New Science Gateways for Advanced Computing Simulations and Visualization Using Vine Toolkit in PL-Grid

A Science Gateway is a connection between scientists and their computational tools in the form of web portal. It creates a space for communities, collaboration and data sharing and visualization in a comprehensive and efficient manner. The main purpose of such a solution is to allow users to access the computational resources, process and analyze their data and get the results in a uniform and user friendly way. In this paper we propose a complex solution based on the Rich Internet Application (RIA) approach consisting of a web portal powered by Vine Toolkit with Adobe Flex/BlazeDs technologies. There are two Science Gateways described in detail one for engineers to manage computationally intensive workflows used in advanced airplane construction simulations, and one for nanotechnology scientists to manage experiments in nano-science field calculated with Density Functional Theory (DFT). In both cases the results show how modern web solution can help scientists in their work. &nbsp

Adaptation of MPDATA Heterogeneous Stencil Computation to Intel Xeon Phi Coprocessor

The multidimensional positive definite advection transport algorithm (MPDATA) belongs to the group of nonoscillatory forward-in-time algorithms and performs a sequence of stencil computations. MPDATA is one of the major parts of the dynamic core of the EULAG geophysical model. In this work, we outline an approach to adaptation of the 3D MPDATA algorithm to the Intel MIC architecture. In order to utilize available computing resources, we propose the (3 + 1)D decomposition of MPDATA heterogeneous stencil computations. This approach is based on combination of the loop tiling and fusion techniques. It allows us to ease memory/communication bounds and better exploit the theoretical floating point efficiency of target computing platforms. An important method of improving the efficiency of the (3 + 1)D decomposition is partitioning of available cores/threads into work teams. It permits for reducing inter-cache communication overheads. This method also increases opportunities for the efficient distribution of MPDATA computation onto available resources of the Intel MIC architecture, as well as Intel CPUs. We discuss preliminary performance results obtained on two hybrid platforms, containing two CPUs and Intel Xeon Phi. The top-of-the-line Intel Xeon Phi 7120P gives the best performance results, and executes MPDATA almost 2 times faster than two Intel Xeon E5-2697v2 CPUs

Reproducibility and repeatability of a semi-automated pipeline to quantify trapeziometacarpal joint angles using dynamic computed tomography

Abstract Background The trapeziometacarpal (TMC) joint is a mechanically complex joint and is commonly affected by musculoskeletal diseases such as osteoarthritis. Quantifying in vivo TMC joint biomechanics, such as joint angles, with traditional reflective marker-based methods can be difficult due to the joint’s location in the hand. Dynamic computed tomography (CT) can facilitate the quantification of TMC joint motion by continuously capturing three-dimensional volumes over time. However, post-processing of dynamic CT datasets can be time intensive and automated methods are needed to reduce processing times to allow for application to larger clinical studies. The purpose of this work is to introduce a fast, semi-automated pipeline to quantify joint angles from dynamic CT scans of the TMC joint and evaluate the associated error in joint angle and translation computation by means of a reproducibility and repeatability study. Methods Ten cadaveric hands were scanned with dynamic CT using a passive motion device to move thumbs in a radial abduction–adduction motion. Static CT scans and high-resolution peripheral quantitative CT scans were also acquired to generate high-resolution bone meshes. Abduction–adduction, flexion–extension, and axial rotation angles were computed using a joint coordinate system. Reproducibility and repeatability were assessed using intraclass correlation coefficients, Bland–Altman analysis, and root mean square errors. Target registration errors were computed to evaluate errors associated with image registration. Results We found good repeatability for flexion–extension, abduction–adduction, and axial rotation angles. Reproducibility was moderate for all three angles. Joint translations exhibited greater repeatability than reproducibility. Specimens with greater joint degeneration had lower repeatability and reproducibility. We found that the difference in resulting joint angles and translations were likely due to differences in segment coordinate system definition between multiple raters, rather than due to registration errors. Conclusions The proposed semi-automatic processing pipeline was fast, repeatable, and moderately reproducible when quantifying TMC joint angles and translations. This work provides a range of errors for TMC joint angles from dynamic CT scans using manually selected anatomical landmarks

Postural control in patients with lumbar disc herniation in the early postoperative period

Chronic spinal disc disease leads to disorders in postural movement coordination. An incorrect asymmetrical movement pattern for the lower limbs loading impairs proprioception and deteriorates postural stability, particularly when the vision is occluded. The standard surgical treatment improves biomechanical conditions in the lumbar spine, reduces pain, yet does it reduce the stability deficit in the upright position? An answer to the latter question would help work out targeted therapy to improve postural stability. We hypothesized that the standard surgical treatment would improve postural stability reflected by decreased sway variability accounting for better use of proprioceptive inputs postoperatively. Thirty-nine patients with lumbar disc herniation participated in the study. Their postural sway was recorded in anterior/posterior and medial/lateral planes with their eyes open or closed (EC) before and after surgery. The variability, range, mean velocity of the recorded time series and the area of the ellipse enclosed by the statokinesiogram were used as measures of postural stability. Preoperatively, EC condition resulted in an increased variability and mean velocity of postural sway, while postoperatively it caused an increase in sway mean velocity and sway area only with no effect on sway variability and range. The comparison of the balance before and after the surgery in the EC condition showed significant decrease in all parameters. In the early postoperative period, the patients recover the ability to control their postural sway in EC within normal limits, however, at the expense of significantly increased frequency of corrective torques. It is probably a transient short-term strategy needed to compensate for the recovery phase when the normal weighting factors for all afferents are being reestablished. We propose that this transient postoperative period may be the best timing of therapeutic intervention targeted at facilitating and reinforcing the acquisition of correct motor patterns