target (1.2 cm{sup 3}), which represents a challenge for VMAT planning and might require the use of more complex non-coplanar VMAT plans. B Palma: None. M Bazalova: None. B Hardemark: Employee, RaySearch Laboratories AB. E Hynning: Employee, RaySearch Laboratories AB. B Qu: None. B Loo Jr.: Research support, RaySearch, Varian. P Maxim: Research support, RaySearch, Varian.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

SU-F-T-540: Comprehensive Fluence Delivery Optimization with Multileaf Collimation

Purpose: Multileaf collimator (MLC) leaf sequencing is performed via commercial black-box implementations, on which a user has limited to no access. We have developed an explicit, generic MLC sequencing model to serve as a tool for future investigations of fluence map optimization, fluence delivery optimization, and rotational collimator delivery methods. Methods: We have developed a novel, comprehensive model to effectively account for a variety of transmission and penumbra effects previously treated on an ad hoc basis in the literature. As the model is capable of quantifying a variety of effects, we utilize the asymmetric leakage intensity across each leaf to deliver fluence maps with pixel size smaller than the narrowest leaf width. Developed using linear programming and mixed integer programming formulations, the model is implemented using state of the art open-source solvers. To demonstrate the versatility of the algorithm, a graphical user interface (GUI) was developed in MATLAB capable of accepting custom leaf specifications and transmission parameters. As a preliminary proof-ofconcept, we have sequenced the leaves of a Varian 120 Leaf Millennium MLC for five prostate cancer patient fields and one head and neck field. Predetermined fluence maps have been processed by data smoothing methods to obtain pixel sizes of 2.5 cm{sup 2}. The quality of output was analyzed using computer simulations. Results: For the prostate fields, an average root mean squared error (RMSE) of 0.82 and gamma (0.5mm/0.5%) of 91.4% were observed compared to RMSE and gamma (0.5mm/0.5%) values of 7.04 and 34.0% when the leakage considerations were omitted. Similar results were observed for the head and neck case. Conclusion: A model to sequence MLC leaves to optimality has been proposed. Future work will involve extensive testing and evaluation of the method on clinical MLCs and comparison with black-box leaf sequencing algorithms currently used by commercial treatment planning systems.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

SU-G-TeP2-15: Feasibility Study of Fiber-Optic Cerenkov Radiation Sensors for in Vivo Measurement: Dosimetric Characterization and Clinical Application in Proton Beams

Purpose: To evaluate the possibility of a fiber-optic Cerenkov radiation sensor (FCRS) for in vivo dose verification in proton therapy. Methods: The Cerenkov radiation due to the proton beam was measured using a homemade phantom, consisting of a plastic optical fiber (POF, PGSCD1001-13-E, Toray, Tokyo, Japan) connected to each channel of a multianode photomultiplier tube (MAPMT:H7546, Hamamatsu Photonics, Shizuoka, Japan). Data were acquired using a multi-anode photomultiplier tube with the NI-DAQ system (National Instruments Texas, USA). The real-time monitoring graphic user interface was programmed using Labview. The FCRS was analyzed for its dosimetrics characteristic in proton beam. To determine the accuracy of the FCRS in proton dose measurements, we compared the ionization chamber dose measurements using a water phantom. We investigated the feasibility of the FCRS for the measurement of dose distributions near the superficial region for proton plans with a varying separation between the target volume and the surface of 3 patients using a humanoid phantom. Results: The dose-response has good linearity. Dose-rate and energy dependence were found to be within 1%. Depth-dose distributions in non-modulated proton beams obtained with the FCRS was in good agreement with the depth-dose measurements from the ionization chamber. To evaluate the dosimetric accuracy of the FCRS, the difference of isocenter dose between the delivery dose calculated by the treatment planning system and that measured by the FCRS was within 3%. With in vivo dosimetry using the humanoid phantom, the calculated surface doses overestimated measurements by 4%–8% using FCRS. Conclusion: In previous study, our results indicate that the performance of the array-type FCRS was comparable to that of the currently used a multi-layer ion chamber system. In this study, we also believe that the fiber-optic Cerenkov radiation sensor has considerable potential for use with in vivo patient proton dosimetry.

07 ISOTOPE AND RADIATION SOURCES↗
DOE OSTI2016

MO-DE-BRA-02: SIMAC: A Simulation Tool for Teaching Linear Accelerator Physics

Purpose: The first goal of this work is to develop software that can simulate the physics of linear accelerators (linac). The second goal is to show that this simulation tool is effective in teaching linac physics to medical physicists and linac service engineers. Methods: Linacs were modeled using analytical expressions that can correctly describe the physical response of a linac to parameter changes in real time. These expressions were programmed with a graphical user interface in order to produce an environment similar to that of linac service mode. The software, “SIMAC”, has been used as a learning aid in a professional development course 3 times (2014 – 2016) as well as in a physics graduate program. Exercises were developed to supplement the didactic components of the courses consisting of activites designed to reinforce the concepts of beam loading; the effect of steering coil currents on beam symmetry; and the relationship between beam energy and flatness. Results: SIMAC was used to teach 35 professionals (medical physicists; regulators; service engineers; 1 week course) as well as 20 graduate students (1 month project). In the student evaluations, 85% of the students rated the effectiveness of SIMAC as very good or outstanding, and 70% rated the software as the most effective part of the courses. Exercise results were collected showing that 100% of the students were able to use the software correctly. In exercises involving gross changes to linac operating points (i.e. energy changes) the majority of students were able to correctly perform these beam adjustments. Conclusion: Software simulation(SIMAC), can be used to effectively teach linac physics. In short courses, students were able to correctly make gross parameter adjustments that typically require much longer training times using conventional training methods.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

MO-FG-CAMPUS-TeP1-03: Pre-Treatment Surface Imaging Based Collision Detection

Purpose: Modern radiotherapy increasingly employs large immobilization devices, gantry attachments, and couch rotations for treatments. All of which raise the risk of collisions between the patient and the gantry / couch. Collision detection is often achieved by manually checking each couch position in the treatment room and sometimes results in extraneous imaging if collisions are detected after image based setup has begun. In the interest of improving efficiency and avoiding extra imaging, we explore the use of a surface imaging based collision detection model. Methods: Surfaces acquired from AlignRT (VisionRT, London, UK) were transferred in wavefront format to a custom Matlab (Mathworks, Natick, MA) software package (CCHECK). Computed tomography (CT) scans acquired at the same time were sent to CCHECK in DICOM format. In CCHECK, binary maps of the surfaces were created and overlaid on the CT images based on the fixed relationship of the AlignRT and CT coordinate systems. Isocenters were added through a graphical user interface (GUI). CCHECK then compares the inputted surfaces to a model of the linear accelerator (linac) to check for collisions at defined gantry and couch positions. Note, CCHECK may be used with or without a CT. Results: The nominal surface image field of view is 650 mm × 900 mm, with variance based on patient position and size. The accuracy of collision detections is primarily based on the linac model and the surface mapping process. The current linac model and mapping process yield detection accuracies on the order of 5 mm, assuming no change in patient posture between surface acquisition and treatment. Conclusions: CCHECK provides a non-ionizing method to check for collisions without the patient in the treatment room. Collision detection accuracy may be improved with more robust linac modeling. Additional gantry attachments (e.g. conical collimators) can be easily added to the model.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Modification and analysis of context-specific genome-scale metabolic models: methane-utilizing microbial chassis as a case study

ABSTRACT Context-specific genome-scale model (CS-GSM) reconstruction is becoming an efficient strategy for integrating and cross-comparing experimental multi-scale data to explore the relationship between cellular genotypes, facilitating fundamental or applied research discoveries. However, the application of CS modeling for non-conventional microbes is still challenging. Here, we present a graphical user interface that integrates COBRApy, EscherPy, and RIPTiDe, Python-based tools within the BioUML platform, and streamlines the reconstruction and interrogation of the CS genome-scale metabolic frameworks via Jupyter Notebook. The approach was tested using -omics data collected for Methylotuvimicrobium alcaliphilum 20Z R , a prominent microbial chassis for methane capturing and valorization. We optimized the previously reconstructed whole genome-scale metabolic network by adjusting the flux distribution using gene expression data. The outputs of the automatically reconstructed CS metabolic network were comparable to manually optimized i IA409 models for Ca-growth conditions. However, the CS model questions the reversibility of the phosphoketolase pathway and suggests higher flux via primary oxidation pathways. The model also highlighted unresolved carbon partitioning between assimilatory and catabolic pathways at the formaldehyde-formate node. Only a very few genes and only one enzyme with a predicted function in C1 metabolism, a homolog of the formaldehyde oxidation enzyme ( fae1-2 ), showed a significant change in expression in La-growth conditions. The CS-GSM predictions agreed with the experimental measurements under the assumption that the Fae1-2 is a part of the tetrahydrofolate-linked pathway. The cellular roles of the tungsten (W)-dependent formate dehydrogenase ( fdhAB ) and fae homologs ( fae1-2 and fae3 ) were investigated via mutagenesis. The phenotype of the f dhAB mutant followed the model prediction. Furthermore, a more significant reduction of the biomass yield was observed during growth in La-supplemented media, confirming a higher flux through formate. M. alcaliphilum 20Z R mutants lacking fae1-2 did not display any significant defects in methane or methanol-dependent growth. However, contrary to fae1, the fae1-2 homolog failed to restore the formaldehyde-activating enzyme function in complementation tests. Overall, the presented data suggest that the developed computational workflow supports the reconstruction and validation of CS-GSM networks of non-model microbes. IMPORTANCE The interrogation of various types of data is a routine strategy to explore the relationship between genotype and phenotype. An efficient approach for integrating and cross-comparing experimental multi-scale data in the context of whole-genome-based metabolic network reconstruction becomes a powerful tool that facilitates fundamental and applied research discoveries. The present study describes the reconstruction of a context-specific (CS) model for the methane-utilizing bacterium, Methylotuvimicrobium alcaliphilum 20Z R . M. alcaliphilum 20Z R is becoming an attractive microbial platform for the production of biofuels, chemicals, pharmaceuticals, and bio-sorbents for capturing atmospheric methane. We demonstrate that this pipeline can help reconstruct metabolic models that are similar to manually curated networks. Furthermore, the model is able to highlight previously overlooked pathways, thus advancing fundamental knowledge of non-model microbial systems or promoting their development toward biotechnological or environmental implementations.

Kulyashov, M. A.↗
DOE OSTI2015

Software package for modeling spin–orbit motion in storage rings

A software package providing a graphical user interface for computer experiments on the motion of charged particle beams in accelerators, as well as analysis of obtained data, is presented. The software package was tested in the framework of the international project on electric dipole moment measurement JEDI (Jülich Electric Dipole moment Investigations). The specific features of particle spin motion imply the requirement to use a cyclic accelerator (storage ring) consisting of electrostatic elements, which makes it possible to preserve horizontal polarization for a long time. Computer experiments study the dynamics of 10{sup 6}–10{sup 9} particles in a beam during 10{sup 9} turns in an accelerator (about 10{sup 12}–10{sup 15} integration steps for the equations of motion). For designing an optimal accelerator structure, a large number of computer experiments on polarized beam dynamics are required. The numerical core of the package is COSY Infinity, a program for modeling spin–orbit dynamics.

43 PARTICLE ACCELERATORS↗
DOE OSTI2016

Fluctuating Hydrodynamics Methods for Dynamic Coarse-Grained Implicit-Solvent Simulations in LAMMPS

We present a software package integrated with the molecular dynamics software LAMMPS for fluctuating hydrodynamics simulations of fluid-structure interactions subject to thermal fluctuations. The package is motivated to provide dynamic thermostats to extend implicit-solvent coarse-grained (IS-CG) models by incorporating kinetic contributions from the solvent to facilitate their use in a wider range of applications. To capture the thermal and hydrodynamic contributions of the solvent to dynamics, we introduce momentum conserving thermostats and computational methods based on fluctuating hydrodynamics and the stochastic Eulerian Lagrangian method (SELM). SELM couples the coarse-grained microstructure degrees of freedom to continuum stochastic fields to capture both the relaxation of hydrodynamic modes and thermal fluctuations. Features of the SELM software include (i) numerical time-step integrators for SELM fluctuating hydrodynamics in inertial and quasi-steady regimes, (ii) Lees--Edwards-style methods for imposing shear, (iii) a Java-based graphical user interface (GUI) for setting up models and simulations, (iv) standardized XML formats for parametrization and data output, and (v) standardized formats VTK for continuum fields and microstructures. The SELM software package facilitates for pre-established models in LAMMPS easy adoption of the SELM fluctuating hydrodynamics thermostats. We offer here an overview of the SELM software package, computational methods, and applications.

97 MATHEMATICS AND COMPUTING↗