Pencil beam dose calculation for proton therapy on graphics processing units

Radiotherapy delivered using scanned beams of protons enables greater conformity between the dose distribution and the tumour than conventional radiotherapy using X rays. However, the dose distributions are more sensitive to changes in patient anatomy, and tend to deteriorate in the presence of motion. Online dose calculation during treatment delivery offers a way of monitoring the delivered dose in real time, and could be used as a basis for mitigating the effects of motion. The aim of this work has therefore been to investigate how the computational power offered by graphics processing units can be harnessed to enable fast analytical dose calculation for online monitoring in proton therapy. The first part of the work consisted of a systematic investigation of various approaches to implementing the most computationally expensive step of the pencil beam algorithm to run on graphics processing units. As a result, it was demonstrated how the kernel superposition operation, or convolution with a spatially varying kernel, can be efficiently implemented using a novel scatter-based approach. For the intended application, this outperformed the conventional gather-based approach suggested in the literature, permitting faster pencil beam dose calculation and potential speedups of related algorithms in other fields. In the second part, a parallelised proton therapy dose calculation engine employing the scatter-based kernel superposition implementation was developed. Such a dose calculation engine, running all of the principal steps of the pencil beam algorithm on a graphics processing unit, had not previously been presented in the literature. The accuracy of the calculation in the high- and medium-dose regions matched that of a clinical treatment planning system whilst the calculation was an order of magnitude faster than previously reported. Importantly, the calculation times were short, both compared to the dead time available during treatment delivery and to the typical motion period, making the implementation suitable for online calculation. In the final part, the beam model of the dose calculation engine was extended to account for the low-dose halo caused by particles travelling at large angles with the beam, making the algorithm comparable to those in current clinical use. By reusing the workflow of the initial calculation but employing a lower resolution for the halo calculation, it was demonstrated how the improved beam model could be included without prohibitively prolonging the calculation time. Since the implementation was based on a widely used algorithm, it was further predicted that by careful tuning, the dose calculation engine would be able to reproduce the dose from a general beamline with sufficient accuracy. Based on the presented results, it was concluded that, by using a single graphics processing unit, dose calculation using the pencil beam algorithm could be made sufficiently fast for online dose monitoring, whilst maintaining the accuracy of current clinical systems.Financial support for this project came from the ENTERVISION Marie Curie Initial Training Network, funded by the European Commission Seventh Framework Programme grant agreement number 264,552. The Tesla K40 graphics processing unit used in parts of this work was donated by Nvidia Corporation through their Hardware Grant Program

Image Processing with MATLAB and GPU

Geology & the lithospher

Sub-second pencil beam dose calculation on GPU for adaptive proton therapy.

This is the author accepted manuscript. The final version is available from IOP via https://iopscience.iop.org/article/10.1088/0031-9155/60/12/4777.Although proton therapy delivered using scanned pencil beams has the potential to produce better dose conformity than conventional radiotherapy, the created dose distributions are more sensitive to anatomical changes and patient motion. Therefore, the introduction of adaptive treatment techniques where the dose can be monitored as it is being delivered is highly desirable. We present a GPU-based dose calculation engine relying on the widely used pencil beam algorithm, developed for on-line dose calculation. The calculation engine was implemented from scratch, with each step of the algorithm parallelized and adapted to run efficiently on the GPU architecture. To ensure fast calculation, it employs several application-specific modifications and simplifications, and a fast scatter-based implementation of the computationally expensive kernel superposition step. The calculation time for a skull base treatment plan using two beam directions was 0.22 s on an Nvidia Tesla K40 GPU, whereas a test case of a cubic target in water from the literature took 0.14 s to calculate. The accuracy of the patient dose distributions was assessed by calculating the γ-index with respect to a gold standard Monte Carlo simulation. The passing rates were 99.2% and 96.7%, respectively, for the 3%/3 mm and 2%/2 mm criteria, matching those produced by a clinical treatment planning system.This research was funded by the European Commission Seventh Framework People Programme through the ENTERVISION project, grant agreement 264552. Dr Jena is funded in part by Cancer Research UK, grant 13716. The Tesla K40 GPU used for benchmarking was donated by the Nvidia Corporation through their Hardware Grant Program

Low Postseroconversion CD4+ T-cell Level Is Associated with Faster Disease Progression and Higher Viral Evolutionary Rate in HIV-2 Infection

L

The Role of TiO2 Doping on RuO2-Coated Electrodes for the Water Oxidation Reaction

Electrochemical water splitting into H2 and O2 presents a significant and challenging energy loss due to the high overpotential required at the anode. Today, in industrially relevant applications, dimensionally stable anodes (DSA) based on the electrocatalytic active RuO2 are conventionally utilized. To enhance the resistance against corrosion, incorporation of TiO2 in the RuO2-coated electrodes is widely employed. In the present work we have used scanning electrochemical microscopy (SECM) to demonstrate that TiO2-doped RuO2-coated electrodes, in addition to being more durable, also show an electrocatalytic activity that is, on average, 13% higher as compared to the pure RuO2-coated electrodes. We also demonstrate that cracks in the pure RuO2 coating are the most active zones, probably because Ti from the Ti support has diffused into the first applied layer of the RuO2 coating. To reveal the nature of this enhanced activity for water oxidation displayed on TiO2-doped RuO2 electrodes, we have employed X-ray photoelectron spectroscopy (XPS) for material characterization. The results show that the electrocatalytic activity enhancement displayed on the mixed (Ru1–x:Tix)O2 coating is promoted through a charge transfer from the RuO2 to the TiO2, which provides new and more reactive sites designated as activated RuO2δ+.This study has partly been carried out in the framework of the European Commission FP7 Initial Training Network “ELCAT”, Grant Agreement No. 214936-2. Portions of this research were performed at SPring-8 with the approval of Japan Synchrotron Radiation Research Institute as Nanotechnology Support Project of the Ministry of Education, Culture, Sports, Science and Technology (Proposal No. 2007A2005 and 2008A1671/BL-47XU)

Frequent CXCR4 tropism of HIV-1 subtype A and CRF02_AG during late-stage disease - indication of an evolving epidemic in West Africa

<p>Abstract</p> <p>Background</p> <p>HIV-1 is one of the fastest evolving pathogens, and is distinguished by geographic and genetic variants that have been classified into different subtypes and circulating recombinant forms (CRFs). Early in infection the primary coreceptor is CCR5, but during disease course CXCR4-using HIV-1 populations may emerge. This has been correlated with accelerated disease progression in HIV-1 subtype B. Basic knowledge of HIV-1 coreceptor tropism is important due to the recent introduction of coreceptor antagonists in antiretroviral therapy, and subtype-specific differences regarding how frequently HIV-1 CXCR4-using populations appear in late-stage disease need to be further investigated. To study how frequently CXCR4-using populations appear in late-stage disease among HIV-1 subtype A and CRF02_AG, we evaluated the accuracy of a recombinant virus phenotypic assay for these subtypes, and used it to determine the HIV-1 coreceptor tropism of plasma samples collected during late-stage disease in Guinea-Bissau. We also performed a genotypic analysis and investigated subtype-specific differences in the appearance of CXCR4 tropism late in disease.</p> <p>Results</p> <p>We found that the recombinant virus phenotypic assay accurately predicted HIV-1 coreceptor tropism of subtype A and CRF02_AG. Over the study period (1997-2007), we found an increasing and generally high frequency of CXCR4 tropism (86%) in CRF02_AG. By sequence analysis of the V3 region of our samples we developed a novel genotypic rule for predicting CXCR4 tropism in CRF02_AG, based on the combined criteria of the total number of charged amino acids and net charge. This rule had higher sensitivity than previously described genotypic rules and may be useful for development of future genotypic tools for this CRF. Finally, we conducted a literature analysis, combining data of 498 individuals in late-stage disease, and found high amounts of CXCR4 tropism for all major HIV-1 subtypes (60-77%), except for subtype C (15%).</p> <p>Conclusions</p> <p>The increase in CXCR4 tropism over time suggests an evolving epidemic of CRF02_AG. The results of the literature analysis demonstrate the need for further studies investigating subtype-specific emergence for CXCR4-tropism; this may be particularly important due to the introduction of CCR5-antagonists in HIV treatment regimens.</p

Production of He-4 and (4) in Pb-Pb collisions at root(NN)-N-S=2.76 TeV at the LHC

Results on the production of He-4 and (4) nuclei in Pb-Pb collisions at root(NN)-N-S = 2.76 TeV in the rapidity range vertical bar y vertical bar <1, using the ALICE detector, are presented in this paper. The rapidity densities corresponding to 0-10% central events are found to be dN/dy4(He) = (0.8 +/- 0.4 (stat) +/- 0.3 (syst)) x 10(-6) and dN/dy4 = (1.1 +/- 0.4 (stat) +/- 0.2 (syst)) x 10(-6), respectively. This is in agreement with the statistical thermal model expectation assuming the same chemical freeze-out temperature (T-chem = 156 MeV) as for light hadrons. The measured ratio of (4)/He-4 is 1.4 +/- 0.8 (stat) +/- 0.5 (syst). (C) 2018 Published by Elsevier B.V.Peer reviewe

Azimuthal anisotropy of charged jet production in root s(NN)=2.76 TeV Pb-Pb collisions

We present measurements of the azimuthal dependence of charged jet production in central and semi-central root s(NN) = 2.76 TeV Pb-Pb collisions with respect to the second harmonic event plane, quantified as nu(ch)(2) (jet). Jet finding is performed employing the anti-k(T) algorithm with a resolution parameter R = 0.2 using charged tracks from the ALICE tracking system. The contribution of the azimuthal anisotropy of the underlying event is taken into account event-by-event. The remaining (statistical) region-to-region fluctuations are removed on an ensemble basis by unfolding the jet spectra for different event plane orientations independently. Significant non-zero nu(ch)(2) (jet) is observed in semi-central collisions (30-50% centrality) for 20 <p(T)(ch) (jet) <90 GeV/c. The azimuthal dependence of the charged jet production is similar to the dependence observed for jets comprising both charged and neutral fragments, and compatible with measurements of the nu(2) of single charged particles at high p(T). Good agreement between the data and predictions from JEWEL, an event generator simulating parton shower evolution in the presence of a dense QCD medium, is found in semi-central collisions. (C) 2015 CERN for the benefit of the ALICE Collaboration. Published by Elsevier B.V. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).Peer reviewe

Forward-central two-particle correlations in p-Pb collisions at root s(NN)=5.02 TeV

Two-particle angular correlations between trigger particles in the forward pseudorapidity range (2.5 2GeV/c. (C) 2015 CERN for the benefit of the ALICE Collaboration. Published by Elsevier B. V.Peer reviewe

Event-shape engineering for inclusive spectra and elliptic flow in Pb-Pb collisions at root(NN)-N-S=2.76 TeV

Peer reviewe