GPU-based ultra-fast direct aperture optimization for online adaptive radiation therapy

Online adaptive radiation therapy (ART) has great promise to significantly reduce normal tissue toxicity and/or improve tumor control through real-time treatment adaptations based on the current patient anatomy. However, the major technical obstacle for clinical realization of online ART, namely the inability to achieve real-time efficiency in treatment re-planning, has yet to be solved. To overcome this challenge, this paper presents our work on the implementation of an intensity modulated radiation therapy (IMRT) direct aperture optimization (DAO) algorithm on graphics processing unit (GPU) based on our previous work on CPU. We formulate the DAO problem as a large-scale convex programming problem, and use an exact method called column generation approach to deal with its extremely large dimensionality on GPU. Five 9-field prostate and five 5-field head-and-neck IMRT clinical cases with 5\times5 mm2 beamlet size and 2.5\times2.5\times2.5 mm3 voxel size were used to evaluate our algorithm on GPU. It takes only 0.7~2.5 seconds for our implementation to generate optimal treatment plans using 50 MLC apertures on an NVIDIA Tesla C1060 GPU card. Our work has therefore solved a major problem in developing ultra-fast (re-)planning technologies for online ART

Student Perceptions of Problem Topics/Concepts in a Traditional Veterinary Embryology

Even though particular attention is paid to the nature and content of anatomy curricula, little has been published about the actual problem topics/concepts experienced by students of anatomy. This information is relevant to modifying existing courses and methods of teaching. The present study thus sought to identify, by means of a questionnaire administered to students of veterinary anatomy, perceived problem topics, the possible reasons for the problems, as well as student suggestions for solving the problems. A wide range of problem topics were identified by this survey, of which the development of heart and cardiovascular system, development of face/head, foetal membrane/placentation particularly 3 D pictures and then the development of body form and urogenital (including external genitalia) recurred most frequently. A major reason given for the problems experienced was an inability to conceptualise 3-dimensional structures. Students requested more time, more lectures and appealed for a reduction in detail of textual information. Many of the problems experienced by this group of students are reflected in other studies of veterinary, medical and dental students, which suggests the existence of ‘universal’ problem topics in the various fields of anatomy. We believe that these universal problem topics exist in many anatomy courses, despite the application of innovative teaching methods and advanced audio-visual technologies. Only by identifying these topics can suitable strategies (within the constraints of the particular curriculum) be devised to resolve them.Keywords: Anatomy, Embryology, Histology, Problem Topics/Concepts, Student Perceptions

GPU-based fast gamma index calcuation

The gamma-index dose comparison tool has been widely used to compare dose distributions in cancer radiotherapy. The accurate calculation of gamma-index requires an exhaustive search of the closest Euclidean distance in the high-resolution dose-distance space. This is a computational intensive task when dealing with 3D dose distributions. In this work, we combine a geometric method with a radial pre-sorting technique , and implement them on computer graphics processing units (GPUs). The developed GPU-based gamma-index computational tool is evaluated on eight pairs of IMRT dose distributions. The GPU implementation achieved 20x~30x speedup factor compared to CPU implementation and gamma-index calculations can be finished within a few seconds for all 3D testing cases. We further investigated the effect of various factors on both CPU and GPU computation time. The strategy of pre-sorting voxels based on their dose difference values speed up the GPU calculation by about 2-4 times. For n-dimensional dose distributions, gamma-index calculation time on CPU is proportional to the summation of gamma^n over all voxels, while that on GPU is effected by gamma^n distributions and is approximately proportional to the gamma^n summation over all voxels. We found increasing dose distributions resolution leads to quadratic increase of computation time on CPU, while less-than-quadratic increase on GPU. The values of dose difference (DD) and distance-to-agreement (DTA) criteria also have their impact on gamma-index calculation time.Comment: 13 pages, 2 figures, and 3 table

Alcohol increases circulatory disease mortality in Russia: acute and chronic effects or misattribution of cause?

Background There is a consensus that the large fluctuations in mortality seen in Russia in the past two decades can be attributed to trends in alcohol consumption. However, the precise mechanisms linking alcohol to mortality from circulatory disease remain unclear. It has recently been argued that a substantial number of such deaths currently ascribed to cardiovascular disorders are misclassified cases of acute alcohol poisoning

Global Health Actors Claim To Support Health System Strengthening—Is This Reality or Rhetoric?

Bruno Marchal and colleagues argue that most current strategies aimed at health systems strengthening remain selectively targeted at specific diseases

Tensile Deformation of Oriented Poly(ε-caprolactone) and Its Miscible Blends with Poly(vinyl methyl ether)

The structural evolution of micromolded poly(ε-caprolactone) (PCL) and its miscible blends with noncrystallizable poly(vinyl methyl ether) (PVME) at the nanoscale was investigated as a function of deformation ratio and blend composition using in situ synchrotron smallangle X-ray scattering (SAXS) and scanning SAXS techniques. It was found that the deformation mechanism of the oriented samples shows a general scheme for the process of tensile deformation: crystal block slips within the lamellae occur at small deformations followed by a stressinduced fragmentation and recrystallization process along the drawing direction at a critical strain where the average thickness of the crystalline lamellae remains essentially constant during stretching. The value of the critical strain depends on the amount of the amorphous component incorporated in the blends, which could be traced back to the lower modulus of the entangled amorphous phase and, therefore, the reduced network stress acting on the crystallites upon addition of PVME. When stretching beyond the critical strain the slippage of the fibrils (stacks of newly formed lamellae) past each other takes place resulting in a relaxation of stretched interlamellar amorphous chains. Because of deformation-induced introduction of the amorphous PVME into the interfibrillar regions in the highly oriented blends, the interactions between fibrils becomes stronger upon further deformation and thus impeding sliding of the fibrils to some extent leading finally to less contraction of the interlamellar amorphous layers compared to the pure PCLNational Natural Science Foundation of China (21204088 and 21134006). This work is within the framework of the RCUK/EPSRC Science Bridges China project of UK−China Advanced Materials Research Institute (AMRI)

Orbital effects of a monochromatic plane gravitational wave with ultra-low frequency incident on a gravitationally bound two-body system

We analytically compute the long-term orbital variations of a test particle orbiting a central body acted upon by an incident monochromatic plane gravitational wave. We assume that the characteristic size of the perturbed two-body system is much smaller than the wavelength of the wave. Moreover, we also suppose that the wave's frequency is much smaller than the particle's orbital one. We make neither a priori assumptions about the direction of the wavevector nor on the orbital geometry of the planet. We find that, while the semi-major axis is left unaffected, the eccentricity, the inclination, the longitude of the ascending node, the longitude of pericenter and the mean anomaly undergo non-vanishing long-term changes. They are not secular trends because of the slow modulation introduced by the tidal matrix coefficients and by the orbital elements themselves. They could be useful to indepenedently constrain the ultra-low frequency waves which may have been indirectly detected in the BICEP2 experiment. Our calculation holds, in general, for any gravitationally bound two-body system whose characteristic frequency is much larger than the frequency of the external wave. It is also valid for a generic perturbation of tidal type with constant coefficients over timescales of the order of the orbital period of the perturbed particle.Comment: LaTex2e, 24 pages, no figures, no tables. Changes suggested by the referees include

Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development.

BACKGROUND: We present the genome sequence of the tammar wallaby, Macropus eugenii, which is a member of the kangaroo family and the first representative of the iconic hopping mammals that symbolize Australia to be sequenced. The tammar has many unusual biological characteristics, including the longest period of embryonic diapause of any mammal, extremely synchronized seasonal breeding and prolonged and sophisticated lactation within a well-defined pouch. Like other marsupials, it gives birth to highly altricial young, and has a small number of very large chromosomes, making it a valuable model for genomics, reproduction and development. RESULTS: The genome has been sequenced to 2 × coverage using Sanger sequencing, enhanced with additional next generation sequencing and the integration of extensive physical and linkage maps to build the genome assembly. We also sequenced the tammar transcriptome across many tissues and developmental time points. Our analyses of these data shed light on mammalian reproduction, development and genome evolution: there is innovation in reproductive and lactational genes, rapid evolution of germ cell genes, and incomplete, locus-specific X inactivation. We also observe novel retrotransposons and a highly rearranged major histocompatibility complex, with many class I genes located outside the complex. Novel microRNAs in the tammar HOX clusters uncover new potential mammalian HOX regulatory elements. CONCLUSIONS: Analyses of these resources enhance our understanding of marsupial gene evolution, identify marsupial-specific conserved non-coding elements and critical genes across a range of biological systems, including reproduction, development and immunity, and provide new insight into marsupial and mammalian biology and genome evolution

IL-6 mediated JAK/STAT3 signaling pathway in cancer patients with cachexia

CONCLUSION: STAT3 may be considered as a therapeutic target for cachectic patients with gastric, lung and breast cancer. Furthermore, IL-6 mediates STAT3 activation in cachectic gastric and breast cancer patients (Tab. 5, Fig. 2, Ref. 62)

Genome-wide association analysis of dementia and its clinical endophenotypes reveal novel loci associated with Alzheimer's disease and three causality networks: The GR@ACE project

INTRODUCTION: Large variability among Alzheimer's disease (AD) cases might impact genetic discoveries and complicate dissection of underlying biological pathways. METHODS: Genome Research at Fundacio ACE (GR@ACE) is a genome-wide study of dementia and its clinical endophenotypes, defined based on AD's clinical certainty and vascular burden. We assessed the impact of known AD loci across endophenotypes to generate loci categories. We incorporated gene coexpression data and conducted pathway analysis per category. Finally, to evaluate the effect of heterogeneity in genetic studies, GR@ACE series were meta-analyzed with additional genome-wide association study data sets. RESULTS: We classified known AD loci into three categories, which might reflect the disease clinical heterogeneity. Vascular processes were only detected as a causal mechanism in probable AD. The meta-analysis strategy revealed the ANKRD31-rs4704171 and NDUFAF6-rs10098778 and confirmed SCIMP-rs7225151 and CD33-rs3865444. DISCUSSION: The regulation of vasculature is a prominent causal component of probable AD. GR@ACE meta-analysis revealed novel AD genetic signals, strongly driven by the presence of clinical heterogeneity in the AD series