Toolkit Version Research Articles

SU‐E‐T‐290: Secondary Dose Monitoring Using Scintillating Fibers in Proton Therapy of Prostate Cancer: A Geant4 Monte Carlo Simulation

Purpose:To monitor the secondary dose distribution originating from a water phantom during proton therapy of prostate cancer using scintillating fibers.Methods:The Geant4 Monte Carlo toolkit version 9.6.p02 was used to simulate prostate cancer proton therapy based treatments. Two cases were studied. In the first case, 8 × 8 = 64 equally spaced fibers inside three 4 × 4 × 2.54 cmm3 DuPont™ Delrin blocks were used to monitor the emission of secondary particles in the transverse (left and right) and distal regions relative to the beam direction. In the second case, a scintillating block with a thickness of 2.54 cm and equal vertical and longitudinal dimensions as the water phantom was used. Geometrical cuts were used to extract the energy deposited in each fiber and the scintillating block.Results:The transverse dose distributions from secondary particles in both cases agree within <5% and with a very good symmetry. The energy deposited not only gradually increases as one moves from the peripheral row fibers towards the center of the block (aligned with the center of the prostate) but also decreases as one goes from the frontal to distal region of the block. The ratio of the doses from the prostate to the ones in the middle two rows of fibers showed a linear relationship with a slope (−3.55±2.26) × 10−5 MeV per treatment Gy. The distal detectors recorded a very small energy deposited due to water attenuation.Conclusion:With a good calibration and the ability to define a good correlation between the dose to the external fibers and the prostate, such fibers can be used for real time dose verification to the target.

SU‐E‐T‐289: Scintillating Fiber Based In‐Vivo Dose Monitoring System to the Rectum in Proton Therapy of Prostate Cancer: A Geant4 Monte Carlo Simulation

Purpose:To construct a dose monitoring system based on an endorectal balloon coupled to thin scintillating fibers to study the dose delivered to the rectum during prostate cancer proton therapyMethods:The Geant4 Monte Carlo toolkit version 9.6p02 was used to simulate prostate cancer proton therapy treatments of an endorectal balloon (for immobilization of a 2.9 cm diameter prostate gland) and a set of 34 scintillating fibers symmetrically placed around the balloon and perpendicular to the proton beam direction (for dosimetry measurements)Results:A linear response of the fibers to the dose delivered was observed within <2%, a property that makes them good candidates for real time dosimetry. Results obtained show that the closest fiber recorded about 1/3 of the dose to the target with a 1/r2 decrease in the dose distribution as one goes toward the frontal and distal top fibers. Very low dose was recorded by the bottom fibers (about 45 times comparatively), which is a clear indication that the overall volume of the rectal wall that is exposed to a higher dose is relatively minimized. Further analysis indicated a simple scaling relationship between the dose to the prostate and the dose to the top fibers (a linear fit gave a slope of −0.07±0.07 MeV per treatment Gy)Conclusion:Thin (1 mm × 1 mm × 100 cm) long scintillating fibers were found to be ideal for real time in‐vivo dose measurement to the rectum for prostate cancer proton therapy. The linear response of the fibers to the dose delivered makes them good candidates of dosimeters. With thorough calibration and the ability to define a good correlation between the dose to the target and the dose to the fibers, such dosimeters can be used for real time dose verification to the target

TH‐A‐19A‐02: Expanding TOPAS Towards Biological Modeling

Purpose:To expand Monte Carlo simulations of TOPAS to directly calculate radiobiological effects using various biological models.Methods:We use the TOPAS toolkit version beta9 and expand the provided scoring system to directly include scorers for relative biological effect (RBE) modeling. A scorer is a class to record a given physical property in the Monte Carlo simulations. We developed a scorer for the dose averaged linear energy transfer (LETd). This scorer was used to compare RBE weighted dose distributions assuming a constant RBE of 1.1 with the RBE weighted dose using a variable RBE based on a model using LETd and dose as input. Additionally, the local effect model (LEM) was implemented in TOPAS to estimate RBE weighted dose distributions. Survival curves for the LEM were simulated for a monoenergetic proton beams impinging on phantoms and for full patient treatment plans.Results:We have implemented radiobiological effect models in TOPAS, providing users with the possibility to directly obtain parameters related to radiobiological dose and use those as additional information to assess the quality of treatment plans. We applied the scorers to clinical patient treatments and phantom simulations. We find that for the proton therapy plans investigated the regions with the highest LETd are generally outside of the target volume, coinciding with the distal edge of treatment fields. LETd‐based variable RBE weighted dose models predict higher doses at the distal edge of over 10% of the prescribed dose than when assuming a constant RBE.Conclusion:By implementing radiobiological effect models into a Monte Carlo simulation package we combine accurate dose calculation with biological modeling. TOPAS thereby provides distributions of multiple physical quantities such as the dose and LETd, and estimates of biological parameters (RBE, survival) thus allowing direct comparison of biological effective dose predictions between different models.

Biomechanical Analysis of Sports Technique Key Elements in Back Double Somersault Dismount off Uneven Bars-Junior Gymnasts 12 to 14 Years Old

The main goal of this work is the computerized video analysis of the characteristic key technical elements of the double somersault dismount off uneven bars in the basic specialization stage in women's artistic gymnastics. The study was conducted during the Masters National Championships, Oneşti, 16-18 November, 2012. The subjects of the research were 7 female gymnasts, 12 to 14 years old, members of the Junior Olympic Team in Deva and finalists on this apparatus. The biomechanical analysis was performed by means of a specialized program called Physics ToolKit Version 6.0, focusing on the key elements of the technique (as per Boloban, V., 1990): starting position (SP), multiplication of body position (MP) and final position (FP) of the body. The biomechanical analysis of double somersault dismount off uneven bars highlighted the characteristics of the key elements and the influence of the biomechanical indicators on the technical execution of the dismount. The analysis of the execution of the dismount in comparison with the requirements of the technical regulations of the International Code of Points for uneven bars will generate new methodological guidelines meant to improve and correct executions, thus confirming the hypotheses proposed and the performances achieved in competition.

PRAND: GPU accelerated parallel random number generation library: Using most reliable algorithms and applying parallelism of modern GPUs and CPUs

The library PRAND for pseudorandom number generation for modern CPUs and GPUs is presented. It contains both single-threaded and multi-threaded realizations of a number of modern and most reliable generators recently proposed and studied in Barash (2011), Matsumoto and Tishimura (1998), L’Ecuyer (1999,1999), Barash and Shchur (2006) and the efficient SIMD realizations proposed in Barash and Shchur (2011). One of the useful features for using PRAND in parallel simulations is the ability to initialize up to 1019 independent streams. Using massive parallelism of modern GPUs and SIMD parallelism of modern CPUs substantially improves performance of the generators. Program summaryProgram title: PRANDCatalogue identifier: AESB_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AESB_v1_0.htmlProgram obtainable from: CPC Program Library, Queen’s University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 45979No. of bytes in distributed program, including test data, etc.: 23953564Distribution format: tar.gzProgramming language: Cuda C, Fortran.Computer: PC, workstation, laptop, or server with NVIDIA GPU (tested on Tesla X2070, Fermi C2050, GeForce GT540M) and with Intel or AMD processor.Operating system: Linux with CUDA version 5.0 or later. Should also run on MacOs, Windows, or UNIX.RAM: 4 MbytesClassification: 4.13.Nature of problem:Any calculation requiring uniform pseudorandom number generator, in particular, Monte Carlo calculations. Any calculation or simulation requiring uncorrelated parallel streams of uniform pseudorandom numbers.Solution method:The library contains realization of a number of modern and reliable generators: MT19937, MRG32K3A and LFSR113. Also new realizations of the method based on parallel evolution of an ensemble of transformations of two-dimensional torus are included in the library: GM19, GM29, GM31, GM61, GM55, GQ58.1, GQ58.3 and GQ58.4. The library contains: single-threaded and multi-threaded realizations for GPU, single-threaded realizations for CPU, realizations for CPU based on SSE command set. Also, the library contains the abilities to jump ahead inside RNG sequence and to initialize independent random number streams with block splitting method for each of the RNGs.Restrictions:Nvidia Cuda Toolkit version 5.0 or later should be installed. To use GPU realizations, Nvidia GPU supporting CUDA and the corresponding Nvidia driver should be installed. For SSE realizations of the generators, Intel or AMD CPU supporting SSE2 command set is required. In order to use the SSE realization of LFSR113, CPU must support SSE4 command set.Additional comments:A version of this program, which only contains the realizations for CPUs, is held in the Library as Catalog Id., AEIT_v2_0 (RNGSSELIB). It does not require a GPU device or CUDA compiler.Running time:The tests and the examples included in the package take less or about one minute to run. Running time is analyzed in detail in Section 8 of the paper.

Monte Carlo dosimetry of high dose rate gynecologic interstitial brachytherapy

PurposeTo assess the dosimetric effects of the presence of the applicator, air pockets in clinical target volume (CTV) and OARs along with tissue heterogeneities using the Monte Carlo (MC) method in high dose rate (HDR) gynecologic interstitial brachytherapy with a Syed-Neblett template. Methods and materialsThe CT based dosimetry has been achieved with the Geant4 MC toolkit version 9.2. DICOM-RT files of 38 patients were imported into our own platform for MC simulations. The dose distributions were then compared to those obtained with a conventional TG-43 calculation. ResultsTaking account of heterogeneities has effects of the order of 1% on the HDR gynecological dose distributions. However, the exclusion of air pockets and applicator from the DVH calculation can lower the CTV D90 and V100 by as much as 8.7% and 5.0% in comparison with TG-43. Rectum dosimetric indices can also be lowered by approximately 3% compared with TG-43 for most cases. Differences for urethra and bladder are for most cases below 1%. ConclusionsExclusion of non-biological material such as air pockets and applicator volume from the CTV is important for both TG-43 and MC calculations. It could be easily implemented and automated in treatment planning systems without affecting computation times.

SU‐E‐T‐254: Tissue Specific Characteristics of Prompt Gamma in Proton Radiotherapy: A GEANT4 Simulation Study

Purpose: An in‐vivo range verification system for proton radiotherapy utilizes prompt gamma photon emitted from the de‐excitation of daughter fragments (e.g. 12C, 16O) produced in an interaction of incident proton in materials with time scales in the range of nano seconds. The goal of the present investigation is to study depth dependency of the yield of emitted prompt gamma rays from energetic proton interactions in different materials. Methods: A coincidence detector system for identifying prompt gamma was simulated with Geant4 Monte Carlo toolkit version 9.4.9 p02. The interaction of 110 MeV protons with target phantom (5 cm × 5 cm × 50 cm) was used. A virtual detector (5 cm × 5 cm × 1 mm) was replicated 500 times to form a bank of detectors. A lower bank was placed 1 cm above the phantom while another bank was placed 1 cm above the lower bank. A coincidence requirement was met when a gamma had passed through both a bottom detector and the corresponding top detector segments directly above it. Our investigation used built‐in physics list consisting of electromagnetic and nuclear interactions. Three different types of phantom materials (Water, PMMA and Bone) were used. Results: The emitted prompt gamma yields from 12C (energy range 4.21 to 4.59 MeV) and 16O (energy range 5.79 to 6.31 MeV) versus depth showed similar distributions irrespective of materials. The depths of the maximum yields from 12C were superficial to that from 16O and Bragg peak depths. The yields from 12C were greater to that from 16O up to 5 mm superficial to Bragg peak; whereas around Bragg peak the yields of 16O dominated. Distal to Bragg peak, the yields from 12C started to dominate. Conclusion: A depth dependent relationship may exist between the characteristic prompt gamma production and Bragg peak. More careful analysis has now been planned.

MO‐G‐137‐01: Proton Therapy Range Verification Using Prompt Gamma Rays: A Simulation Study with the Geant4 Monte Carlo Toolkit

Purpose: To simulate a coincidence detector system for in vivo range verification using prompt gamma (PG) emission technique for proton radiation therapy and to compare the results with the alternative technique utilizing the positron‐emitting nuclei (PEN). Methods: A coincidence detector system for characterizing both emitted and registered prompt gamma spectrum was simulated by Geant4 Monte Carlo toolkit version 9.4.9 p02. The interaction of 110 MeV protons with target phantom of PMMA (5 cm × 5 cm × 50 cm) was used in the simulation. A virtual detector (5 cm × 5 cm × 1 mm) was replicated 500 times to form a bank of detectors. A lower bank was placed 1 cm above the phantom while another bank was placed 1 cm above the lower bank. A coincidence requirement was met when a gamma had passed through both a bottom detector segment and the corresponding top detector segment directly above it. Our investigation used the built‐in physics list consisting of electromagnetic as well as nuclear interactions. Results: The depths corresponding to the maximum prompt gamma counts were found to be in close proximity to the range of protons as determined by the Bragg Peak. We noted that the PEN yields had their maximum and distal 50% yield more superficially than the Bragg Peak. This is clearly different compared to PG yields that showed their maximum in closer proximity to the Bragg Peak. The 50% distal PEN yields also lied shallower to the Bragg peak whereas the 50% distal PG yields lied deeper with respect to the Bragg Peak. Conclusion: This work shows clearly that the range of the incident protons can be measured in vivo via a suitable detector system utilizing the PG technique. More realistic simulations by implementing and optimizing various detector materials are now being planned.

Resting - state functional MR changes in Alzheimer's disease patients visualized by amplitude of low - frequency fluctuation and fraction of amplitude of low - frequency fluctuation

Objective To investigate the difference of amplitude of low-frequency fluctuation (ALFF) and fraction of amplitude of low-frequency fluctuation (f ALFF) between Alzheimer's disease (AD) patients and normal aging (NA) controls by voxel-based analysis. Methods Thirty-one AD patients and 44 NA controls were enrolled in the study.Blood oxygen level dependent functional (BOLD) EPI data were obtained during resting-state by using 32-channel head coil.Data were realigned,normalized and then smoothed with 8 mm FWHM kernel.Resting-state f MRI toolkit (version 1.6) was used to generate ALFF and f ALFF images.Independent two sample t-test was performed with SPM5 to compare ALFF and f ALFF of AD and NA controls.Pearsoncorrelation analysis was performed to examine the relationship between MMSE score and ALFF,f ALFF parameters.The significance level was set to be uncorrected 0.001 on the voxel level and 0.05 on the cluster level. Results AD patients showed increased ALFF in left temporal lobe (0.492±0.119) and right cingulated cortex (0.434±0.093) of AD patients,which were 0.443±0.068 and 0.380±0.081 in NA controls (t=2.658,2.227,P<0.05).Decreased f ALFF was found in bilateral posterior cingulate cortices (1.167±0.203) and increased f ALFF was found in bilateral temporal lobes (left 1.226±0.127,right 1.146±0.214) with left side dominance,which were 1.453±0.269,1.134±0.088,1.014±0.132 in NA controls (t=5.001,3.695,3.285,P<0.05).Bilateral temporal ALFF and f ALFF correlated with MMSE positively (r=0.768—0.909,P<0.05) with left dominance. Conclusion AD patients showed increased resting-state functional MRI changes correlated with MMSE scorein the temporal lobes with left dominance,which indicated left temporal lobe may be the best location for the observation of disease progression in AD patients. Key words: Alzheimer disease; Magnetic resonance imaging

2044 DIFFUSION TENSOR MAGNETIC RESONANCE TRACTOGRAPHY OF THE PROSTATE: FEASIBILITY FOR NEUROANATOMIC MAPPING

You have accessJournal of UrologyImaging/Radiology: Uroradiology I1 Apr 20122044 DIFFUSION TENSOR MAGNETIC RESONANCE TRACTOGRAPHY OF THE PROSTATE: FEASIBILITY FOR NEUROANATOMIC MAPPING David S. Finley, Benjamin Ellingson, Shyam Natarajan, Taryar Zaw, Steven Raman, Peter Schulam, Robert Reiter, and Daniel Margolis David S. FinleyDavid S. Finley Los Angeles, CA More articles by this author , Benjamin EllingsonBenjamin Ellingson Los Angeles, CA More articles by this author , Shyam NatarajanShyam Natarajan Los Angeles, CA More articles by this author , Taryar ZawTaryar Zaw Los Angeles, CA More articles by this author , Steven RamanSteven Raman Los Angeles, CA More articles by this author , Peter SchulamPeter Schulam Los Angeles, CA More articles by this author , Robert ReiterRobert Reiter Los Angeles, CA More articles by this author , and Daniel MargolisDaniel Margolis Los Angeles, CA More articles by this author View All Author Informationhttps://doi.org/10.1016/j.juro.2012.02.2208AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookTwitterLinked InEmail INTRODUCTION AND OBJECTIVES Present knowledge of periprostatic neuroanatomy is based largely on gross dissection of the prostate gland. We evaluated the feasibility of in-vivo diffusion tensor magnetic resonance imaging (DTI) tractography of the prostate to visualize and map periprostatic neurovascular anatomy. METHODS Eight men scheduled to undergo robot-assisted radical prostatectomy underwent 3.0Tesla endorectal multiparametric magnetic resonance imaging (MRI) of the prostate with DTI. Tract mapping was accomplished by positioning spherical regions of interest (ROI), with a radius of 1.5 mm contiguously along the prostatic capsule on axial T2W images at standardized locations at the prostatic apex, mid-gland, and base. Image processing was performed using the Diffusion Toolkit version 0.6.1 and TrackVis version (5.1, TrackVis.org, Mass General). Fiber tracts were constructed for each patient using an angle threshold of 35° and a Tensorline propagation algorithm with bootstrapping from multiple directions and averages. RESULTS DTI tractography was successfully performed in all eight patients, visualizing fiber tracts around the prostate. A dense network of fibers was identified around the entire border in the region between the prostatic capsule and lateral prostatic fascia (Figure 1A). Variation in total tract number (range: 709-2855, SD=875) was observed between patients and regions of the prostate (Figure 1B). Posterolateral fiber bundle mass varied between the right and left sides within individual patients (range 25.5%-74.5%). The total tract mass, corrected for prostate volume, was significantly larger for the lower prostate hemisphere compared with the upper hemisphere at the prostatic base (Fig 1C). The postero-lateral sectors, representing the putative “classic” region of the dominant NVB, accounted for only 32.3% of the total tract mass. Fiber tracts were seen crossing-over from the right and left sides of the prostate. CONCLUSIONS DTI tractography of the prostate effectively visualized periprostatic fiber tract anatomy. Variation in tract distribution and fiber cross-over was observed. © 2012 by American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 187Issue 4SApril 2012Page: e824-e825 Advertisement Copyright & Permissions© 2012 by American Urological Association Education and Research, Inc.MetricsAuthor Information David S. Finley Los Angeles, CA More articles by this author Benjamin Ellingson Los Angeles, CA More articles by this author Shyam Natarajan Los Angeles, CA More articles by this author Taryar Zaw Los Angeles, CA More articles by this author Steven Raman Los Angeles, CA More articles by this author Peter Schulam Los Angeles, CA More articles by this author Robert Reiter Los Angeles, CA More articles by this author Daniel Margolis Los Angeles, CA More articles by this author Expand All Advertisement Advertisement PDF downloadLoading ...

Computation of Availability and Performance of Wind Turbine with Markov Analysis in India

This paper deals with the availability analysis for the wind turbines (WT) located in hill and main pass having uncertainty in wind. Availability is a key performance index for WTs. In this paper, the concept of Markov analysis (MA) is used to model the failure characteristics of the WTs for calculating probability and reliability of reaching various system states of WT having the capacities of 225 kW, 250 kW, and 400 kW. Due to uncertainty in the wind, the probability of component failure is independent of the past history. Hence MA is considered as the best mathematical tool for modelling WT with complex system. The field data obtained from the Muppandal site in India such as Mean time between failure (MTBF), Mean time to repair (MTTR), failure rate and repair rate are used to compute the WT availability, using ITEM Toolkit version 8.0.2 as a measure of performance. No attempt is made to analyze the individual state of the WT system. In this paper, for seven critical components, a resultant of 128 states has been analyzed. This analysis yields some surprising results that some WTs are the most unreliable due to the rapid failure of its sub assemblies in view of the very high uncertainty in the wind and frequent grid failures.

Application of Non-uniform Sampling to Three Dimensional Carbon Direct-detection NMR Experiment

In this study, the combined use of 2 new techniques, nonuniform sampling (NUS) and carbon direct-detection (CDD), for the measurement of multidimensional NMR has been demonstrated. NUS is a method for sampling time domain data of indirect dimensions at random sparse points, whereas canonical multidimensional NMR spectra require all the regular grids as sampling points. Of several sparse sampling methods, NUS is advantageous, because it can reduce the errors that originate from the lack of sampling points by randomizing the sampling points. NUS can have denser sampling points at the beginning, where signals decay less than those in the end of sampling, and in turn enhance the signal-to-noise ratio (SNR) in the frequency dimensions per unit time. NUS is applicable to proteins that have been difficult to study using conventional NMR approaches. CDD is another area where applications have advanced considerably over the last several years. CDD is an effective technique for detecting NMR signals from proteins that exist under unfavorable conditions to observe or discriminate proton signals, which include paramagnetic proteins, highly deuterated samples, proteins of high salts, and disordered proteins. Despite the advances in NMR hardware, however, CDD has not been easily employed for practical applications, because the SNR of its result is insufficient. In this paper, NUS and CDD have been used in a combination in a 3D CBCACON experiment, expecting the supporting role of NUS in improving the SNR of CDD. The 3D CBCACON experiment provides the chemical shifts information of Cα/β(i-1)-N(i)-C'(i-1). The Bruker’s default pulse sequence of “c_cbcacon_ia3d” was modified to incorporate the NUS scheme. The sample used in the present study was ubiquitin (approximately 2.0 mM) and the reference and NUS experiments were performed using a Bruker AV 600 MHz NMR machine equipped with a TCI cryoprobe. The time domains of reference 3D CBCACON data consisted of 256* (F3: C') × 28* (F2: N) × 24* (F1: Cα/β) × 2 (IPAP) (*means complex point), and the number of transients was 8, leading to the total measurement time of 26 hours. The NUS schedule comprised 270 points, and it corresponded to about 40% of the intact points and required an 11-hour measuring time. As the chemical shifts of the Cα/β atoms evolved under constant time, the points for the Cα/β dimension were designed to have equal distribution, whereas the points for N dimension distributed to a Gaussian shape with higher density at the beginning (Fig. S1). To process the NUS data, multidimensional Fourier transformation (MFT) and the maximum entropy (MaxEnt) algorithms by using in-house written MFT processing program (J-G. Jee, unpublished data) and the Rowland NMR Toolkit (version 3.0), respectively, were employed. For conventional fast discrete Fourier transformation (FFT) processing and analyses of spectra, NMRPipe software was used. The overlaid 2D spectra of [C', N] and [C, Cα/β] in FFT, MFT, and MaxEnt results are shown in Figure 1. Because the number of sampling points in the current NUS decreased more than a half, a lower SNR was expected in the results. Although some noise peaks were observed in both the MFT and MaxEnt data due to the lower sensitivity caused by smaller points (Fig. 1), they are tolerable for the backbone chemical shifts assignment. Generally, the spectra reproduced by MaxEnt display a better resolution than those reproduced by MFT. However, insufficient quality or quantity of the input data may alter the chemical shifts. MFT is expected to generate fewer erroneous results despite its

Establishment of the genetic/genomic competency center for education.

Develop a trans-disciplinary repository of genomics education resources using a Web-based learning management system. The repository maps and organizes genetic-genomic information and materials relevant to educators by healthcare discipline-specific competencies and performance indicators. An interdisciplinary project team was established to guide toolkit repository building and usability testing. The toolkit was built using the X-CREDIT software on the Moodle learning management platform, which includes a mapping matrix and browsing function that captures teaching resources in a searchable database linked to competencies, knowledge areas, performance indicators, learning activities and resources, and outcome assessments. Discipline-specific advisory groups assisted in resource identification, competency mapping, and peer review. The toolkit is multidisciplinary, currently including physician assistants and nurses, and provides a resource crosslink to discipline-specific competencies. All resources have a detailed description, and users may contribute new resources, which are peer reviewed for relevance and accuracy by an editorial board. Alpha and beta testing using online usability surveys that included toolkit exercises helped refine the structure, look, and navigation of the final website. One hundred thirty faculty-124 nursing and 6 physician assistant faculty-agreed to participate. Of those, 59 users (45.4% response rate) completed the online usability survey. Nearly all users (94.9%) were able to find a competency that was relevant to their topic, and 85.4% were able to locate the relevant performance indicators. The majority (86.5%) felt the model adequately described the relationships between competencies, performance indicators, learning activities-resources, and assessments, and made conceptual sense. Survey respondents reported font color and size made the information difficult to read, windows were not large enough, and the "shopping cart" concept was confusing; all of these areas have been modified for the final toolkit version. Alpha and beta testing of the toolkit revealed that users can successfully obtain educational materials by searching competencies and performance indicators. The platform is accessible on the Internet at http://www.g-2-c-2.org and can be continually updated as new resources become available. Faculty members need easy access to a wide range of accurate, current resources to facilitate integration of genomics into the curriculum.

The ProteoRed MIAPE web toolkit: A User-friendly Framework to Connect and Share Proteomics Standards

The development of the HUPO-PSI's (Proteomics Standards Initiative) standard data formats and MIAPE (Minimum Information About a Proteomics Experiment) guidelines should improve proteomics data sharing within the scientific community. Proteomics journals have encouraged the use of these standards and guidelines to improve the quality of experimental reporting and ease the evaluation and publication of manuscripts. However, there is an evident lack of bioinformatics tools specifically designed to create and edit standard file formats and reports, or embed them within proteomics workflows. In this article, we describe a new web-based software suite (The ProteoRed MIAPE web toolkit) that performs several complementary roles related to proteomic data standards. First, it can verify that the reports fulfill the minimum information requirements of the corresponding MIAPE modules, highlighting inconsistencies or missing information. Second, the toolkit can convert several XML-based data standards directly into human readable MIAPE reports stored within the ProteoRed MIAPE repository. Finally, it can also perform the reverse operation, allowing users to export from MIAPE reports into XML files for computational processing, data sharing, or public database submission. The toolkit is thus the first application capable of automatically linking the PSI's MIAPE modules with the corresponding XML data exchange standards, enabling bidirectional conversions. This toolkit is freely available at http://www.proteored.org/MIAPE/.

Monte Carlo Simulations of Prompt-Gamma Emission During Carbon Ion Irradiation

Monte Carlo simulations based on the Geant4 toolkit (version 9.1) were performed to study the emission of secondary prompt-gamma rays produced by nuclear reactions during carbon ion-beam therapy. These simulations were performed along with an experimental program and instrumentation developments which aim at designing a prompt-gamma ray device for real-time control of hadrontherapy. The objective of the present study is twofold: firstly, to present the features of the prompt-gamma radiation in the case of carbon ion irradiation; secondly, to simulate the experimental setup and to compare measured and simulated counting rates corresponding to four different experiments. For each experiment, we found that simulations overestimate prompt-gamma ray detection yields by a factor of 12. Uncertainties in fragmentation cross sections and binary cascade model cannot explain such discrepancies. The so-called “photon evaporation” model is therefore questionable and its modification is currently in progress.

Validation of recent Geant4 physics models for application in carbon ion therapy

Abstract Cancer treatment with energetic carbon ions has distinct advantages over proton or photon irradiation. In this paper we present a simulation model integrated into the Geant4 Monte Carlo toolkit (version 9.3) which enables the use of ICRU 73 stopping powers for ion transport calculations. For a few materials, revised ICRU 73 stopping power tables recently published by ICRU (P. Sigmund, A. Schinner, H. Paul, Errata and Addenda: ICRU Report 73 (Stopping of Ions Heavier than Helium), International Commission on Radiation Units and Measurements, 2009) were incorporated into Geant4, also covering media like water which are of importance in radiotherapeutical applications. We examine, with particular attention paid to the recent developments, the accuracy of current Geant4 models for simulating Bragg peak profiles of 12 C ions incident on water and polyethylene targets. Simulated dose distributions are validated against experimental data available in the literature, where the focus is on beam energies relevant to ion therapy applications (90–400 MeV/u). A quantitative analysis is performed which addresses the precision of the Bragg peak position and proportional features of the dose distribution. It is shown that experimental peak positions can be reproduced within 0.2% of the particle range in the case of water, and within 0.9% in the case of polyethylene. The comparisons also demonstrate that the simulations accurately render the full width at half maximum (FWHM) of the measured Bragg peaks in water. For polyethylene slight deviations from experimental peak widths are partly attributed to systematic effects due to a simplified geometry model adopted in the simulation setup.

Accelerating numerical solution of stochastic differential equations with CUDA

Numerical integration of stochastic differential equations is commonly used in many branches of science. In this paper we present how to accelerate this kind of numerical calculations with popular NVIDIA Graphics Processing Units using the CUDA programming environment. We address general aspects of numerical programming on stream processors and illustrate them by two examples: the noisy phase dynamics in a Josephson junction and the noisy Kuramoto model. In presented cases the measured speedup can be as high as 675× compared to a typical CPU, which corresponds to several billion integration steps per second. This means that calculations which took weeks can now be completed in less than one hour. This brings stochastic simulation to a completely new level, opening for research a whole new range of problems which can now be solved interactively. Program summary Program title: SDE Catalogue identifier: AEFG_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEFG_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Gnu GPL v3 No. of lines in distributed program, including test data, etc.: 978 No. of bytes in distributed program, including test data, etc.: 5905 Distribution format: tar.gz Programming language: CUDA C Computer: any system with a CUDA-compatible GPU Operating system: Linux RAM: 64 MB of GPU memory Classification: 4.3 External routines: The program requires the NVIDIA CUDA Toolkit Version 2.0 or newer and the GNU Scientific Library v1.0 or newer. Optionally gnuplot is recommended for quick visualization of the results. Nature of problem: Direct numerical integration of stochastic differential equations is a computationally intensive problem, due to the necessity of calculating multiple independent realizations of the system. We exploit the inherent parallelism of this problem and perform the calculations on GPUs using the CUDA programming environment. The GPU's ability to execute hundreds of threads simultaneously makes it possible to speed up the computation by over two orders of magnitude, compared to a typical modern CPU. Solution method: The stochastic Runge–Kutta method of the second order is applied to integrate the equation of motion. Ensemble-averaged quantities of interest are obtained through averaging over multiple independent realizations of the system. Unusual features: The numerical solution of the stochastic differential equations in question is performed on a GPU using the CUDA environment. Running time: < 1 minute

BaBar MC production on the Canadian grid using a web services approach

The present paper highlights the approach used to design and implement a web services based BaBar Monte Carlo (MC) production grid using Globus Toolkit version 4. The grid integrates the resources of two clusters at the University of Victoria, using the ClassAd mechanism provided by the Condor-G metascheduler. Each cluster uses the Portable Batch System (PBS) as its local resource management system (LRMS). Resource brokering is provided by the Condor matchmaking process, whereby the job and resource attributes are expressed as ClassAds. The important features of the grid are automatic registering of resource ClassAds to the central registry, ClassAds extraction from the registry to the metascheduler for matchmaking, and the incorporation of input/output file staging. Web-based monitoring is employed to track the status of grid resources and the jobs for an efficient operation of the grid. The performance of this new grid for BaBar jobs, and the existing Canadian computational grid (GridX1) based on Globus Toolkit version 2 is found to be consistent.

Wide area data replication for scientific collaborations

Scientific applications require sophisticated data management capabilities. We present the design and implementation of a data replication service (DRS), one of a planned set of higher-level data management services for Grids. The capabilities of the DRS are based on the publication capability of the lightweight data replicator (LDR) system developed for the LIGO Scientific Collaboration. We describe LIGO publication requirements and LDR functionality. We also describe the design and implementation of the DRS in the Globus Toolkit Version 4.0 environment and present performance results.

Towards semantic-aware management of security services in GT4

Globus Toolkit version 4 (GT4) leads to a set of new services and tools. This is the culmination of a first step towards the migration to web services from previous Globus Toolkit versions. GT4 directly addresses basic issues, in the form of services, inherent to any distributed system like, for example, security, resource discovery, data movement and management, etc. However, we believe that an advanced management is still needed in the framework, in order to provide a system-wide view of these services. This is especially true in the case of security related services. They must be properly managed all across different collaborating organizations within the grid infrastructure. This paper presents the major achievements when designing and developing a semantic-aware management framework for GT4 security services.