Parallel preconditioning techniques for sparse CG solvers
Energy Technology Data Exchange (ETDEWEB)
Basermann, A.; Reichel, B.; Schelthoff, C. [Central Institute for Applied Mathematics, Juelich (Germany)
1996-12-31
Conjugate gradient (CG) methods to solve sparse systems of linear equations play an important role in numerical methods for solving discretized partial differential equations. The large size and the condition of many technical or physical applications in this area result in the need for efficient parallelization and preconditioning techniques of the CG method. In particular for very ill-conditioned matrices, sophisticated preconditioner are necessary to obtain both acceptable convergence and accuracy of CG. Here, we investigate variants of polynomial and incomplete Cholesky preconditioners that markedly reduce the iterations of the simply diagonally scaled CG and are shown to be well suited for massively parallel machines.
Longoni, Gianluca
In the nuclear science and engineering field, radiation transport calculations play a key-role in the design and optimization of nuclear devices. The linear Boltzmann equation describes the angular, energy and spatial variations of the particle or radiation distribution. The discrete ordinates method (S N) is the most widely used technique for solving the linear Boltzmann equation. However, for realistic problems, the memory and computing time require the use of supercomputers. This research is devoted to the development of new formulations for the SN method, especially for highly angular dependent problems, in parallel environments. The present research work addresses two main issues affecting the accuracy and performance of SN transport theory methods: quadrature sets and acceleration techniques. New advanced quadrature techniques which allow for large numbers of angles with a capability for local angular refinement have been developed. These techniques have been integrated into the 3-D SN PENTRAN (Parallel Environment Neutral-particle TRANsport) code and applied to highly angular dependent problems, such as CT-Scan devices, that are widely used to obtain detailed 3-D images for industrial/medical applications. In addition, the accurate simulation of core physics and shielding problems with strong heterogeneities and transport effects requires the numerical solution of the transport equation. In general, the convergence rate of the solution methods for the transport equation is reduced for large problems with optically thick regions and scattering ratios approaching unity. To remedy this situation, new acceleration algorithms based on the Even-Parity Simplified SN (EP-SSN) method have been developed. A new stand-alone code system, PENSSn (Parallel Environment Neutral-particle Simplified SN), has been developed based on the EP-SSN method. The code is designed for parallel computing environments with spatial, angular and hybrid (spatial/angular) domain
A Hybrid Parallel Preconditioning Algorithm For CFD
Barth,Timothy J.; Tang, Wei-Pai; Kwak, Dochan (Technical Monitor)
1995-01-01
A new hybrid preconditioning algorithm will be presented which combines the favorable attributes of incomplete lower-upper (ILU) factorization with the favorable attributes of the approximate inverse method recently advocated by numerous researchers. The quality of the preconditioner is adjustable and can be increased at the cost of additional computation while at the same time the storage required is roughly constant and approximately equal to the storage required for the original matrix. In addition, the preconditioning algorithm suggests an efficient and natural parallel implementation with reduced communication. Sample calculations will be presented for the numerical solution of multi-dimensional advection-diffusion equations. The matrix solver has also been embedded into a Newton algorithm for solving the nonlinear Euler and Navier-Stokes equations governing compressible flow. The full paper will show numerous examples in CFD to demonstrate the efficiency and robustness of the method.
Parallelization of the preconditioned IDR solver for modern multicore computer systems
Bessonov, O. A.; Fedoseyev, A. I.
2012-10-01
This paper present the analysis, parallelization and optimization approach for the large sparse matrix solver CNSPACK for modern multicore microprocessors. CNSPACK is an advanced solver successfully used for coupled solution of stiff problems arising in multiphysics applications such as CFD, semiconductor transport, kinetic and quantum problems. It employs iterative IDR algorithm with ILU preconditioning (user chosen ILU preconditioning order). CNSPACK has been successfully used during last decade for solving problems in several application areas, including fluid dynamics and semiconductor device simulation. However, there was a dramatic change in processor architectures and computer system organization in recent years. Due to this, performance criteria and methods have been revisited, together with involving the parallelization of the solver and preconditioner using Open MP environment. Results of the successful implementation for efficient parallelization are presented for the most advances computer system (Intel Core i7-9xx or two-processor Xeon 55xx/56xx).
Parallel preconditioned conjugate gradient algorithm applied to neutron diffusion problem
International Nuclear Information System (INIS)
Majumdar, A.; Martin, W.R.
1992-01-01
Numerical solution of the neutron diffusion problem requires solving a linear system of equations such as Ax = b, where A is an n x n symmetric positive definite (SPD) matrix; x and b are vectors with n components. The preconditioned conjugate gradient (PCG) algorithm is an efficient iterative method for solving such a linear system of equations. In this paper, the authors describe the implementation of a parallel PCG algorithm on a shared memory machine (BBN TC2000) and on a distributed workstation (IBM RS6000) environment created by the parallel virtual machine parallelization software
Parallelized preconditioned BiCGStab solution of sparse linear system equations in F-COBRA-TF
International Nuclear Information System (INIS)
Geemert, Rene van; Glück, Markus; Riedmann, Michael; Gabriel, Harry
2011-01-01
Recently, the in-house development of a preconditioned and parallelized BiCGStab solver has been pursued successfully in AREVA’s advanced sub-channel code F-COBRA-TF. This solver can be run either in a sequential computation mode on a single CPU, or in a parallel computation mode on multiple parallel CPUs. The developed procedure enables the computation of several thousands of successive sparse linear system solutions in F-COBRA-TF with acceptable wall clock run times. The current paper provides general information about F-COBRA-TF in terms of modeling capabilities and application areas, and points out where the relevance arises for the efficient iterative solution of sparse linear systems. Furthermore, the preconditioning and parallelization strategies in the developed BiCGStab iterative solution approach are discussed. The paper is concluded with a number of verification examples. (author)
An M-step preconditioned conjugate gradient method for parallel computation
Adams, L.
1983-01-01
This paper describes a preconditioned conjugate gradient method that can be effectively implemented on both vector machines and parallel arrays to solve sparse symmetric and positive definite systems of linear equations. The implementation on the CYBER 203/205 and on the Finite Element Machine is discussed and results obtained using the method on these machines are given.
Koldan, Jelena; Puzyrev, Vladimir; de la Puente, Josep; Houzeaux, Guillaume; Cela, José María
2014-06-01
We present an elaborate preconditioning scheme for Krylov subspace methods which has been developed to improve the performance and reduce the execution time of parallel node-based finite-element (FE) solvers for 3-D electromagnetic (EM) numerical modelling in exploration geophysics. This new preconditioner is based on algebraic multigrid (AMG) that uses different basic relaxation methods, such as Jacobi, symmetric successive over-relaxation (SSOR) and Gauss-Seidel, as smoothers and the wave front algorithm to create groups, which are used for a coarse-level generation. We have implemented and tested this new preconditioner within our parallel nodal FE solver for 3-D forward problems in EM induction geophysics. We have performed series of experiments for several models with different conductivity structures and characteristics to test the performance of our AMG preconditioning technique when combined with biconjugate gradient stabilized method. The results have shown that, the more challenging the problem is in terms of conductivity contrasts, ratio between the sizes of grid elements and/or frequency, the more benefit is obtained by using this preconditioner. Compared to other preconditioning schemes, such as diagonal, SSOR and truncated approximate inverse, the AMG preconditioner greatly improves the convergence of the iterative solver for all tested models. Also, when it comes to cases in which other preconditioners succeed to converge to a desired precision, AMG is able to considerably reduce the total execution time of the forward-problem code-up to an order of magnitude. Furthermore, the tests have confirmed that our AMG scheme ensures grid-independent rate of convergence, as well as improvement in convergence regardless of how big local mesh refinements are. In addition, AMG is designed to be a black-box preconditioner, which makes it easy to use and combine with different iterative methods. Finally, it has proved to be very practical and efficient in the
Constraint treatment techniques and parallel algorithms for multibody dynamic analysis. Ph.D. Thesis
Chiou, Jin-Chern
1990-01-01
Computational procedures for kinematic and dynamic analysis of three-dimensional multibody dynamic (MBD) systems are developed from the differential-algebraic equations (DAE's) viewpoint. Constraint violations during the time integration process are minimized and penalty constraint stabilization techniques and partitioning schemes are developed. The governing equations of motion, a two-stage staggered explicit-implicit numerical algorithm, are treated which takes advantage of a partitioned solution procedure. A robust and parallelizable integration algorithm is developed. This algorithm uses a two-stage staggered central difference algorithm to integrate the translational coordinates and the angular velocities. The angular orientations of bodies in MBD systems are then obtained by using an implicit algorithm via the kinematic relationship between Euler parameters and angular velocities. It is shown that the combination of the present solution procedures yields a computationally more accurate solution. To speed up the computational procedures, parallel implementation of the present constraint treatment techniques, the two-stage staggered explicit-implicit numerical algorithm was efficiently carried out. The DAE's and the constraint treatment techniques were transformed into arrowhead matrices to which Schur complement form was derived. By fully exploiting the sparse matrix structural analysis techniques, a parallel preconditioned conjugate gradient numerical algorithm is used to solve the systems equations written in Schur complement form. A software testbed was designed and implemented in both sequential and parallel computers. This testbed was used to demonstrate the robustness and efficiency of the constraint treatment techniques, the accuracy of the two-stage staggered explicit-implicit numerical algorithm, and the speed up of the Schur-complement-based parallel preconditioned conjugate gradient algorithm on a parallel computer.
Preconditioned conjugate gradient technique for the analysis of symmetric anisotropic structures
Noor, Ahmed K.; Peters, Jeanne M.
1987-01-01
An efficient preconditioned conjugate gradient (PCG) technique and a computational procedure are presented for the analysis of symmetric anisotropic structures. The technique is based on selecting the preconditioning matrix as the orthotropic part of the global stiffness matrix of the structure, with all the nonorthotropic terms set equal to zero. This particular choice of the preconditioning matrix results in reducing the size of the analysis model of the anisotropic structure to that of the corresponding orthotropic structure. The similarities between the proposed PCG technique and a reduction technique previously presented by the authors are identified and exploited to generate from the PCG technique direct measures for the sensitivity of the different response quantities to the nonorthotropic (anisotropic) material coefficients of the structure. The effectiveness of the PCG technique is demonstrated by means of a numerical example of an anisotropic cylindrical panel.
A Preconditioning Technique for First-Order Primal-Dual Splitting Method in Convex Optimization
Directory of Open Access Journals (Sweden)
Meng Wen
2017-01-01
Full Text Available We introduce a preconditioning technique for the first-order primal-dual splitting method. The primal-dual splitting method offers a very general framework for solving a large class of optimization problems arising in image processing. The key idea of the preconditioning technique is that the constant iterative parameters are updated self-adaptively in the iteration process. We also give a simple and easy way to choose the diagonal preconditioners while the convergence of the iterative algorithm is maintained. The efficiency of the proposed method is demonstrated on an image denoising problem. Numerical results show that the preconditioned iterative algorithm performs better than the original one.
International Nuclear Information System (INIS)
Hwang, F-N; Wei, Z-H; Huang, T-M; Wang Weichung
2010-01-01
We develop a parallel Jacobi-Davidson approach for finding a partial set of eigenpairs of large sparse polynomial eigenvalue problems with application in quantum dot simulation. A Jacobi-Davidson eigenvalue solver is implemented based on the Portable, Extensible Toolkit for Scientific Computation (PETSc). The eigensolver thus inherits PETSc's efficient and various parallel operations, linear solvers, preconditioning schemes, and easy usages. The parallel eigenvalue solver is then used to solve higher degree polynomial eigenvalue problems arising in numerical simulations of three dimensional quantum dots governed by Schroedinger's equations. We find that the parallel restricted additive Schwarz preconditioner in conjunction with a parallel Krylov subspace method (e.g. GMRES) can solve the correction equations, the most costly step in the Jacobi-Davidson algorithm, very efficiently in parallel. Besides, the overall performance is quite satisfactory. We have observed near perfect superlinear speedup by using up to 320 processors. The parallel eigensolver can find all target interior eigenpairs of a quintic polynomial eigenvalue problem with more than 32 million variables within 12 minutes by using 272 Intel 3.0 GHz processors.
Weighted graph based ordering techniques for preconditioned conjugate gradient methods
Clift, Simon S.; Tang, Wei-Pai
1994-01-01
We describe the basis of a matrix ordering heuristic for improving the incomplete factorization used in preconditioned conjugate gradient techniques applied to anisotropic PDE's. Several new matrix ordering techniques, derived from well-known algorithms in combinatorial graph theory, which attempt to implement this heuristic, are described. These ordering techniques are tested against a number of matrices arising from linear anisotropic PDE's, and compared with other matrix ordering techniques. A variation of RCM is shown to generally improve the quality of incomplete factorization preconditioners.
Energy Technology Data Exchange (ETDEWEB)
Choi, Kwan Woo; Son, Soon Yong [Dept. of Radiology, Asan Medical Center, Seoul (Korea, Republic of); Min, Jung Whan [Dept. of Radiological Technology, Shingu University, Sungnam (Korea, Republic of); Kwon, Kyung Tae [Dept. of Radiological Technology, Dongnam Health University, Suwon (Korea, Republic of); Yoo, Beong Gyu; Lee, Jong Seok [Dept. of Radiotechnology, Wonkwang Health Science University, Iksan (Korea, Republic of)
2015-12-15
The purpose of this study was to investigate the problems of a signal to noise ratio measurement using a two region measurement method that is conventionally used when using a multi-channel coil and a parallel imaging technique. As a research method, after calculating the standard SNR using a single channel head coil of which coil satisfies three preconditions when using a two region measurement method, we made comparisons and evaluations after calculating an SNR by using a two region measurement method of which method is problematic because it is used without considering the methods recommended by reputable organizations and the preconditions at the time of using a multi-channel coil and a parallel imaging technique. We found that a two region measurement method using a multi-channel coil and a parallel imaging technique shows the highest relative standard deviation, and thus shows a low degree of precision. In addition, we found out that the difference of SNR according to ROI location was very high, and thus a spatial noise distribution was not uniform. Also, 95% confidence interval through Blend-Altman plot is the widest, and thus the conformity degree with a two region measurement method using the standard single channel head coil is low. By directly comparing an AAPM method, which serves as a standard of a performance evaluation test of a magnetic resonance imaging device under the same image acquisition conditions, an NEMA method which can accurately determine the noise level in a signal region and the methods recommended by manufacturers of a magnetic resonance imaging device, there is a significance in that we quantitatively verified the inaccurate problems of a signal to noise ratio using a two region measurement method when using a multi-channel coil and a parallel imaging technique of which method does not satisfy the preconditions that researchers could overlook.
CSIR Research Space (South Africa)
Toper, AZ
1998-01-01
Full Text Available This research report discusses the development of preconditioning techniques to control face bursts, for safer mining in seismically hazardous areas. Preconditioning involves regularly setting off carefully tailored blasts in the fractured rock...
The multigrid preconditioned conjugate gradient method
Tatebe, Osamu
1993-01-01
A multigrid preconditioned conjugate gradient method (MGCG method), which uses the multigrid method as a preconditioner of the PCG method, is proposed. The multigrid method has inherent high parallelism and improves convergence of long wavelength components, which is important in iterative methods. By using this method as a preconditioner of the PCG method, an efficient method with high parallelism and fast convergence is obtained. First, it is considered a necessary condition of the multigrid preconditioner in order to satisfy requirements of a preconditioner of the PCG method. Next numerical experiments show a behavior of the MGCG method and that the MGCG method is superior to both the ICCG method and the multigrid method in point of fast convergence and high parallelism. This fast convergence is understood in terms of the eigenvalue analysis of the preconditioned matrix. From this observation of the multigrid preconditioner, it is realized that the MGCG method converges in very few iterations and the multigrid preconditioner is a desirable preconditioner of the conjugate gradient method.
Matrix preconditioning: a robust operation for optical linear algebra processors.
Ghosh, A; Paparao, P
1987-07-15
Analog electrooptical processors are best suited for applications demanding high computational throughput with tolerance for inaccuracies. Matrix preconditioning is one such application. Matrix preconditioning is a preprocessing step for reducing the condition number of a matrix and is used extensively with gradient algorithms for increasing the rate of convergence and improving the accuracy of the solution. In this paper, we describe a simple parallel algorithm for matrix preconditioning, which can be implemented efficiently on a pipelined optical linear algebra processor. From the results of our numerical experiments we show that the efficacy of the preconditioning algorithm is affected very little by the errors of the optical system.
Energy Technology Data Exchange (ETDEWEB)
Chen, Ke [Univ. of Liverpool (United Kingdom)
1996-12-31
We study various preconditioning techniques for the iterative solution of boundary integral equations, and aim to provide a theory for a class of sparse preconditioners. Two related ideas are explored here: singularity separation and inverse approximation. Our preliminary conclusion is that singularity separation based preconditioners perform better than approximate inverse based while it is desirable to have both features.
Kronecker Products on Preconditioning
Gao, Longfei
2013-01-01
techniques have become increasingly popular due to their great potential on large scale computation. In this work, we present preconditioning techniques for linear systems built with tensor product basis functions. Efficient algorithms are designed
Solving the Stokes problem on a massively parallel computer
DEFF Research Database (Denmark)
Axelsson, Owe; Barker, Vincent A.; Neytcheva, Maya
2001-01-01
boundary value problem for each velocity component, are solved by the conjugate gradient method with a preconditioning based on the algebraic multi‐level iteration (AMLI) technique. The velocity is found from the computed pressure. The method is optimal in the sense that the computational work...... is proportional to the number of unknowns. Further, it is designed to exploit a massively parallel computer with distributed memory architecture. Numerical experiments on a Cray T3E computer illustrate the parallel performance of the method....
Kronecker Products on Preconditioning
Gao, Longfei
2013-08-01
Numerical techniques for linear systems arising from discretization of partial differential equations are nowadays essential for understanding the physical world. Among these techniques, iterative methods and the accompanying preconditioning techniques have become increasingly popular due to their great potential on large scale computation. In this work, we present preconditioning techniques for linear systems built with tensor product basis functions. Efficient algorithms are designed for various problems by exploiting the Kronecker product structure in the matrices, inherited from tensor product basis functions. Specifically, we design preconditioners for mass matrices to remove the complexity from the basis functions used in isogeometric analysis, obtaining numerical performance independent of mesh size, polynomial order and continuity order; we also present a compound iteration preconditioner for stiffness matrices in two dimensions, obtaining fast convergence speed; lastly, for the Helmholtz problem, we present a strategy to `hide\\' its indefiniteness from Krylov subspace methods by eliminating the part of initial error that corresponds to those negative generalized eigenvalues. For all three cases, the Kronecker product structure in the matrices is exploited to achieve high computational efficiency.
Hejranfar, Kazem; Parseh, Kaveh
2017-09-01
The preconditioned characteristic boundary conditions based on the artificial compressibility (AC) method are implemented at artificial boundaries for the solution of two- and three-dimensional incompressible viscous flows in the generalized curvilinear coordinates. The compatibility equations and the corresponding characteristic variables (or the Riemann invariants) are mathematically derived and then applied as suitable boundary conditions in a high-order accurate incompressible flow solver. The spatial discretization of the resulting system of equations is carried out by the fourth-order compact finite-difference (FD) scheme. In the preconditioning applied here, the value of AC parameter in the flow field and also at the far-field boundary is automatically calculated based on the local flow conditions to enhance the robustness and performance of the solution algorithm. The code is fully parallelized using the Concurrency Runtime standard and Parallel Patterns Library (PPL) and its performance on a multi-core CPU is analyzed. The incompressible viscous flows around a 2-D circular cylinder, a 2-D NACA0012 airfoil and also a 3-D wavy cylinder are simulated and the accuracy and performance of the preconditioned characteristic boundary conditions applied at the far-field boundaries are evaluated in comparison to the simplified boundary conditions and the non-preconditioned characteristic boundary conditions. It is indicated that the preconditioned characteristic boundary conditions considerably improve the convergence rate of the solution of incompressible flows compared to the other boundary conditions and the computational costs are significantly decreased.
Shao, Meiyue; Aktulga, H. Metin; Yang, Chao; Ng, Esmond G.; Maris, Pieter; Vary, James P.
2018-01-01
We describe a number of recently developed techniques for improving the performance of large-scale nuclear configuration interaction calculations on high performance parallel computers. We show the benefit of using a preconditioned block iterative method to replace the Lanczos algorithm that has traditionally been used to perform this type of computation. The rapid convergence of the block iterative method is achieved by a proper choice of starting guesses of the eigenvectors and the construction of an effective preconditioner. These acceleration techniques take advantage of special structure of the nuclear configuration interaction problem which we discuss in detail. The use of a block method also allows us to improve the concurrency of the computation, and take advantage of the memory hierarchy of modern microprocessors to increase the arithmetic intensity of the computation relative to data movement. We also discuss the implementation details that are critical to achieving high performance on massively parallel multi-core supercomputers, and demonstrate that the new block iterative solver is two to three times faster than the Lanczos based algorithm for problems of moderate sizes on a Cray XC30 system.
Large-Scale Parallel Finite Element Analysis of the Stress Singular Problems
International Nuclear Information System (INIS)
Noriyuki Kushida; Hiroshi Okuda; Genki Yagawa
2002-01-01
In this paper, the convergence behavior of large-scale parallel finite element method for the stress singular problems was investigated. The convergence behavior of iterative solvers depends on the efficiency of the pre-conditioners. However, efficiency of pre-conditioners may be influenced by the domain decomposition that is necessary for parallel FEM. In this study the following results were obtained: Conjugate gradient method without preconditioning and the diagonal scaling preconditioned conjugate gradient method were not influenced by the domain decomposition as expected. symmetric successive over relaxation method preconditioned conjugate gradient method converged 6% faster as maximum if the stress singular area was contained in one sub-domain. (authors)
Synchronization Techniques in Parallel Discrete Event Simulation
Lindén, Jonatan
2018-01-01
Discrete event simulation is an important tool for evaluating system models in many fields of science and engineering. To improve the performance of large-scale discrete event simulations, several techniques to parallelize discrete event simulation have been developed. In parallel discrete event simulation, the work of a single discrete event simulation is distributed over multiple processing elements. A key challenge in parallel discrete event simulation is to ensure that causally dependent ...
Parallel pic plasma simulation through particle decomposition techniques
International Nuclear Information System (INIS)
Briguglio, S.; Vlad, G.; Di Martino, B.; Naples, Univ. 'Federico II'
1998-02-01
Particle-in-cell (PIC) codes are among the major candidates to yield a satisfactory description of the detail of kinetic effects, such as the resonant wave-particle interaction, relevant in determining the transport mechanism in magnetically confined plasmas. A significant improvement of the simulation performance of such codes con be expected from parallelization, e.g., by distributing the particle population among several parallel processors. Parallelization of a hybrid magnetohydrodynamic-gyrokinetic code has been accomplished within the High Performance Fortran (HPF) framework, and tested on the IBM SP2 parallel system, using a 'particle decomposition' technique. The adopted technique requires a moderate effort in porting the code in parallel form and results in intrinsic load balancing and modest inter processor communication. The performance tests obtained confirm the hypothesis of high effectiveness of the strategy, if targeted towards moderately parallel architectures. Optimal use of resources is also discussed with reference to a specific physics problem [it
Algorithms for computational fluid dynamics n parallel processors
International Nuclear Information System (INIS)
Van de Velde, E.F.
1986-01-01
A study of parallel algorithms for the numerical solution of partial differential equations arising in computational fluid dynamics is presented. The actual implementation on parallel processors of shared and nonshared memory design is discussed. The performance of these algorithms is analyzed in terms of machine efficiency, communication time, bottlenecks and software development costs. For elliptic equations, a parallel preconditioned conjugate gradient method is described, which has been used to solve pressure equations discretized with high order finite elements on irregular grids. A parallel full multigrid method and a parallel fast Poisson solver are also presented. Hyperbolic conservation laws were discretized with parallel versions of finite difference methods like the Lax-Wendroff scheme and with the Random Choice method. Techniques are developed for comparing the behavior of an algorithm on different architectures as a function of problem size and local computational effort. Effective use of these advanced architecture machines requires the use of machine dependent programming. It is shown that the portability problems can be minimized by introducing high level operations on vectors and matrices structured into program libraries
Energy Technology Data Exchange (ETDEWEB)
Kohn, S.; Weare, J.; Ong, E.; Baden, S.
1997-05-01
We have applied structured adaptive mesh refinement techniques to the solution of the LDA equations for electronic structure calculations. Local spatial refinement concentrates memory resources and numerical effort where it is most needed, near the atomic centers and in regions of rapidly varying charge density. The structured grid representation enables us to employ efficient iterative solver techniques such as conjugate gradient with FAC multigrid preconditioning. We have parallelized our solver using an object- oriented adaptive mesh refinement framework.
An efficient preconditioning technique using Krylov subspace methods for 3D characteristics solvers
International Nuclear Information System (INIS)
Dahmani, M.; Le Tellier, R.; Roy, R.; Hebert, A.
2005-01-01
The Generalized Minimal RESidual (GMRES) method, using a Krylov subspace projection, is adapted and implemented to accelerate a 3D iterative transport solver based on the characteristics method. Another acceleration technique called the self-collision rebalancing technique (SCR) can also be used to accelerate the solution or as a left preconditioner for GMRES. The GMRES method is usually used to solve a linear algebraic system (Ax=b). It uses K(r (o) ,A) as projection subspace and AK(r (o) ,A) for the orthogonalization of the residual. This paper compares the performance of these two combined methods on various problems. To implement the GMRES iterative method, the characteristics equations are derived in linear algebra formalism by using the equivalence between the method of characteristics and the method of collision probability to end up with a linear algebraic system involving fluxes and currents. Numerical results show good performance of the GMRES technique especially for the cases presenting large material heterogeneity with a scattering ratio close to 1. Similarly, the SCR preconditioning slightly increases the GMRES efficiency
Parallelizable approximate solvers for recursions arising in preconditioning
Energy Technology Data Exchange (ETDEWEB)
Shapira, Y. [Israel Inst. of Technology, Haifa (Israel)
1996-12-31
For the recursions used in the Modified Incomplete LU (MILU) preconditioner, namely, the incomplete decomposition, forward elimination and back substitution processes, a parallelizable approximate solver is presented. The present analysis shows that the solutions of the recursions depend only weakly on their initial conditions and may be interpreted to indicate that the inexact solution is close, in some sense, to the exact one. The method is based on a domain decomposition approach, suitable for parallel implementations with message passing architectures. It requires a fixed number of communication steps per preconditioned iteration, independently of the number of subdomains or the size of the problem. The overlapping subdomains are either cubes (suitable for mesh-connected arrays of processors) or constructed by the data-flow rule of the recursions (suitable for line-connected arrays with possibly SIMD or vector processors). Numerical examples show that, in both cases, the overhead in the number of iterations required for convergence of the preconditioned iteration is small relatively to the speed-up gained.
Barth, Timothy J.; Chan, Tony F.; Tang, Wei-Pai
1998-01-01
This paper considers an algebraic preconditioning algorithm for hyperbolic-elliptic fluid flow problems. The algorithm is based on a parallel non-overlapping Schur complement domain-decomposition technique for triangulated domains. In the Schur complement technique, the triangulation is first partitioned into a number of non-overlapping subdomains and interfaces. This suggests a reordering of triangulation vertices which separates subdomain and interface solution unknowns. The reordering induces a natural 2 x 2 block partitioning of the discretization matrix. Exact LU factorization of this block system yields a Schur complement matrix which couples subdomains and the interface together. The remaining sections of this paper present a family of approximate techniques for both constructing and applying the Schur complement as a domain-decomposition preconditioner. The approximate Schur complement serves as an algebraic coarse space operator, thus avoiding the known difficulties associated with the direct formation of a coarse space discretization. In developing Schur complement approximations, particular attention has been given to improving sequential and parallel efficiency of implementations without significantly degrading the quality of the preconditioner. A computer code based on these developments has been tested on the IBM SP2 using MPI message passing protocol. A number of 2-D calculations are presented for both scalar advection-diffusion equations as well as the Euler equations governing compressible fluid flow to demonstrate performance of the preconditioning algorithm.
International Nuclear Information System (INIS)
Longoni, G.; Haghighat, A.; Sjoden, G.
2005-01-01
This paper discusses a new preconditioned Sn algorithm referred to as FAST (Flux Acceleration Sn Transport). This algorithm uses the PENSSn code as the pre-conditioner, and the PENTRANSSn code system as the transport solver. PENSSn is developed based on the even-parity simplified Sn formulation in a parallel environment, and PENTRAN-SSn is a version of PENTRAN that uses PENSSn as the pre-conditioner with the FAST system. The paper briefly discusses the EP-SSn formulation and important numerical features of PENSSn. The FAST algorithm is discussed and tested for the C5G7 MOX eigenvalue benchmark problem. It is demonstrated that FAST leads to significant speedups (∼7) over the standard PENTRAN code. Moreover, FAST shows closer agreement with a reference Monte Carlo simulation. (authors)
Tian, Shan; Zhu, Fengping; Hu, Ruiping; Tian, Song; Chen, Xingxing; Lou, Dan; Cao, Bing; Chen, Qiulei; Li, Bai; Li, Fang; Bai, Yulong; Wu, Yi; Zhu, Yulian
2018-01-01
Exercise preconditioning is a simple and effective way to prevent ischemia. This paper further provided the mechanism in hemodynamic aspects at the cellular level. To study the anti-apoptotic effects of fluid mechanics preconditioning, Cultured rats brain microvascular endothelial cells were given fluid intervention in a parallel plate flow chamber before oxygen glucose deprivation. It showed that fluid mechanics preconditioning could inhibit the apoptosis of endothelial cells, and this process might be mediated by the shear stress activation of Tie-2 on cells membrane surface and Bcl-2 on the mitochondria surface. Copyright © 2017 Elsevier B.V. All rights reserved.
40 CFR 80.52 - Vehicle preconditioning.
2010-07-01
... 40 Protection of Environment 16 2010-07-01 2010-07-01 false Vehicle preconditioning. 80.52 Section...) REGULATION OF FUELS AND FUEL ADDITIVES Reformulated Gasoline § 80.52 Vehicle preconditioning. (a) Initial vehicle preconditioning and preconditioning between tests with different fuels shall be performed in...
International Nuclear Information System (INIS)
Brown, P.; Chang, B.
1998-01-01
The linear Boltzmann transport equation (BTE) is an integro-differential equation arising in deterministic models of neutral and charged particle transport. In slab (one-dimensional Cartesian) geometry and certain higher-dimensional cases, Diffusion Synthetic Acceleration (DSA) is known to be an effective algorithm for the iterative solution of the discretized BTE. Fourier and asymptotic analyses have been applied to various idealizations (e.g., problems on infinite domains with constant coefficients) to obtain sharp bounds on the convergence rate of DSA in such cases. While DSA has been shown to be a highly effective acceleration (or preconditioning) technique in one-dimensional problems, it has been observed to be less effective in higher dimensions. This is due in part to the expense of solving the related diffusion linear system. We investigate here the effectiveness of a parallel semicoarsening multigrid (SMG) solution approach to DSA preconditioning in several three dimensional problems. In particular, we consider the algorithmic and implementation scalability of a parallel SMG-DSA preconditioner on several types of test problems
Parallel Implicit Algorithms for CFD
Keyes, David E.
1998-01-01
The main goal of this project was efficient distributed parallel and workstation cluster implementations of Newton-Krylov-Schwarz (NKS) solvers for implicit Computational Fluid Dynamics (CFD.) "Newton" refers to a quadratically convergent nonlinear iteration using gradient information based on the true residual, "Krylov" to an inner linear iteration that accesses the Jacobian matrix only through highly parallelizable sparse matrix-vector products, and "Schwarz" to a domain decomposition form of preconditioning the inner Krylov iterations with primarily neighbor-only exchange of data between the processors. Prior experience has established that Newton-Krylov methods are competitive solvers in the CFD context and that Krylov-Schwarz methods port well to distributed memory computers. The combination of the techniques into Newton-Krylov-Schwarz was implemented on 2D and 3D unstructured Euler codes on the parallel testbeds that used to be at LaRC and on several other parallel computers operated by other agencies or made available by the vendors. Early implementations were made directly in Massively Parallel Integration (MPI) with parallel solvers we adapted from legacy NASA codes and enhanced for full NKS functionality. Later implementations were made in the framework of the PETSC library from Argonne National Laboratory, which now includes pseudo-transient continuation Newton-Krylov-Schwarz solver capability (as a result of demands we made upon PETSC during our early porting experiences). A secondary project pursued with funding from this contract was parallel implicit solvers in acoustics, specifically in the Helmholtz formulation. A 2D acoustic inverse problem has been solved in parallel within the PETSC framework.
Iterative algorithms for large sparse linear systems on parallel computers
Adams, L. M.
1982-01-01
Algorithms for assembling in parallel the sparse system of linear equations that result from finite difference or finite element discretizations of elliptic partial differential equations, such as those that arise in structural engineering are developed. Parallel linear stationary iterative algorithms and parallel preconditioned conjugate gradient algorithms are developed for solving these systems. In addition, a model for comparing parallel algorithms on array architectures is developed and results of this model for the algorithms are given.
A subspace preconditioning algorithm for eigenvector/eigenvalue computation
Energy Technology Data Exchange (ETDEWEB)
Bramble, J.H.; Knyazev, A.V.; Pasciak, J.E.
1996-12-31
We consider the problem of computing a modest number of the smallest eigenvalues along with orthogonal bases for the corresponding eigen-spaces of a symmetric positive definite matrix. In our applications, the dimension of a matrix is large and the cost of its inverting is prohibitive. In this paper, we shall develop an effective parallelizable technique for computing these eigenvalues and eigenvectors utilizing subspace iteration and preconditioning. Estimates will be provided which show that the preconditioned method converges linearly and uniformly in the matrix dimension when used with a uniform preconditioner under the assumption that the approximating subspace is close enough to the span of desired eigenvectors.
Kaporin, I. E.
2012-02-01
In order to precondition a sparse symmetric positive definite matrix, its approximate inverse is examined, which is represented as the product of two sparse mutually adjoint triangular matrices. In this way, the solution of the corresponding system of linear algebraic equations (SLAE) by applying the preconditioned conjugate gradient method (CGM) is reduced to performing only elementary vector operations and calculating sparse matrix-vector products. A method for constructing the above preconditioner is described and analyzed. The triangular factor has a fixed sparsity pattern and is optimal in the sense that the preconditioned matrix has a minimum K-condition number. The use of polynomial preconditioning based on Chebyshev polynomials makes it possible to considerably reduce the amount of scalar product operations (at the cost of an insignificant increase in the total number of arithmetic operations). The possibility of an efficient massively parallel implementation of the resulting method for solving SLAEs is discussed. For a sequential version of this method, the results obtained by solving 56 test problems from the Florida sparse matrix collection (which are large-scale and ill-conditioned) are presented. These results show that the method is highly reliable and has low computational costs.
Itoh, Shoji; Sugihara, Masaaki
2016-01-01
We present a theorem that defines the direction of a preconditioned system for the bi-conjugate gradient (BiCG) method, and we extend it to preconditioned bi-Lanczos-type algorithms. We show that the direction of a preconditioned system is switched by construction and by the settings of the initial shadow residual vector. We analyze and compare the polynomial structures of four preconditioned BiCG algorithms.
Design Considerations for a Flexible Multigrid Preconditioning Library
Directory of Open Access Journals (Sweden)
Jérémie Gaidamour
2012-01-01
Full Text Available MueLu is a library within the Trilinos software project [An overview of Trilinos, Technical Report SAND2003-2927, Sandia National Laboratories, 2003] and provides a framework for parallel multigrid preconditioning methods for large sparse linear systems. While providing efficient implementations of modern multigrid methods based on smoothed aggregation and energy minimization concepts, MueLu is designed to be customized and extended. This article gives an overview of design considerations for the MueLu package: user interfaces, internal design, data management, usage of modern software constructs, leveraging Trilinos capabilities, linear algebra operations and advanced application.
Ischemic preconditioning protects against ischemic brain injury
Directory of Open Access Journals (Sweden)
Xiao-meng Ma
2016-01-01
Full Text Available In this study, we hypothesized that an increase in integrin αv ß 3 and its co-activator vascular endothelial growth factor play important neuroprotective roles in ischemic injury. We performed ischemic preconditioning with bilateral common carotid artery occlusion for 5 minutes in C57BL/6J mice. This was followed by ischemic injury with bilateral common carotid artery occlusion for 30 minutes. The time interval between ischemic preconditioning and lethal ischemia was 48 hours. Histopathological analysis showed that ischemic preconditioning substantially diminished damage to neurons in the hippocampus 7 days after ischemia. Evans Blue dye assay showed that ischemic preconditioning reduced damage to the blood-brain barrier 24 hours after ischemia. This demonstrates the neuroprotective effect of ischemic preconditioning. Western blot assay revealed a significant reduction in protein levels of integrin αv ß 3, vascular endothelial growth factor and its receptor in mice given ischemic preconditioning compared with mice not given ischemic preconditioning 24 hours after ischemia. These findings suggest that the neuroprotective effect of ischemic preconditioning is associated with lower integrin αv ß 3 and vascular endothelial growth factor levels in the brain following ischemia.
Parallel computing techniques for rotorcraft aerodynamics
Ekici, Kivanc
The modification of unsteady three-dimensional Navier-Stokes codes for application on massively parallel and distributed computing environments is investigated. The Euler/Navier-Stokes code TURNS (Transonic Unsteady Rotor Navier-Stokes) was chosen as a test bed because of its wide use by universities and industry. For the efficient implementation of TURNS on parallel computing systems, two algorithmic changes are developed. First, main modifications to the implicit operator, Lower-Upper Symmetric Gauss Seidel (LU-SGS) originally used in TURNS, is performed. Second, application of an inexact Newton method, coupled with a Krylov subspace iterative method (Newton-Krylov method) is carried out. Both techniques have been tried previously for the Euler equations mode of the code. In this work, we have extended the methods to the Navier-Stokes mode. Several new implicit operators were tried because of convergence problems of traditional operators with the high cell aspect ratio (CAR) grids needed for viscous calculations on structured grids. Promising results for both Euler and Navier-Stokes cases are presented for these operators. For the efficient implementation of Newton-Krylov methods to the Navier-Stokes mode of TURNS, efficient preconditioners must be used. The parallel implicit operators used in the previous step are employed as preconditioners and the results are compared. The Message Passing Interface (MPI) protocol has been used because of its portability to various parallel architectures. It should be noted that the proposed methodology is general and can be applied to several other CFD codes (e.g. OVERFLOW).
Ghosh, A
1988-08-01
Lanczos and conjugate gradient algorithms are important in computational linear algebra. In this paper, a parallel pipelined realization of these algorithms on a ring of optical linear algebra processors is described. The flow of data is designed to minimize the idle times of the optical multiprocessor and the redundancy of computations. The effects of optical round-off errors on the solutions obtained by the optical Lanczos and conjugate gradient algorithms are analyzed, and it is shown that optical preconditioning can improve the accuracy of these algorithms substantially. Algorithms for optical preconditioning and results of numerical experiments on solving linear systems of equations arising from partial differential equations are discussed. Since the Lanczos algorithm is used mostly with sparse matrices, a folded storage scheme to represent sparse matrices on spatial light modulators is also described.
Ren, Chuancheng; Gao, Xuwen; Steinberg, Gary K.; Zhao, Heng
2009-01-01
Remote ischemic preconditioning is an emerging concept for stroke treatment, but its protection against focal stroke has not been established. We tested whether remote preconditioning, performed in the ipsilateral hind limb, protects against focal stroke and explored its protective parameters. Stroke was generated by a permanent occlusion of the left distal middle cerebral artery (MCA) combined with a 30 minute occlusion of the bilateral common carotid arteries (CCA) in male rats. Limb preconditioning was generated by 5 or 15 minute occlusion followed with the same period of reperfusion of the left hind femoral artery, and repeated for 2 or 3 cycles. Infarct was measured 2 days later. The results showed that rapid preconditioning with 3 cycles of 15 minutes performed immediately before stroke reduced infarct size from 47.7±7.6% of control ischemia to 9.8±8.6%; at 2 cycles of 15 minutes, infarct was reduced to 24.7±7.3%; at 2 cycles of 5 minutes, infarct was not reduced. Delayed preconditioning with 3 cycles of 15 minutes conducted 2 days before stroke also reduced infarct to 23.0 ±10.9%, but with 2 cycles of 15 minutes it offered no protection. The protective effects at these two therapeutic time windows of remote preconditioning are consistent with those of conventional preconditioning, in which the preconditioning ischemia is induced in the brain itself. Unexpectedly, intermediate preconditioning with 3 cycles of 15 minutes performed 12 hours before stroke also reduced infarct to 24.7±4.7%, which contradicts the current dogma for therapeutic time windows for the conventional preconditioning that has no protection at this time point. In conclusion, remote preconditioning performed in one limb protected against ischemic damage after focal cerebral ischemia. PMID:18201834
Distributed Memory Parallel Computing with SEAWAT
Verkaik, J.; Huizer, S.; van Engelen, J.; Oude Essink, G.; Ram, R.; Vuik, K.
2017-12-01
Fresh groundwater reserves in coastal aquifers are threatened by sea-level rise, extreme weather conditions, increasing urbanization and associated groundwater extraction rates. To counteract these threats, accurate high-resolution numerical models are required to optimize the management of these precious reserves. The major model drawbacks are long run times and large memory requirements, limiting the predictive power of these models. Distributed memory parallel computing is an efficient technique for reducing run times and memory requirements, where the problem is divided over multiple processor cores. A new Parallel Krylov Solver (PKS) for SEAWAT is presented. PKS has recently been applied to MODFLOW and includes Conjugate Gradient (CG) and Biconjugate Gradient Stabilized (BiCGSTAB) linear accelerators. Both accelerators are preconditioned by an overlapping additive Schwarz preconditioner in a way that: a) subdomains are partitioned using Recursive Coordinate Bisection (RCB) load balancing, b) each subdomain uses local memory only and communicates with other subdomains by Message Passing Interface (MPI) within the linear accelerator, c) it is fully integrated in SEAWAT. Within SEAWAT, the PKS-CG solver replaces the Preconditioned Conjugate Gradient (PCG) solver for solving the variable-density groundwater flow equation and the PKS-BiCGSTAB solver replaces the Generalized Conjugate Gradient (GCG) solver for solving the advection-diffusion equation. PKS supports the third-order Total Variation Diminishing (TVD) scheme for computing advection. Benchmarks were performed on the Dutch national supercomputer (https://userinfo.surfsara.nl/systems/cartesius) using up to 128 cores, for a synthetic 3D Henry model (100 million cells) and the real-life Sand Engine model ( 10 million cells). The Sand Engine model was used to investigate the potential effect of the long-term morphological evolution of a large sand replenishment and climate change on fresh groundwater resources
Preconditioning, postconditioning and their application to clinical cardiology.
Kloner, Robert A; Rezkalla, Shereif H
2006-05-01
Ischemic preconditioning is a well-established phenomenon first described in experimental preparations in which brief episodes of ischemia/reperfusion applied prior to a longer coronary artery occlusion reduce myocardial infarct size. There are ample correlates of ischemic preconditioning in the clinical realm. Preconditioning mimetic agents that stimulate the biochemical pathways of ischemic preconditioning and protect the heart without inducing ischemia have been examined in numerous experimental studies. However, despite the effectiveness of ischemic preconditioning and preconditioning mimetics for protecting ischemic myocardium, there are no preconditioning-based therapies that are routinely used in clinical medicine at the current time. Part of the problem is the need to administer therapy prior to the known ischemic event. Other issues are that percutaneous coronary intervention technology has advanced so far (with the development of stents and drug-eluting stents) that ischemic preconditioning or preconditioning mimetics have not been needed in most interventional cases. Recent clinical trials such as AMISTAD I and II (Acute Myocardial Infarction STudy of ADenosine) suggest that some preconditioning mimetics may reduce myocardial infarct size when given along with reperfusion or, as in the IONA trial, have benefit on clinical events when administered chronically in patients with known coronary artery disease. It is possible that some of the benefit described for adenosine in the AMISTAD 1 and 2 trials represents a manifestation of the recently described postconditioning phenomenon. It is probable that postconditioning--in which reperfusion is interrupted with brief coronary occlusions and reperfusion sequences--is more likely than preconditioning to be feasible as a clinical application to patients undergoing percutaneous coronary intervention for acute myocardial infarction.
GPU acceleration of preconditioned solvers for ill-conditioned linear systems
Gupta, R.
2015-01-01
In this work we study the implementations of deflation and preconditioning techniques for solving ill-conditioned linear systems using iterative methods. Solving such systems can be a time-consuming process because of the jumps in the coefficients due to large difference in material properties. We
Preconditioned iterations to calculate extreme eigenvalues
Energy Technology Data Exchange (ETDEWEB)
Brand, C.W.; Petrova, S. [Institut fuer Angewandte Mathematik, Leoben (Austria)
1994-12-31
Common iterative algorithms to calculate a few extreme eigenvalues of a large, sparse matrix are Lanczos methods or power iterations. They converge at a rate proportional to the separation of the extreme eigenvalues from the rest of the spectrum. Appropriate preconditioning improves the separation of the eigenvalues. Davidson`s method and its generalizations exploit this fact. The authors examine a preconditioned iteration that resembles a truncated version of Davidson`s method with a different preconditioning strategy.
Energy Technology Data Exchange (ETDEWEB)
Franz, A., LLNL
1998-02-17
The numerical simulation of chemically reacting flows is a topic, that has attracted a great deal of current research At the heart of numerical reactive flow simulations are large sets of coupled, nonlinear Partial Differential Equations (PDES). Due to the stiffness that is usually present, explicit time differencing schemes are not used despite their inherent simplicity and efficiency on parallel and vector machines, since these schemes require prohibitively small numerical stepsizes. Implicit time differencing schemes, although possessing good stability characteristics, introduce a great deal of computational overhead necessary to solve the simultaneous algebraic system at each timestep. This thesis examines an algorithm based on a preconditioned time differencing scheme. The algorithm is explicit and permits a large stable time step. An investigation of the algorithm`s accuracy, stability and performance on a parallel architecture is presented
AZTEC: A parallel iterative package for the solving linear systems
Energy Technology Data Exchange (ETDEWEB)
Hutchinson, S.A.; Shadid, J.N.; Tuminaro, R.S. [Sandia National Labs., Albuquerque, NM (United States)
1996-12-31
We describe a parallel linear system package, AZTEC. The package incorporates a number of parallel iterative methods (e.g. GMRES, biCGSTAB, CGS, TFQMR) and preconditioners (e.g. Jacobi, Gauss-Seidel, polynomial, domain decomposition with LU or ILU within subdomains). Additionally, AZTEC allows for the reuse of previous preconditioning factorizations within Newton schemes for nonlinear methods. Currently, a number of different users are using this package to solve a variety of PDE applications.
Directory of Open Access Journals (Sweden)
Ahmad Sukari Halim
2013-11-01
Full Text Available BackgroundIschemic preconditioning has been shown to improve the outcomes of hypoxic tolerance of the heart, brain, lung, liver, jejunum, skin, and muscle tissues. However, to date, no report of ischemic preconditioning on vascularized bone grafts has been published.MethodsSixteen rabbits were divided into four groups with ischemic times of 2, 6, 14, and 18 hours. Half of the rabbits in each group underwent ischemic preconditioning. The osteomyocutaneous flaps consisted of the tibia bone, from which the overlying muscle and skin were raised. The technique of ischemic preconditioning involved applying a vascular clamp to the pedicle for 3 cycles of 10 minutes each. The rabbits then underwent serial plain radiography and computed tomography imaging on the first, second, fourth, and sixth postoperative weeks. Following this, all of the rabbits were sacrificed and histological examinations were performed.ResultsThe results showed that for clinical analysis of the skin flaps and bone grafts, the preconditioned groups showed better survivability. In the plain radiographs, except for two non-preconditioned rabbits with intraoperative ischemic times of 6 hours, all began to show early callus formation at the fourth week. The computed tomography findings showed more callus formation in the preconditioned groups for all of the ischemic times except for the 18-hour group. The histological findings correlated with the radiological findings. There was no statistical significance in the difference between the two groups.ConclusionsIn conclusion, ischemic preconditioning improved the survivability of skin flaps and increased callus formation during the healing process of vascularized bone grafts.
A Parallel Solver for Large-Scale Markov Chains
Czech Academy of Sciences Publication Activity Database
Benzi, M.; Tůma, Miroslav
2002-01-01
Roč. 41, - (2002), s. 135-153 ISSN 0168-9274 R&D Projects: GA AV ČR IAA2030801; GA ČR GA101/00/1035 Keywords : parallel preconditioning * iterative methods * discrete Markov chains * generalized inverses * singular matrices * graph partitioning * AINV * Bi-CGSTAB Subject RIV: BA - General Mathematics Impact factor: 0.504, year: 2002
Energy Technology Data Exchange (ETDEWEB)
Gates, I.D. [Gushor Inc., Calgary, AB (Canada)]|[Calgary Univ., AB (Canada). Dept. of Chemical and Petroleum Engineering; Larter, S.R.; Adams, J.J.; Snowdon, L.; Jiang, C. [Gushor Inc., Calgary, AB (Canada)]|[Calgary Univ., Calgary, AB (Canada). Dept. of Geoscience
2008-10-15
This study investigated preconditioning techniques for altering reservoir fluid properties prior to steam assisted gravity drainage (SAGD) recovery processes. Viscosity-reducing agents were distributed in mobile reservoir water. Simulations were conducted to demonstrate the method's ability to modify oil viscosity prior to steam injection. The study simulated the action of water soluble organic solvents that preferentially partitioned in the oil phase. The solvent was injected with water into the reservoir in a slow waterflood that did not displace oil from the near wellbore region. A reservoir simulation model was used to investigate the technique. Shu's correlation was used to establish a viscosity correlation for the bitumen and solvent mixtures. Solvent injection was modelled by converting the oil phase viscosity through time. Over the first 2 years, oil rates of the preconditioned case were double that of the non-preconditioned case study. However, after 11 years, the preconditioned case's rates declined below rates observed in the non-preconditioned case. The model demonstrated that oil viscosity distributions were significantly altered using the preconditioners. The majority of the most viscous oil surrounding the production well was significantly reduced. It was concluded that accelerated steam chamber growth provided faster access to lower viscosity materials at the top of the reservoir. 12 refs., 9 figs.
Preconditioning for Mixed Finite Element Formulations of Elliptic Problems
Wildey, Tim; Xue, Guangri
2013-01-01
In this paper, we discuss a preconditioning technique for mixed finite element discretizations of elliptic equations. The technique is based on a block-diagonal approximation of the mass matrix which maintains the sparsity and positive definiteness of the corresponding Schur complement. This preconditioner arises from the multipoint flux mixed finite element method and is robust with respect to mesh size and is better conditioned for full permeability tensors than a preconditioner based on a diagonal approximation of the mass matrix. © Springer-Verlag Berlin Heidelberg 2013.
Ischemic Preconditioning of One Forearm Enhances Static and Dynamic Apnea
DEFF Research Database (Denmark)
Kjeld, Thomas; Rasmussen, Mads Reinholdt; Jattu, Timo
2014-01-01
INTRODUCTION: Ischemic preconditioning enhances ergometer cycling and swimming performance. We evaluated whether ischemic preconditioning of one forearm (four times for 5 min) also affects static breath hold and underwater swimming, whereas the effect of similar preconditioning on ergometer rowing...... preconditioning reduced the forearm oxygen saturation from 65% ± 7% to 19% ± 7% (mean ± SD; P right thigh.......05). CONCLUSIONS: We conclude that while the effect of ischemic preconditioning (of one forearm) on ergometer rowing was minimal, probably because of reduced muscle oxygenation during the warm-up, ischemic preconditioning does enhance both static and dynamic apnea, supporting that muscle ischemia is an important...
Parallel pathways for cross-modal memory retrieval in Drosophila.
Zhang, Xiaonan; Ren, Qingzhong; Guo, Aike
2013-05-15
Memory-retrieval processing of cross-modal sensory preconditioning is vital for understanding the plasticity underlying the interactions between modalities. As part of the sensory preconditioning paradigm, it has been hypothesized that the conditioned response to an unreinforced cue depends on the memory of the reinforced cue via a sensory link between the two cues. To test this hypothesis, we studied cross-modal memory-retrieval processing in a genetically tractable model organism, Drosophila melanogaster. By expressing the dominant temperature-sensitive shibire(ts1) (shi(ts1)) transgene, which blocks synaptic vesicle recycling of specific neural subsets with the Gal4/UAS system at the restrictive temperature, we specifically blocked visual and olfactory memory retrieval, either alone or in combination; memory acquisition remained intact for these modalities. Blocking the memory retrieval of the reinforced olfactory cues did not impair the conditioned response to the unreinforced visual cues or vice versa, in contrast to the canonical memory-retrieval processing of sensory preconditioning. In addition, these conditioned responses can be abolished by blocking the memory retrieval of the two modalities simultaneously. In sum, our results indicated that a conditioned response to an unreinforced cue in cross-modal sensory preconditioning can be recalled through parallel pathways.
Parallel CFD Algorithms for Aerodynamical Flow Solvers on Unstructured Meshes. Parts 1 and 2
Barth, Timothy J.; Kwak, Dochan (Technical Monitor)
1995-01-01
The Advisory Group for Aerospace Research and Development (AGARD) has requested my participation in the lecture series entitled Parallel Computing in Computational Fluid Dynamics to be held at the von Karman Institute in Brussels, Belgium on May 15-19, 1995. In addition, a request has been made from the US Coordinator for AGARD at the Pentagon for NASA Ames to hold a repetition of the lecture series on October 16-20, 1995. I have been asked to be a local coordinator for the Ames event. All AGARD lecture series events have attendance limited to NATO allied countries. A brief of the lecture series is provided in the attached enclosure. Specifically, I have been asked to give two lectures of approximately 75 minutes each on the subject of parallel solution techniques for the fluid flow equations on unstructured meshes. The title of my lectures is "Parallel CFD Algorithms for Aerodynamical Flow Solvers on Unstructured Meshes" (Parts I-II). The contents of these lectures will be largely review in nature and will draw upon previously published work in this area. Topics of my lectures will include: (1) Mesh partitioning algorithms. Recursive techniques based on coordinate bisection, Cuthill-McKee level structures, and spectral bisection. (2) Newton's method for large scale CFD problems. Size and complexity estimates for Newton's method, modifications for insuring global convergence. (3) Techniques for constructing the Jacobian matrix. Analytic and numerical techniques for Jacobian matrix-vector products, constructing the transposed matrix, extensions to optimization and homotopy theories. (4) Iterative solution algorithms. Practical experience with GIVIRES and BICG-STAB matrix solvers. (5) Parallel matrix preconditioning. Incomplete Lower-Upper (ILU) factorization, domain-decomposed ILU, approximate Schur complement strategies.
Preconditioned Krylov subspace methods for eigenvalue problems
Energy Technology Data Exchange (ETDEWEB)
Wu, Kesheng; Saad, Y.; Stathopoulos, A. [Univ. of Minnesota, Minneapolis, MN (United States)
1996-12-31
Lanczos algorithm is a commonly used method for finding a few extreme eigenvalues of symmetric matrices. It is effective if the wanted eigenvalues have large relative separations. If separations are small, several alternatives are often used, including the shift-invert Lanczos method, the preconditioned Lanczos method, and Davidson method. The shift-invert Lanczos method requires direct factorization of the matrix, which is often impractical if the matrix is large. In these cases preconditioned schemes are preferred. Many applications require solution of hundreds or thousands of eigenvalues of large sparse matrices, which pose serious challenges for both iterative eigenvalue solver and preconditioner. In this paper we will explore several preconditioned eigenvalue solvers and identify the ones suited for finding large number of eigenvalues. Methods discussed in this paper make up the core of a preconditioned eigenvalue toolkit under construction.
International Nuclear Information System (INIS)
McGhee, J.M.; Roberts, R.M.; Morel, J.E.
1997-01-01
A spherical harmonics research code (DANTE) has been developed which is compatible with parallel computer architectures. DANTE provides 3-D, multi-material, deterministic, transport capabilities using an arbitrary finite element mesh. The linearized Boltzmann transport equation is solved in a second order self-adjoint form utilizing a Galerkin finite element spatial differencing scheme. The core solver utilizes a preconditioned conjugate gradient algorithm. Other distinguishing features of the code include options for discrete-ordinates and simplified spherical harmonics angular differencing, an exact Marshak boundary treatment for arbitrarily oriented boundary faces, in-line matrix construction techniques to minimize memory consumption, and an effective diffusion based preconditioner for scattering dominated problems. Algorithm efficiency is demonstrated for a massively parallel SIMD architecture (CM-5), and compatibility with MPP multiprocessor platforms or workstation clusters is anticipated
Energy Technology Data Exchange (ETDEWEB)
McLay, R.T.; Carey, G.F.
1996-12-31
In this study we consider parallel solution of sparse linear systems arising from discretized PDE`s. As part of our continuing work on our parallel PCG Solver package, we have made improvements in two areas. The first is improving the performance of the matrix-vector product. Here on regular finite-difference grids, we are able to use the cache memory more efficiently for smaller domains or where there are multiple degrees of freedom. The second problem of interest in the present work is the construction of preconditioners in the context of the parallel PCG solver we are developing. Here the problem is partitioned over a set of processors subdomains and the matrix-vector product for PCG is carried out in parallel for overlapping grid subblocks. For problems of scaled speedup, the actual rate of convergence of the unpreconditioned system deteriorates as the mesh is refined. Multigrid and subdomain strategies provide a logical approach to resolving the problem. We consider the parallel trade-offs between communication and computation and provide a complexity analysis of a representative algorithm. Some preliminary calculations using the parallel package and comparisons with other preconditioners are provided together with parallel performance results.
Isoflurane preconditions myocardium against infarction via release of free radicals
Müllenheim, Jost; Ebel, Dirk; Frässdorf, Jan; Preckel, Benedikt; Thämer, Volker; Schlack, Wolfgang
2002-01-01
BACKGROUND: Isoflurane exerts cardioprotective effects that mimic the ischemic preconditioning phenomenon. Generation of free radicals is implicated in ischemic preconditioning. The authors investigated whether isoflurane-induced preconditioning may involve release of free radicals. METHODS:
Chabory, A.; Hon, de B.P.; Schilders, W.H.A.; Tijhuis, A.G.
2008-01-01
Finite-difference techniques are very popular and versatile numerical tools in computational electromagnetics. In this paper, we propose a preconditioned finite-difference frequency-domain method (FDFD) to model periodic structures in 2D and 3D. The preconditioner follows from a modal decoupling
Chabory, A.; Hon, de B.P.; Schilders, W.H.A.; Tijhuis, A.G.
2008-01-01
Finite-difference techniques are very popular and versatile numerical tools in computational electromagnetics. In this paper, we propose a preconditioned finite-difference frequency-domain method (FDFD) to model periodic structures in 2D and 3D. The preconditioner follows from a modal decoupling
He, Zhijie; Lu, Hongyang; Yang, Xiaojiao; Zhang, Li; Wu, Yi; Niu, Wenxiu; Ding, Li; Wang, Guili; Tong, Shanbao; Jia, Jie
2018-01-01
Exercise preconditioning induces neuroprotective effects during cerebral ischemia and reperfusion, which involves the recovery of cerebral blood flow (CBF). Mechanisms underlying the neuroprotective effects of re-established CBF following ischemia and reperfusion are unclear. The present study investigated CBF in hyper-early stage of reperfusion by laser speckle contrast imaging, a full-field high-resolution optical imaging technique. Rats with or without treadmill training were subjected to middle cerebral artery occlusion followed by reperfusion. CBF in arteries, veins, and capillaries in hyper-early stage of reperfusion (1, 2, and 3 h after reperfusion) and in subacute stage (24 h after reperfusion) were measured. Neurological scoring and 2,3,5-triphenyltetrazolium chloride staining were further applied to determine the neuroprotective effects of exercise preconditioning. In hyper-early stage of reperfusion, CBF in the rats with exercise preconditioning was reduced significantly in arteries and veins, respectively, compared to rats with no exercise preconditioning. Capillary CBF remained stable in the hyper-early stage of reperfusion, though it increased significantly 24 h after reperfusion in the rats with exercise preconditioning. As a neuroprotective strategy, exercise preconditioning reduced the blood perfusion of arteries and veins in the hyper-early stage of reperfusion, which indicated intervention-induced neuroprotective hypoperfusion after reperfusion onset.
A Parallel Algebraic Multigrid Solver on Graphics Processing Units
Haase, Gundolf
2010-01-01
The paper presents a multi-GPU implementation of the preconditioned conjugate gradient algorithm with an algebraic multigrid preconditioner (PCG-AMG) for an elliptic model problem on a 3D unstructured grid. An efficient parallel sparse matrix-vector multiplication scheme underlying the PCG-AMG algorithm is presented for the many-core GPU architecture. A performance comparison of the parallel solver shows that a singe Nvidia Tesla C1060 GPU board delivers the performance of a sixteen node Infiniband cluster and a multi-GPU configuration with eight GPUs is about 100 times faster than a typical server CPU core. © 2010 Springer-Verlag.
40 CFR 86.532-78 - Vehicle preconditioning.
2010-07-01
... 40 Protection of Environment 18 2010-07-01 2010-07-01 false Vehicle preconditioning. 86.532-78... (CONTINUED) CONTROL OF EMISSIONS FROM NEW AND IN-USE HIGHWAY VEHICLES AND ENGINES Emission Regulations for 1978 and Later New Motorcycles; Test Procedures § 86.532-78 Vehicle preconditioning. (a) The vehicle...
Projection preconditioning for Lanczos-type methods
Energy Technology Data Exchange (ETDEWEB)
Bielawski, S.S.; Mulyarchik, S.G.; Popov, A.V. [Belarusian State Univ., Minsk (Belarus)
1996-12-31
We show how auxiliary subspaces and related projectors may be used for preconditioning nonsymmetric system of linear equations. It is shown that preconditioned in such a way (or projected) system is better conditioned than original system (at least if the coefficient matrix of the system to be solved is symmetrizable). Two approaches for solving projected system are outlined. The first one implies straightforward computation of the projected matrix and consequent using some direct or iterative method. The second approach is the projection preconditioning of conjugate gradient-type solver. The latter approach is developed here in context with biconjugate gradient iteration and some related Lanczos-type algorithms. Some possible particular choices of auxiliary subspaces are discussed. It is shown that one of them is equivalent to using colorings. Some results of numerical experiments are reported.
The protective effect of ischemic preconditioning on rat testis
Directory of Open Access Journals (Sweden)
Ciralik Harun
2007-12-01
Full Text Available Abstract Background It has been demonstrated that brief episodes of sublethal ischemia-reperfusion, so-called ischemic preconditioning, provide powerful tissue protection in different tissues such as heart, brain, skeletal muscle, lung, liver, intestine, kidney, retina, and endothelial cells. Although a recent study has claimed that there are no protective effects of ischemic preconditioning in rat testis, the protective effects of ischemic preconditioning on testicular tissue have not been investigated adequately. The present study was thus planned to investigate whether ischemic preconditioning has a protective effect on testicular tissue. Methods Rats were divided into seven groups that each contained seven rats. In group 1 (control group, only unilateral testicular ischemia was performed by creating a testicular torsion by a 720 degree clockwise rotation for 180 min. In group 2, group 3, group 4, group 5, group 6, and group 7, unilateral testicular ischemia was performed for 180 min following different periods of ischemic preconditioning. The ischemic preconditioning periods were as follows: 10 minutes of ischemia with 10 minutes of reperfusion in group 2; 20 minutes of ischemia with 10 minutes of reperfusion in group 3; 30 minutes of ischemia with 10 minutes of reperfusion in group 4; multiple preconditioning periods were used (3 × 10 min early phase transient ischemia with 10 min reperfusion in all episodes in group 5; multiple preconditioning periods were used (5, 10, and 15 min early phase transient ischemia with 10 min reperfusion in all episodes in group 6; and, multiple preconditioning periods were used (10, 20, and 30 min early phase transient ischemia with 10 min reperfusion in all episodes in group 7. After the ischemic protocols were carried out, animals were sacrificed by cervical dislocation and testicular tissue samples were taken for biochemical measurements (protein, malondialdehyde, nitric oxide and histological examination
New partially parallel acquisition technique in cerebral imaging: preliminary findings
International Nuclear Information System (INIS)
Tintera, Jaroslav; Gawehn, Joachim; Bauermann, Thomas; Vucurevic, Goran; Stoeter, Peter
2004-01-01
In MRI applications where short acquisition time is necessary, the increase of acquisition speed is often at the expense of image resolution and SNR. In such cases, the newly developed parallel acquisition techniques could provide images without mentioned limitations and in reasonably shortened measurement time. A newly designed eight-channel head coil array (i-PAT coil) allowing for parallel acquisition of independently reconstructed images (GRAPPA mode) has been tested for its applicability in neuroradiology. Image homogeneity was tested in standard phantom and healthy volunteers. BOLD signal changes were studied in a group of six volunteers using finger tapping stimulation. Phantom studies revealed an important drop of signal even after the use of a normalization filter in the center of the image and an important increase of artifact power with reduction of measurement time strongly depending on the combination of acceleration parameters. The additional application of a parallel acquisition technique such as GRAPPA decreases measurement time in the range of about 30%, but further reduction is often possible only at the expense of SNR. This technique performs best in conditions in which imaging speed is important, such as CE MRA, but time resolution still does not allow the acquisition of angiograms separating the arterial and venous phase. Significantly larger areas of BOLD activation were found using the i-PAT coil compared to the standard head coil. Being an eight-channel surface coil array, peripheral cortical structures profit from high SNR as high-resolution imaging of small cortical dysplasias and functional activation of cortical areas imaged by BOLD contrast. In BOLD contrast imaging, susceptibility artifacts are reduced, but only if an appropriate combination of acceleration parameters is used. (orig.)
New partially parallel acquisition technique in cerebral imaging: preliminary findings
Energy Technology Data Exchange (ETDEWEB)
Tintera, Jaroslav [Institute for Clinical and Experimental Medicine, Prague (Czech Republic); Gawehn, Joachim; Bauermann, Thomas; Vucurevic, Goran; Stoeter, Peter [University Clinic Mainz, Institute of Neuroradiology, Mainz (Germany)
2004-12-01
In MRI applications where short acquisition time is necessary, the increase of acquisition speed is often at the expense of image resolution and SNR. In such cases, the newly developed parallel acquisition techniques could provide images without mentioned limitations and in reasonably shortened measurement time. A newly designed eight-channel head coil array (i-PAT coil) allowing for parallel acquisition of independently reconstructed images (GRAPPA mode) has been tested for its applicability in neuroradiology. Image homogeneity was tested in standard phantom and healthy volunteers. BOLD signal changes were studied in a group of six volunteers using finger tapping stimulation. Phantom studies revealed an important drop of signal even after the use of a normalization filter in the center of the image and an important increase of artifact power with reduction of measurement time strongly depending on the combination of acceleration parameters. The additional application of a parallel acquisition technique such as GRAPPA decreases measurement time in the range of about 30%, but further reduction is often possible only at the expense of SNR. This technique performs best in conditions in which imaging speed is important, such as CE MRA, but time resolution still does not allow the acquisition of angiograms separating the arterial and venous phase. Significantly larger areas of BOLD activation were found using the i-PAT coil compared to the standard head coil. Being an eight-channel surface coil array, peripheral cortical structures profit from high SNR as high-resolution imaging of small cortical dysplasias and functional activation of cortical areas imaged by BOLD contrast. In BOLD contrast imaging, susceptibility artifacts are reduced, but only if an appropriate combination of acceleration parameters is used. (orig.)
Preconditioned conjugate-gradient methods for low-speed flow calculations
Ajmani, Kumud; Ng, Wing-Fai; Liou, Meng-Sing
1993-01-01
An investigation is conducted into the viability of using a generalized Conjugate Gradient-like method as an iterative solver to obtain steady-state solutions of very low-speed fluid flow problems. Low-speed flow at Mach 0.1 over a backward-facing step is chosen as a representative test problem. The unsteady form of the two dimensional, compressible Navier-Stokes equations is integrated in time using discrete time-steps. The Navier-Stokes equations are cast in an implicit, upwind finite-volume, flux split formulation. The new iterative solver is used to solve a linear system of equations at each step of the time-integration. Preconditioning techniques are used with the new solver to enhance the stability and convergence rate of the solver and are found to be critical to the overall success of the solver. A study of various preconditioners reveals that a preconditioner based on the Lower-Upper Successive Symmetric Over-Relaxation iterative scheme is more efficient than a preconditioner based on Incomplete L-U factorizations of the iteration matrix. The performance of the new preconditioned solver is compared with a conventional Line Gauss-Seidel Relaxation (LGSR) solver. Overall speed-up factors of 28 (in terms of global time-steps required to converge to a steady-state solution) and 20 (in terms of total CPU time on one processor of a CRAY-YMP) are found in favor of the new preconditioned solver, when compared with the LGSR solver.
Preconditioned Conjugate Gradient methods for low speed flow calculations
Ajmani, Kumud; Ng, Wing-Fai; Liou, Meng-Sing
1993-01-01
An investigation is conducted into the viability of using a generalized Conjugate Gradient-like method as an iterative solver to obtain steady-state solutions of very low-speed fluid flow problems. Low-speed flow at Mach 0.1 over a backward-facing step is chosen as a representative test problem. The unsteady form of the two dimensional, compressible Navier-Stokes equations are integrated in time using discrete time-steps. The Navier-Stokes equations are cast in an implicit, upwind finite-volume, flux split formulation. The new iterative solver is used to solve a linear system of equations at each step of the time-integration. Preconditioning techniques are used with the new solver to enhance the stability and the convergence rate of the solver and are found to be critical to the overall success of the solver. A study of various preconditioners reveals that a preconditioner based on the lower-upper (L-U)-successive symmetric over-relaxation iterative scheme is more efficient than a preconditioner based on incomplete L-U factorizations of the iteration matrix. The performance of the new preconditioned solver is compared with a conventional line Gauss-Seidel relaxation (LGSR) solver. Overall speed-up factors of 28 (in terms of global time-steps required to converge to a steady-state solution) and 20 (in terms of total CPU time on one processor of a CRAY-YMP) are found in favor of the new preconditioned solver, when compared with the LGSR solver.
Preconditioned conjugate gradient methods for the Navier-Stokes equations
Ajmani, Kumud; Ng, Wing-Fai; Liou, Meng-Sing
1994-01-01
A preconditioned Krylov subspace method (GMRES) is used to solve the linear systems of equations formed at each time-integration step of the unsteady, two-dimensional, compressible Navier-Stokes equations of fluid flow. The Navier-Stokes equations are cast in an implicit, upwind finite-volume, flux-split formulation. Several preconditioning techniques are investigated to enhance the efficiency and convergence rate of the implicit solver based on the GMRES algorithm. The superiority of the new solver is established by comparisons with a conventional implicit solver, namely line Gauss-Seidel relaxation (LGSR). Computational test results for low-speed (incompressible flow over a backward-facing step at Mach 0.1), transonic flow (trailing edge flow in a transonic turbine cascade), and hypersonic flow (shock-on-shock interactions on a cylindrical leading edge at Mach 6.0) are presented. For the Mach 0.1 case, overall speedup factors of up to 17 (in terms of time-steps) and 15 (in terms of CPU time on a CRAY-YMP/8) are found in favor of the preconditioned GMRES solver, when compared with the LGSR solver. The corresponding speedup factors for the transonic flow case are 17 and 23, respectively. The hypersonic flow case shows slightly lower speedup factors of 9 and 13, respectively. The study of preconditioners conducted in this research reveals that a new LUSGS-type preconditioner is much more efficient than a conventional incomplete LU-type preconditioner.
GPU Parallel Bundle Block Adjustment
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ZHENG Maoteng
2017-09-01
Full Text Available To deal with massive data in photogrammetry, we introduce the GPU parallel computing technology. The preconditioned conjugate gradient and inexact Newton method are also applied to decrease the iteration times while solving the normal equation. A brand new workflow of bundle adjustment is developed to utilize GPU parallel computing technology. Our method can avoid the storage and inversion of the big normal matrix, and compute the normal matrix in real time. The proposed method can not only largely decrease the memory requirement of normal matrix, but also largely improve the efficiency of bundle adjustment. It also achieves the same accuracy as the conventional method. Preliminary experiment results show that the bundle adjustment of a dataset with about 4500 images and 9 million image points can be done in only 1.5 minutes while achieving sub-pixel accuracy.
Xenon preconditioning: molecular mechanisms and biological effects
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Liu Wenwu
2013-01-01
Full Text Available Abstract Xenon is one of noble gases and has been recognized as an anesthetic for more than 50 years. Xenon possesses many of the characteristics of an ideal anesthetic, but it is not widely applied in clinical practice mainly because of its high cost. In recent years, numerous studies have demonstrated that xenon as an anesthetic can exert neuroprotective and cardioprotective effects in different models. Moreover, xenon has been applied in the preconditioning, and the neuroprotective and cardioprotective effects of xenon preconditioning have been investigated in a lot of studies in which some mechanisms related to these protections are proposed. In this review, we summarized these mechanisms and the biological effects of xenon preconditioning.
The Conceptual Preconditions of Studying Collective Professional Mobility of Management Personnel
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Doronin Andrii V.
2016-08-01
Full Text Available The preconditions and problems of developing the concept of the study and transformation of collective professional mobility of management personnel are generalized. The necessity of specifying the content and structure of the scientific and methodological concept of «paradigm» is justified. The possibility of using philosophy and economic theory to determine the initial ideas on the development of technique for studying collective professional mobility of management personnel are analyzed; contradictions, which resolution would create a constructive theoretical basis of such a study are revealed. The need to focus on the interdisciplinary approach in the development of the conceptual preconditions of studying collective professional mobility is substantiated. The versions of the world view allowing to ensure productive discussions of representatives of various scientific disciplines at the phenomenological stage of building a new paradigm are developed.
Preconditioned Krylov and Gauss-Seidel solutions of response matrix equations
International Nuclear Information System (INIS)
Lewis, E.E.; Smith, M.A.; Yang, W.S.; Wollaber, A.
2011-01-01
The use of preconditioned Krylov methods is examined as an alternative to the partitioned matrix acceleration applied to red-black Gauss Seidel (RBGS) iteration that is presently used in the variational nodal code, VARIANT. We employ the GMRES algorithm to treat non-symmetric response matrix equations. A pre conditioner is formulated for the within-group diffusion equation which is equivalent to partitioned matrix acceleration of RBGS iterations. We employ the pre conditioner, which closely parallels two-level p multigrid, to improve RBGS and GMRES algorithms. Of the accelerated algorithms, GMRES converges with less computational effort than RBGS and therefore is chosen for further development. The p multigrid pre conditioner requires response matrices with two or more degrees of freedom (DOF) per interface that are polynomials, which are both orthogonal and hierarchical. It is therefore not directly applicable to very fine mesh calculations that are both slow to converge and that are often modeled with response matrices with only one DOF per interface. Orthogonal matrix aggregation (OMA) is introduced to circumvent this difficulty by combining N×N fine mesh response matrices with one DOF per interface into a coarse mesh response matrix with N orthogonal DOF per interface. Numerical results show that OMA used alone or in combination with p multigrid preconditioning substantially accelerates GMRES solutions. (author)
Preconditioned Krylov and Gauss-Seidel solutions of response matrix equations
Energy Technology Data Exchange (ETDEWEB)
Lewis, E.E., E-mail: e-lewis@northwestern.edu [Department of Mechanical Engineering, Northwestern University, Evanston, IL (United States); Smith, M.A.; Yang, W.S.; Wollaber, A., E-mail: masmith@anl.gov, E-mail: wsyang@anl.gov, E-mail: wollaber@lanl.gov [Nuclear Engineering Division, Argonne National Laboratory, Argonne, IL (United States)
2011-07-01
The use of preconditioned Krylov methods is examined as an alternative to the partitioned matrix acceleration applied to red-black Gauss Seidel (RBGS) iteration that is presently used in the variational nodal code, VARIANT. We employ the GMRES algorithm to treat non-symmetric response matrix equations. A pre conditioner is formulated for the within-group diffusion equation which is equivalent to partitioned matrix acceleration of RBGS iterations. We employ the pre conditioner, which closely parallels two-level p multigrid, to improve RBGS and GMRES algorithms. Of the accelerated algorithms, GMRES converges with less computational effort than RBGS and therefore is chosen for further development. The p multigrid pre conditioner requires response matrices with two or more degrees of freedom (DOF) per interface that are polynomials, which are both orthogonal and hierarchical. It is therefore not directly applicable to very fine mesh calculations that are both slow to converge and that are often modeled with response matrices with only one DOF per interface. Orthogonal matrix aggregation (OMA) is introduced to circumvent this difficulty by combining N×N fine mesh response matrices with one DOF per interface into a coarse mesh response matrix with N orthogonal DOF per interface. Numerical results show that OMA used alone or in combination with p multigrid preconditioning substantially accelerates GMRES solutions. (author)
Solving large mixed linear models using preconditioned conjugate gradient iteration.
Strandén, I; Lidauer, M
1999-12-01
Continuous evaluation of dairy cattle with a random regression test-day model requires a fast solving method and algorithm. A new computing technique feasible in Jacobi and conjugate gradient based iterative methods using iteration on data is presented. In the new computing technique, the calculations in multiplication of a vector by a matrix were recorded to three steps instead of the commonly used two steps. The three-step method was implemented in a general mixed linear model program that used preconditioned conjugate gradient iteration. Performance of this program in comparison to other general solving programs was assessed via estimation of breeding values using univariate, multivariate, and random regression test-day models. Central processing unit time per iteration with the new three-step technique was, at best, one-third that needed with the old technique. Performance was best with the test-day model, which was the largest and most complex model used. The new program did well in comparison to other general software. Programs keeping the mixed model equations in random access memory required at least 20 and 435% more time to solve the univariate and multivariate animal models, respectively. Computations of the second best iteration on data took approximately three and five times longer for the animal and test-day models, respectively, than did the new program. Good performance was due to fast computing time per iteration and quick convergence to the final solutions. Use of preconditioned conjugate gradient based methods in solving large breeding value problems is supported by our findings.
Helium induces preconditioning in human endothelium in vivo
Smit, Kirsten F.; Oei, Gezina T. M. L.; Brevoord, Daniel; Stroes, Erik S.; Nieuwland, Rienk; Schlack, Wolfgang S.; Hollmann, Markus W.; Weber, Nina C.; Preckel, Benedikt
2013-01-01
Helium protects myocardium by inducing preconditioning in animals. We investigated whether human endothelium is preconditioned by helium inhalation in vivo. Forearm ischemia-reperfusion (I/R) in healthy volunteers (each group n = 10) was performed by inflating a blood pressure cuff for 20 min.
Ischemic preconditioning protects against gap junctional uncoupling in cardiac myofibroblasts.
Sundset, Rune; Cooper, Marie; Mikalsen, Svein-Ole; Ytrehus, Kirsti
2004-01-01
Ischemic preconditioning increases the heart's tolerance to a subsequent longer ischemic period. The purpose of this study was to investigate the role of gap junction communication in simulated preconditioning in cultured neonatal rat cardiac myofibroblasts. Gap junctional intercellular communication was assessed by Lucifer yellow dye transfer. Preconditioning preserved intercellular coupling after prolonged ischemia. An initial reduction in coupling in response to the preconditioning stimulus was also observed. This may protect neighboring cells from damaging substances produced during subsequent regional ischemia in vivo, and may preserve gap junctional communication required for enhanced functional recovery during subsequent reperfusion.
International Nuclear Information System (INIS)
Ullmann, P.
2007-06-01
The primary objective of this work was the first experimental realization of parallel RF transmission for accelerating spatially selective excitation in magnetic resonance imaging. Furthermore, basic aspects regarding the performance of this technique were investigated, potential risks regarding the specific absorption rate (SAR) were considered and feasibility studies under application-oriented conditions as first steps towards a practical utilisation of this technique were undertaken. At first, based on the RF electronics platform of the Bruker Avance MRI systems, the technical foundations were laid to perform simultaneous transmission of individual RF waveforms on different RF channels. Another essential requirement for the realization of Parallel Excitation (PEX) was the design and construction of suitable RF transmit arrays with elements driven by separate transmit channels. In order to image the PEX results two imaging methods were implemented based on a spin-echo and a gradient-echo sequence, in which a parallel spatially selective pulse was included as an excitation pulse. In the course of this work PEX experiments were successfully performed on three different MRI systems, a 4.7 T and a 9.4 T animal system and a 3 T human scanner, using 5 different RF coil setups in total. In the last part of this work investigations regarding possible applications of Parallel Excitation were performed. A first study comprised experiments of slice-selective B1 inhomogeneity correction by using 3D-selective Parallel Excitation. The investigations were performed in a phantom as well as in a rat fixed in paraformaldehyde solution. In conjunction with these experiments a novel method of calculating RF pulses for spatially selective excitation based on a so-called Direct Calibration approach was developed, which is particularly suitable for this type of experiments. In the context of these experiments it was demonstrated how to combine the advantages of parallel transmission
Preconditioned iterative methods for space-time fractional advection-diffusion equations
Zhao, Zhi; Jin, Xiao-Qing; Lin, Matthew M.
2016-08-01
In this paper, we propose practical numerical methods for solving a class of initial-boundary value problems of space-time fractional advection-diffusion equations. First, we propose an implicit method based on two-sided Grünwald formulae and discuss its stability and consistency. Then, we develop the preconditioned generalized minimal residual (preconditioned GMRES) method and preconditioned conjugate gradient normal residual (preconditioned CGNR) method with easily constructed preconditioners. Importantly, because resulting systems are Toeplitz-like, fast Fourier transform can be applied to significantly reduce the computational cost. We perform numerical experiments to demonstrate the efficiency of our preconditioners, even in cases with variable coefficients.
Directory of Open Access Journals (Sweden)
Rovini Massimo
2009-01-01
Full Text Available This is a reply to the comments by Gunnam et al. "Comments on 'Techniques and architectures for hazard-free semi-parallel decoding of LDPC codes'", EURASIP Journal on Embedded Systems, vol. 2009, Article ID 704174 on our recent work "Techniques and architectures for hazard-free semi-parallel decoding of LDPC codes", EURASIP Journal on Embedded Systems, vol. 2009, Article ID 723465.
Parallel halftoning technique using dot diffusion optimization
Molina-Garcia, Javier; Ponomaryov, Volodymyr I.; Reyes-Reyes, Rogelio; Cruz-Ramos, Clara
2017-05-01
In this paper, a novel approach for halftone images is proposed and implemented for images that are obtained by the Dot Diffusion (DD) method. Designed technique is based on an optimization of the so-called class matrix used in DD algorithm and it consists of generation new versions of class matrix, which has no baron and near-baron in order to minimize inconsistencies during the distribution of the error. Proposed class matrix has different properties and each is designed for two different applications: applications where the inverse-halftoning is necessary, and applications where this method is not required. The proposed method has been implemented in GPU (NVIDIA GeForce GTX 750 Ti), multicore processors (AMD FX(tm)-6300 Six-Core Processor and in Intel core i5-4200U), using CUDA and OpenCV over a PC with linux. Experimental results have shown that novel framework generates a good quality of the halftone images and the inverse halftone images obtained. The simulation results using parallel architectures have demonstrated the efficiency of the novel technique when it is implemented in real-time processing.
The parallel-sequential field subtraction technique for coherent nonlinear ultrasonic imaging
Cheng, Jingwei; Potter, Jack N.; Drinkwater, Bruce W.
2018-06-01
Nonlinear imaging techniques have recently emerged which have the potential to detect cracks at a much earlier stage than was previously possible and have sensitivity to partially closed defects. This study explores a coherent imaging technique based on the subtraction of two modes of focusing: parallel, in which the elements are fired together with a delay law and sequential, in which elements are fired independently. In the parallel focusing a high intensity ultrasonic beam is formed in the specimen at the focal point. However, in sequential focusing only low intensity signals from individual elements enter the sample and the full matrix of transmit-receive signals is recorded and post-processed to form an image. Under linear elastic assumptions, both parallel and sequential images are expected to be identical. Here we measure the difference between these images and use this to characterise the nonlinearity of small closed fatigue cracks. In particular we monitor the change in relative phase and amplitude at the fundamental frequencies for each focal point and use this nonlinear coherent imaging metric to form images of the spatial distribution of nonlinearity. The results suggest the subtracted image can suppress linear features (e.g. back wall or large scatters) effectively when instrumentation noise compensation in applied, thereby allowing damage to be detected at an early stage (c. 15% of fatigue life) and reliably quantified in later fatigue life.
Techniques and Architectures for Hazard-Free Semi-Parallel Decoding of LDPC Codes
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Rovini Massimo
2009-01-01
Full Text Available The layered decoding algorithm has recently been proposed as an efficient means for the decoding of low-density parity-check (LDPC codes, thanks to the remarkable improvement in the convergence speed (2x of the decoding process. However, pipelined semi-parallel decoders suffer from violations or "hazards" between consecutive updates, which not only violate the layered principle but also enforce the loops in the code, thus spoiling the error correction performance. This paper describes three different techniques to properly reschedule the decoding updates, based on the careful insertion of "idle" cycles, to prevent the hazards of the pipeline mechanism. Also, different semi-parallel architectures of a layered LDPC decoder suitable for use with such techniques are analyzed. Then, taking the LDPC codes for the wireless local area network (IEEE 802.11n as a case study, a detailed analysis of the performance attained with the proposed techniques and architectures is reported, and results of the logic synthesis on a 65 nm low-power CMOS technology are shown.
Operator-Based Preconditioning of Stiff Hyperbolic Systems
International Nuclear Information System (INIS)
Reynolds, Daniel R.; Samtaney, Ravi; Woodward, Carol S.
2009-01-01
We introduce an operator-based scheme for preconditioning stiff components encountered in implicit methods for hyperbolic systems of partial differential equations posed on regular grids. The method is based on a directional splitting of the implicit operator, followed by a characteristic decomposition of the resulting directional parts. This approach allows for solution to any number of characteristic components, from the entire system to only the fastest, stiffness-inducing waves. We apply the preconditioning method to stiff hyperbolic systems arising in magnetohydro- dynamics and gas dynamics. We then present numerical results showing that this preconditioning scheme works well on problems where the underlying stiffness results from the interaction of fast transient waves with slowly-evolving dynamics, scales well to large problem sizes and numbers of processors, and allows for additional customization based on the specific problems under study
Minimal residual method stronger than polynomial preconditioning
Energy Technology Data Exchange (ETDEWEB)
Faber, V.; Joubert, W.; Knill, E. [Los Alamos National Lab., NM (United States)] [and others
1994-12-31
Two popular methods for solving symmetric and nonsymmetric systems of equations are the minimal residual method, implemented by algorithms such as GMRES, and polynomial preconditioning methods. In this study results are given on the convergence rates of these methods for various classes of matrices. It is shown that for some matrices, such as normal matrices, the convergence rates for GMRES and for the optimal polynomial preconditioning are the same, and for other matrices such as the upper triangular Toeplitz matrices, it is at least assured that if one method converges then the other must converge. On the other hand, it is shown that matrices exist for which restarted GMRES always converges but any polynomial preconditioning of corresponding degree makes no progress toward the solution for some initial error. The implications of these results for these and other iterative methods are discussed.
Directory of Open Access Journals (Sweden)
Wu Ann
2011-01-01
Full Text Available Abstract Background A preconditioning stimulus can trigger a neuroprotective phenotype in the nervous system - a preconditioning nerve lesion causes a significant increase in axonal regeneration, and cerebral preconditioning protects against subsequent ischemia. We hypothesized that a preconditioning nerve lesion induces gene/protein modifications, neuronal changes, and immune activation that may affect pain sensation following subsequent nerve injury. We examined whether a preconditioning lesion affects neuropathic pain and neuroinflammation after peripheral nerve injury. Results We found that a preconditioning crush injury to a terminal branch of the sciatic nerve seven days before partial ligation of the sciatic nerve (PSNL; a model of neuropathic pain induced a significant attenuation of pain hypersensitivity, particularly mechanical allodynia. A preconditioning lesion of the tibial nerve induced a long-term significant increase in paw-withdrawal threshold to mechanical stimuli and paw-withdrawal latency to thermal stimuli, after PSNL. A preconditioning lesion of the common peroneal induced a smaller but significant short-term increase in paw-withdrawal threshold to mechanical stimuli, after PSNL. There was no difference between preconditioned and unconditioned animals in neuronal damage and macrophage and T-cell infiltration into the dorsal root ganglia (DRGs or in astrocyte and microglia activation in the spinal dorsal and ventral horns. Conclusions These results suggest that prior exposure to a mild nerve lesion protects against adverse effects of subsequent neuropathic injury, and that this conditioning-induced inhibition of pain hypersensitivity is not dependent on neuroinflammation in DRGs and spinal cord. Identifying the underlying mechanisms may have important implications for the understanding of neuropathic pain due to nerve injury.
Super-low dose endotoxin pre-conditioning exacerbates sepsis mortality.
Chen, Keqiang; Geng, Shuo; Yuan, Ruoxi; Diao, Na; Upchurch, Zachary; Li, Liwu
2015-04-01
Sepsis mortality varies dramatically in individuals of variable immune conditions, with poorly defined mechanisms. This phenomenon complements the hypothesis that innate immunity may adopt rudimentary memory, as demonstrated in vitro with endotoxin priming and tolerance in cultured monocytes. However, previous in vivo studies only examined the protective effect of endotoxin tolerance in the context of sepsis. In sharp contrast, we report herein that pre-conditionings with super-low or low dose endotoxin lipopolysaccharide (LPS) cause strikingly opposite survival outcomes. Mice pre-conditioned with super-low dose LPS experienced severe tissue damage, inflammation, increased bacterial load in circulation, and elevated mortality when they were subjected to cecal-ligation and puncture (CLP). This is in opposite to the well-reported protective phenomenon with CLP mice pre-conditioned with low dose LPS. Mechanistically, we demonstrated that super-low and low dose LPS differentially modulate the formation of neutrophil extracellular trap (NET) in neutrophils. Instead of increased ERK activation and NET formation in neutrophils pre-conditioned with low dose LPS, we observed significantly reduced ERK activation and compromised NET generation in neutrophils pre-conditioned with super-low dose LPS. Collectively, our findings reveal a novel mechanism potentially responsible for the dynamic programming of innate immunity in vivo as it relates to sepsis risks.
Super-low Dose Endotoxin Pre-conditioning Exacerbates Sepsis Mortality
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Keqiang Chen
2015-04-01
Full Text Available Sepsis mortality varies dramatically in individuals of variable immune conditions, with poorly defined mechanisms. This phenomenon complements the hypothesis that innate immunity may adopt rudimentary memory, as demonstrated in vitro with endotoxin priming and tolerance in cultured monocytes. However, previous in vivo studies only examined the protective effect of endotoxin tolerance in the context of sepsis. In sharp contrast, we report herein that pre-conditioning with super-low or low dose endotoxin lipopolysaccharide (LPS cause strikingly opposite survival outcomes. Mice pre-conditioned with super-low dose LPS experienced severe tissue damage, inflammation, increased bacterial load in circulation, and elevated mortality when they were subjected to cecal-ligation and puncture (CLP. This is in contrast to the well-reported protective phenomenon with CLP mice pre-conditioned with low dose LPS. Mechanistically, we demonstrated that super-low and low dose LPS differentially modulate the formation of neutrophil extracellular trap (NET in neutrophils. Instead of increased ERK activation and NET formation in neutrophils pre-conditioned with low dose LPS, we observed significantly reduced ERK activation and compromised NET generation in neutrophils pre-conditioned with super-low dose LPS. Collectively, our findings reveal a mechanism potentially responsible for the dynamic programming of innate immunity in vivo as it relates to sepsis risks.
10-channel fiber array fabrication technique for parallel optical coherence tomography system
Arauz, Lina J.; Luo, Yuan; Castillo, Jose E.; Kostuk, Raymond K.; Barton, Jennifer
2007-02-01
Optical Coherence Tomography (OCT) shows great promise for low intrusive biomedical imaging applications. A parallel OCT system is a novel technique that replaces mechanical transverse scanning with electronic scanning. This will reduce the time required to acquire image data. In this system an array of small diameter fibers is required to obtain an image in the transverse direction. Each fiber in the array is configured in an interferometer and is used to image one pixel in the transverse direction. In this paper we describe a technique to package 15μm diameter fibers on a siliconsilica substrate to be used in a 2mm endoscopic probe tip. Single mode fibers are etched to reduce the cladding diameter from 125μm to 15μm. Etched fibers are placed into a 4mm by 150μm trench in a silicon-silica substrate and secured with UV glue. Active alignment was used to simplify the lay out of the fibers and minimize unwanted horizontal displacement of the fibers. A 10-channel fiber array was built, tested and later incorporated into a parallel optical coherence system. This paper describes the packaging, testing, and operation of the array in a parallel OCT system.
van Caster, Patrick; Eiling, Sandra; Boekholt, Yvonne; Behmenburg, Friederike; Dorsch, Marianne; Heinen, André; Hollmann, Markus W.; Huhn, Ragnar
2018-01-01
Prior studies have suggested that the antifibrinolytic drug aprotinin increases the infarct size after ischemia and reperfusion (I/R) and attenuates the effect of ischemic preconditioning (IPC). Aprotinin was replaced by tranexamic acid (TXA) in clinical practice. Here, we investigated whether TXA
International Nuclear Information System (INIS)
Kreitner, K.F.; Romaneehsen, Bernd; Oberholzer, Katja; Dueber, Christoph; Krummenauer, Frank; Mueller, L.P.
2006-01-01
The performance of a magnetic resonance (MR) imaging strategy that uses multiple receiver coil elements and integrated parallel imaging techniques (iPAT) in traumatic and degenerative disorders of the knee and to compare this technique with a standard MR imaging protocol was evaluated. Ninety patients with suspected internal derangements of the knee joint prospectively underwent MR imaging at 1.5 T. For signal detection, a 6-channel array coil was used. All patients were investigated with a standard imaging protocol consisting of different turbo spin-echo sequences proton density (PD), T 2 -weighted turbo spin echo (TSE) with and without fat suppression in three imaging planes. All sequences were repeated with an integrated parallel acquisition technique (iPAT) using the modified sensitivity encoding (mSENSE) algorithm with an acceleration factor of 2. Two radiologists independently evaluated and scored all images with regard to overall image quality, artefacts and pathologic findings. Agreement of the parallel ratings between readers and imaging techniques, respectively, was evaluated by means of pairwise kappa coefficients that were stratified for the area of evaluation. Agreement between the parallel readers for both the iPAT imaging and the conventional technique, respectively, as well as between imaging techniques was found encouraging with inter-observer kappa values ranging between 0.78 and 0.98 for both imaging techniques, and the inter-method kappa values ranging between 0.88 and 1.00 for both clinical readers. All pathological findings (e.g. occult fractures, meniscal and cruciate ligament tears, torn and interpositioned Hoffa's cleft, cartilage damage) were detected by both techniques with comparable performance. The use of iPAT lead to a 48% reduction of acquisition time compared with standard technique. Parallel imaging using mSENSE proved to be an efficient and economic tool for fast musculoskeletal MR imaging of the knee joint with comparable
International Nuclear Information System (INIS)
Chiueh, C.C.; Andoh, Tsugunobu; Chock, P. Boon
2005-01-01
Hormesis, a stress tolerance, can be induced by ischemic preconditioning stress. In addition to preconditioning, it may be induced by other means, such as gas anesthetics. Preconditioning mechanisms, which may be mediated by reprogramming survival genes and proteins, are obscure. A known neurotoxicant, 1-Methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP), causes less neurotoxicity in the mice that are preconditioned. Pharmacological evidences suggest that the signaling pathway of ·NO-cGMP-PKG (protein kinase G) may mediate preconditioning phenomenon. We developed a human SH-SY5Y cell model for investigating · NO-mediated signaling pathway, gene regulation, and protein expression following a sublethal preconditioning stress caused by a brief 2-h serum deprivation. Preconditioned human SH-SY5Y cells are more resistant against severe oxidative stress and apoptosis caused by lethal serum deprivation and 1-mehtyl-4-phenylpyridinium (MPP + ). Both sublethal and lethal oxidative stress caused by serum withdrawal increased neuronal nitric oxide synthase (nNOS/NOS1) expression and · NO levels to a similar extent. In addition to free radical scavengers, inhibition of nNOS, guanylyl cyclase, and PKG blocks hormesis induced by preconditioning. S-nitrosothiols and 6-Br-cGMP produce a cytoprotection mimicking the action of preconditioning tolerance. There are two distinct cGMP-mediated survival pathways: (i) the up-regulation of a redox protein thioredoxin (Trx) for elevating mitochondrial levels of antioxidant protein Mn superoxide dismutase (MnSOD) and antiapoptotic protein Bcl-2, and (ii) the activation of mitochondrial ATP-sensitive potassium channels [K(ATP)]. Preconditioning induction of Trx increased tolerance against MPP + , which was blocked by Trx mRNA antisense oligonucleotide and Trx reductase inhibitor. It is concluded that Trx plays a pivotal role in · NO-dependent preconditioning hormesis against MPTP/MPP +
Macro-elementwise preconditioning methods
Czech Academy of Sciences Publication Activity Database
Axelsson, Owe
2012-01-01
Roč. 82, č. 10 (2012), s. 1952-1963 ISSN 0378-4754 Institutional research plan: CEZ:AV0Z30860518 Keywords : heterogeniety * elementwise preconditioning * block matrix partitioning * macro-elements Subject RIV: BA - General Mathematics Impact factor: 0.836, year: 2012 http://www.sciencedirect.com/science/journal/03784754
Parallel-vector algorithms for particle simulations on shared-memory multiprocessors
International Nuclear Information System (INIS)
Nishiura, Daisuke; Sakaguchi, Hide
2011-01-01
Over the last few decades, the computational demands of massive particle-based simulations for both scientific and industrial purposes have been continuously increasing. Hence, considerable efforts are being made to develop parallel computing techniques on various platforms. In such simulations, particles freely move within a given space, and so on a distributed-memory system, load balancing, i.e., assigning an equal number of particles to each processor, is not guaranteed. However, shared-memory systems achieve better load balancing for particle models, but suffer from the intrinsic drawback of memory access competition, particularly during (1) paring of contact candidates from among neighboring particles and (2) force summation for each particle. Here, novel algorithms are proposed to overcome these two problems. For the first problem, the key is a pre-conditioning process during which particle labels are sorted by a cell label in the domain to which the particles belong. Then, a list of contact candidates is constructed by pairing the sorted particle labels. For the latter problem, a table comprising the list indexes of the contact candidate pairs is created and used to sum the contact forces acting on each particle for all contacts according to Newton's third law. With just these methods, memory access competition is avoided without additional redundant procedures. The parallel efficiency and compatibility of these two algorithms were evaluated in discrete element method (DEM) simulations on four types of shared-memory parallel computers: a multicore multiprocessor computer, scalar supercomputer, vector supercomputer, and graphics processing unit. The computational efficiency of a DEM code was found to be drastically improved with our algorithms on all but the scalar supercomputer. Thus, the developed parallel algorithms are useful on shared-memory parallel computers with sufficient memory bandwidth.
Energy Technology Data Exchange (ETDEWEB)
Ullmann, P.
2007-06-15
The primary objective of this work was the first experimental realization of parallel RF transmission for accelerating spatially selective excitation in magnetic resonance imaging. Furthermore, basic aspects regarding the performance of this technique were investigated, potential risks regarding the specific absorption rate (SAR) were considered and feasibility studies under application-oriented conditions as first steps towards a practical utilisation of this technique were undertaken. At first, based on the RF electronics platform of the Bruker Avance MRI systems, the technical foundations were laid to perform simultaneous transmission of individual RF waveforms on different RF channels. Another essential requirement for the realization of Parallel Excitation (PEX) was the design and construction of suitable RF transmit arrays with elements driven by separate transmit channels. In order to image the PEX results two imaging methods were implemented based on a spin-echo and a gradient-echo sequence, in which a parallel spatially selective pulse was included as an excitation pulse. In the course of this work PEX experiments were successfully performed on three different MRI systems, a 4.7 T and a 9.4 T animal system and a 3 T human scanner, using 5 different RF coil setups in total. In the last part of this work investigations regarding possible applications of Parallel Excitation were performed. A first study comprised experiments of slice-selective B1 inhomogeneity correction by using 3D-selective Parallel Excitation. The investigations were performed in a phantom as well as in a rat fixed in paraformaldehyde solution. In conjunction with these experiments a novel method of calculating RF pulses for spatially selective excitation based on a so-called Direct Calibration approach was developed, which is particularly suitable for this type of experiments. In the context of these experiments it was demonstrated how to combine the advantages of parallel transmission
A nonrecursive order N preconditioned conjugate gradient: Range space formulation of MDOF dynamics
Kurdila, Andrew J.
1990-01-01
While excellent progress has been made in deriving algorithms that are efficient for certain combinations of system topologies and concurrent multiprocessing hardware, several issues must be resolved to incorporate transient simulation in the control design process for large space structures. Specifically, strategies must be developed that are applicable to systems with numerous degrees of freedom. In addition, the algorithms must have a growth potential in that they must also be amenable to implementation on forthcoming parallel system architectures. For mechanical system simulation, this fact implies that algorithms are required that induce parallelism on a fine scale, suitable for the emerging class of highly parallel processors; and transient simulation methods must be automatically load balancing for a wider collection of system topologies and hardware configurations. These problems are addressed by employing a combination range space/preconditioned conjugate gradient formulation of multi-degree-of-freedom dynamics. The method described has several advantages. In a sequential computing environment, the method has the features that: by employing regular ordering of the system connectivity graph, an extremely efficient preconditioner can be derived from the 'range space metric', as opposed to the system coefficient matrix; because of the effectiveness of the preconditioner, preliminary studies indicate that the method can achieve performance rates that depend linearly upon the number of substructures, hence the title 'Order N'; and the method is non-assembling. Furthermore, the approach is promising as a potential parallel processing algorithm in that the method exhibits a fine parallel granularity suitable for a wide collection of combinations of physical system topologies/computer architectures; and the method is easily load balanced among processors, and does not rely upon system topology to induce parallelism.
Directory of Open Access Journals (Sweden)
Mehiddin Al-Baali
2015-12-01
Full Text Available We deal with the design of parallel algorithms by using variable partitioning techniques to solve nonlinear optimization problems. We propose an iterative solution method that is very efficient for separable functions, our scope being to discuss its performance for general functions. Experimental results on an illustrative example have suggested some useful modifications that, even though they improve the efficiency of our parallel method, leave some questions open for further investigation.
Application of preconditioned conjugate gradient-like methods to reactor kinetics
International Nuclear Information System (INIS)
Yang, D.Y.; Chen, G.S.; Chou, H.P.
1993-01-01
Several conjugate gradient-like (CG-like) methods are applied to solve the nonsymmetric linear systems of equations derived from the time-dependent two-dimensional two-energy-group neutron diffusion equations by a finite difference approximation. The methods are: the generalized conjugate residual method; the generalized conjugate gradient least-square method; the generalized minimal residual method (GMRES); the conjugate gradient square method; and a variant of bi-conjugate gradient method (Bi-CGSTAB). In order to accelerate these methods, six preconditioning techniques are investigated. Two are based on pointwise incomplete factorization: the incomplete LU (ILU) and the modified incomplete LU (MILU) decompositions; two, based on the block tridiagonal structure of the coefficient matrix, are blockwise and modified blockwise incomplete factorizations, BILU and MBILU; two are the alternating-direction implicit and symmetric successive overrelaxation (SSOR) preconditioners, derived from the basic iterative schemes. Comparisons are made by using CG-like methods combined with different preconditioners to solve a sequence of time-step reactor transient problems. Numerical tests indicate that preconditioned BI-CGSTAB with the preconditioner MBILU requires less CPU time and fewer iterations than other methods. The preconditioned CG-like methods are less sensitive to the time-step size used than the Chebyshev semi-iteration method and line SOR method. The indication is that the CGS, Bi-CGSTAB and GMRES methods are, on average, better than the other methods in reactor kinetics computation and that a good preconditioner is more important than the choice of CG-like methods. The MILU decomposition based on the conventional row-sum criterion has difficulty yielding a convergent solution and an improved version is introduced. (author)
[Anaesthetic-induced myocardial preconditioning: fundamental basis and clinical implications].
Chiari, P; Bouvet, F; Piriou, V
2005-04-01
Volatile halogenated anaesthetics offer a myocardial protection when they are administrated before a myocardial ischaemia. Cellular mechanisms involved in anaesthetic preconditioning are now better understood. The objectives of this review are to understand the anaesthetic-induced preconditioning underlying mechanisms and to know the clinical implications. References were obtained from PubMed data bank (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi) using the following keywords: volatile anaesthetic, isoflurane, halothane, sevoflurane, desflurane, preconditioning, protection, myocardium. Ischaemic preconditioning (PC) is a myocardial endogenous protection against ischaemia. It has been described as one or several short ischaemia before a sustained ischemia. These short ischaemia trigger a protective signal against this longer ischaemia. An ischemic organ is able to precondition a remote organ. It is possible to replace the short ischaemia by a preadministration of halogenated volatile anaesthetic with the same protective effect, this is called anaesthetic PC (APC). APC and ischaemic PC share similar underlying biochemical mechanisms including protein kinase C, tyrosine kinase activation and mitochondrial and sarcolemnal K(ATP) channels opening. All halogenated anaesthetics can produce an anaesthetic PC effect. Myocardial protection during reperfusion, after the long ischaemia, has been shown by successive short ischaemia or volatile anaesthetic administration, this is called postconditioning. Ischaemic PC has been described in humans in 1993. Clinical studies in human cardiac surgery have shown the possibility of anaesthetic PC with volatile anaesthetics. These studies have shown a decrease of postoperative troponin in patient receiving halogenated anaesthetics.
Parallel Computing Characteristics of CUPID code under MPI and Hybrid environment
Energy Technology Data Exchange (ETDEWEB)
Lee, Jae Ryong; Yoon, Han Young [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of); Jeon, Byoung Jin; Choi, Hyoung Gwon [Seoul National Univ. of Science and Technology, Seoul (Korea, Republic of)
2014-05-15
In this paper, a characteristic of parallel algorithm is presented for solving an elliptic type equation of CUPID via domain decomposition method using the MPI and the parallel performance is estimated in terms of a scalability which shows the speedup ratio. In addition, the time-consuming pattern of major subroutines is studied. Two different grid systems are taken into account: 40,000 meshes for coarse system and 320,000 meshes for fine system. Since the matrix of the CUPID code differs according to whether the flow is single-phase or two-phase, the effect of matrix shape is evaluated. Finally, the effect of the preconditioner for matrix solver is also investigated. Finally, the hybrid (OpenMP+MPI) parallel algorithm is introduced and discussed in detail for solving pressure solver. Component-scale thermal-hydraulics code, CUPID has been developed for two-phase flow analysis, which adopts a three-dimensional, transient, three-field model, and parallelized to fulfill a recent demand for long-transient and highly resolved multi-phase flow behavior. In this study, the parallel performance of the CUPID code was investigated in terms of scalability. The CUPID code was parallelized with domain decomposition method. The MPI library was adopted to communicate the information at the neighboring domain. For managing the sparse matrix effectively, the CSR storage format is used. To take into account the characteristics of the pressure matrix which turns to be asymmetric for two-phase flow, both single-phase and two-phase calculations were run. In addition, the effect of the matrix size and preconditioning was also investigated. The fine mesh calculation shows better scalability than the coarse mesh because the number of coarse mesh does not need to decompose the computational domain excessively. The fine mesh can be present good scalability when dividing geometry with considering the ratio between computation and communication time. For a given mesh, single-phase flow
Radiographers' preconditions for evidence-based radiography
International Nuclear Information System (INIS)
Ahonen, Sanna-Mari; Liikanen, Eeva
2010-01-01
Evidence-based practice (EBP) is essential in today's health care, but its establishment requires several preconditions from individuals and organizations (e.g. knowledge, understanding, attitudes, abilities, self-confidence, support, and resources). Previous studies suggest that radiographers do generate and use evidence in their work, but evidence-based radiography (EBR) is not yet used routinely as established practice, especially in terms of research utilization. This paper aims to describe radiographers' preconditions for EBR, and their participation in research activities. Main focus is on research utilization. Using an electronic questionnaire developed for this study, a survey was conducted: data collected from Finnish radiographers and radiotherapists (N = 438) were analysed both statistically and qualitatively. The final response rate was 39%. The results suggest radiographers' preconditions for EBR to consist of knowledge of research, significance of research activities, research-orientated way of working, and support. In addition, adequate resourcing is essential. Reading scientific journals, participation in research activities, a higher degree of education, and senior post seem to be significant promoters of EBR and research utilization. The results support the notion that EBR, and especially research utilization, are not yet well-established in Finland, and radiographers' viewpoints concerning the role and significance of research evidence and research activities still seem to vary.
Weston, Brian; Nourgaliev, Robert; Delplanque, Jean-Pierre
2017-11-01
We present a new block-based Schur complement preconditioner for simulating all-speed compressible flow with phase change. The conservation equations are discretized with a reconstructed Discontinuous Galerkin method and integrated in time with fully implicit time discretization schemes. The resulting set of non-linear equations is converged using a robust Newton-Krylov framework. Due to the stiffness of the underlying physics associated with stiff acoustic waves and viscous material strength effects, we solve for the primitive-variables (pressure, velocity, and temperature). To enable convergence of the highly ill-conditioned linearized systems, we develop a physics-based preconditioner, utilizing approximate block factorization techniques to reduce the fully-coupled 3×3 system to a pair of reduced 2×2 systems. We demonstrate that our preconditioned Newton-Krylov framework converges on very stiff multi-physics problems, corresponding to large CFL and Fourier numbers, with excellent algorithmic and parallel scalability. Results are shown for the classic lid-driven cavity flow problem as well as for 3D laser-induced phase change. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.
Orderings for conjugate gradient preconditionings
Ortega, James M.
1991-01-01
The effect of orderings on the rate of convergence of the conjugate gradient method with SSOR or incomplete Cholesky preconditioning is examined. Some results also are presented that help to explain why red/black ordering gives an inferior rate of convergence.
Decentralisation in developing countries: preconditions for successful implementation
Directory of Open Access Journals (Sweden)
Yasin Olum
2014-07-01
Full Text Available Decentralisation has been implemented and is being implemented in many developing countries without much success. Although several unique factors inhibit the implementation of decentralisation in individual countries, the paper argues that there are six pre-conditions that these countries should fulfill before decentralisation can be successfully implemented. These preconditions are: institutional mechanisms; creation of spaces for participation; political will and civil will; capacity development at the local level; careful implementation; and democratic governance.
Preconditioned Inexact Newton for Nonlinear Sparse Electromagnetic Imaging
Desmal, Abdulla
2014-05-04
Newton-type algorithms have been extensively studied in nonlinear microwave imaging due to their quadratic convergence rate and ability to recover images with high contrast values. In the past, Newton methods have been implemented in conjunction with smoothness promoting optimization/regularization schemes. However, this type of regularization schemes are known to perform poorly when applied in imagining domains with sparse content or sharp variations. In this work, an inexact Newton algorithm is formulated and implemented in conjunction with a linear sparse optimization scheme. A novel preconditioning technique is proposed to increase the convergence rate of the optimization problem. Numerical results demonstrate that the proposed framework produces sharper and more accurate images when applied in sparse/sparsified domains.
Preconditioned Inexact Newton for Nonlinear Sparse Electromagnetic Imaging
Desmal, Abdulla
2014-01-06
Newton-type algorithms have been extensively studied in nonlinear microwave imaging due to their quadratic convergence rate and ability to recover images with high contrast values. In the past, Newton methods have been implemented in conjunction with smoothness promoting optimization/regularization schemes. However, this type of regularization schemes are known to perform poorly when applied in imagining domains with sparse content or sharp variations. In this work, an inexact Newton algorithm is formulated and implemented in conjunction with a linear sparse optimization scheme. A novel preconditioning technique is proposed to increase the convergence rate of the optimization problem. Numerical results demonstrate that the proposed framework produces sharper and more accurate images when applied in sparse/sparsified domains.
Preconditioned Inexact Newton for Nonlinear Sparse Electromagnetic Imaging
Desmal, Abdulla; Bagci, Hakan
2014-01-01
Newton-type algorithms have been extensively studied in nonlinear microwave imaging due to their quadratic convergence rate and ability to recover images with high contrast values. In the past, Newton methods have been implemented in conjunction with smoothness promoting optimization/regularization schemes. However, this type of regularization schemes are known to perform poorly when applied in imagining domains with sparse content or sharp variations. In this work, an inexact Newton algorithm is formulated and implemented in conjunction with a linear sparse optimization scheme. A novel preconditioning technique is proposed to increase the convergence rate of the optimization problem. Numerical results demonstrate that the proposed framework produces sharper and more accurate images when applied in sparse/sparsified domains.
Management of Preconditioned Calves and Impacts of Preconditioning.
Hilton, W Mark
2015-07-01
When studying the practice of preconditioning (PC) calves, many factors need to be examined to determine if cow-calf producers should make this investment. Factors such as average daily gain, feed efficiency, available labor, length of the PC period, genetics, and marketing options must be analyzed. The health sales price advantage is an additional benefit in producing and selling PC calves but not the sole determinant of PC's financially feasibility. Studies show that a substantial advantage of PC is the selling of additional pounds at a cost of gain well below the marginal return of producing those additional pounds. Copyright © 2015 Elsevier Inc. All rights reserved.
Techniques and environments for big data analysis parallel, cloud, and grid computing
Dehuri, Satchidananda; Kim, Euiwhan; Wang, Gi-Name
2016-01-01
This volume is aiming at a wide range of readers and researchers in the area of Big Data by presenting the recent advances in the fields of Big Data Analysis, as well as the techniques and tools used to analyze it. The book includes 10 distinct chapters providing a concise introduction to Big Data Analysis and recent Techniques and Environments for Big Data Analysis. It gives insight into how the expensive fitness evaluation of evolutionary learning can play a vital role in big data analysis by adopting Parallel, Grid, and Cloud computing environments.
Logical inference techniques for loop parallelization
Oancea, Cosmin E.; Rauchwerger, Lawrence
2012-01-01
This paper presents a fully automatic approach to loop parallelization that integrates the use of static and run-time analysis and thus overcomes many known difficulties such as nonlinear and indirect array indexing and complex control flow. Our hybrid analysis framework validates the parallelization transformation by verifying the independence of the loop's memory references. To this end it represents array references using the USR (uniform set representation) language and expresses the independence condition as an equation, S = Ø, where S is a set expression representing array indexes. Using a language instead of an array-abstraction representation for S results in a smaller number of conservative approximations but exhibits a potentially-high runtime cost. To alleviate this cost we introduce a language translation F from the USR set-expression language to an equally rich language of predicates (F(S) ⇒ S = Ø). Loop parallelization is then validated using a novel logic inference algorithm that factorizes the obtained complex predicates (F(S)) into a sequence of sufficient-independence conditions that are evaluated first statically and, when needed, dynamically, in increasing order of their estimated complexities. We evaluate our automated solution on 26 benchmarks from PERFECTCLUB and SPEC suites and show that our approach is effective in parallelizing large, complex loops and obtains much better full program speedups than the Intel and IBM Fortran compilers. Copyright © 2012 ACM.
Logical inference techniques for loop parallelization
Oancea, Cosmin E.
2012-01-01
This paper presents a fully automatic approach to loop parallelization that integrates the use of static and run-time analysis and thus overcomes many known difficulties such as nonlinear and indirect array indexing and complex control flow. Our hybrid analysis framework validates the parallelization transformation by verifying the independence of the loop\\'s memory references. To this end it represents array references using the USR (uniform set representation) language and expresses the independence condition as an equation, S = Ø, where S is a set expression representing array indexes. Using a language instead of an array-abstraction representation for S results in a smaller number of conservative approximations but exhibits a potentially-high runtime cost. To alleviate this cost we introduce a language translation F from the USR set-expression language to an equally rich language of predicates (F(S) ⇒ S = Ø). Loop parallelization is then validated using a novel logic inference algorithm that factorizes the obtained complex predicates (F(S)) into a sequence of sufficient-independence conditions that are evaluated first statically and, when needed, dynamically, in increasing order of their estimated complexities. We evaluate our automated solution on 26 benchmarks from PERFECTCLUB and SPEC suites and show that our approach is effective in parallelizing large, complex loops and obtains much better full program speedups than the Intel and IBM Fortran compilers. Copyright © 2012 ACM.
Improved parallel solution techniques for the integral transport matrix method
Energy Technology Data Exchange (ETDEWEB)
Zerr, R. Joseph, E-mail: rjz116@psu.edu [Department of Mechanical and Nuclear Engineering, The Pennsylvania State University, University Park, PA (United States); Azmy, Yousry Y., E-mail: yyazmy@ncsu.edu [Department of Nuclear Engineering, North Carolina State University, Burlington Engineering Laboratories, Raleigh, NC (United States)
2011-07-01
Alternative solution strategies to the parallel block Jacobi (PBJ) method for the solution of the global problem with the integral transport matrix method operators have been designed and tested. The most straightforward improvement to the Jacobi iterative method is the Gauss-Seidel alternative. The parallel red-black Gauss-Seidel (PGS) algorithm can improve on the number of iterations and reduce work per iteration by applying an alternating red-black color-set to the subdomains and assigning multiple sub-domains per processor. A parallel GMRES(m) method was implemented as an alternative to stationary iterations. Computational results show that the PGS method can improve on the PBJ method execution time by up to 10´ when eight sub-domains per processor are used. However, compared to traditional source iterations with diffusion synthetic acceleration, it is still approximately an order of magnitude slower. The best-performing cases are optically thick because sub-domains decouple, yielding faster convergence. Further tests revealed that 64 sub-domains per processor was the best performing level of sub-domain division. An acceleration technique that improves the convergence rate would greatly improve the ITMM. The GMRES(m) method with a diagonal block pre conditioner consumes approximately the same time as the PBJ solver but could be improved by an as yet undeveloped, more efficient pre conditioner. (author)
Improved parallel solution techniques for the integral transport matrix method
International Nuclear Information System (INIS)
Zerr, R. Joseph; Azmy, Yousry Y.
2011-01-01
Alternative solution strategies to the parallel block Jacobi (PBJ) method for the solution of the global problem with the integral transport matrix method operators have been designed and tested. The most straightforward improvement to the Jacobi iterative method is the Gauss-Seidel alternative. The parallel red-black Gauss-Seidel (PGS) algorithm can improve on the number of iterations and reduce work per iteration by applying an alternating red-black color-set to the subdomains and assigning multiple sub-domains per processor. A parallel GMRES(m) method was implemented as an alternative to stationary iterations. Computational results show that the PGS method can improve on the PBJ method execution time by up to 10´ when eight sub-domains per processor are used. However, compared to traditional source iterations with diffusion synthetic acceleration, it is still approximately an order of magnitude slower. The best-performing cases are optically thick because sub-domains decouple, yielding faster convergence. Further tests revealed that 64 sub-domains per processor was the best performing level of sub-domain division. An acceleration technique that improves the convergence rate would greatly improve the ITMM. The GMRES(m) method with a diagonal block pre conditioner consumes approximately the same time as the PBJ solver but could be improved by an as yet undeveloped, more efficient pre conditioner. (author)
Nonlinear Multiplicative Schwarz Preconditioning in Natural Convection Cavity Flow
Liu, Lulu
2017-03-17
A natural convection cavity flow problem is solved using nonlinear multiplicative Schwarz preconditioners, as a Gauss-Seidel-like variant of additive Schwarz preconditioned inexact Newton (ASPIN). The nonlinear preconditioning extends the domain of convergence of Newton’s method to high Rayleigh numbers. Convergence performance varies widely with respect to different groupings of the fields of this multicomponent problem, and with respect to different orderings of the groupings.
Nonlinear Multiplicative Schwarz Preconditioning in Natural Convection Cavity Flow
Liu, Lulu; Zhang, Wei; Keyes, David E.
2017-01-01
A natural convection cavity flow problem is solved using nonlinear multiplicative Schwarz preconditioners, as a Gauss-Seidel-like variant of additive Schwarz preconditioned inexact Newton (ASPIN). The nonlinear preconditioning extends the domain of convergence of Newton’s method to high Rayleigh numbers. Convergence performance varies widely with respect to different groupings of the fields of this multicomponent problem, and with respect to different orderings of the groupings.
International Nuclear Information System (INIS)
Rosa, M.; Warsa, J. S.; Chang, J. H.
2007-01-01
A Fourier analysis is conducted in two-dimensional (2D) Cartesian geometry for the discrete-ordinates (SN) approximation of the neutron transport problem solved with Richardson iteration (Source Iteration) and Richardson iteration preconditioned with Transport Synthetic Acceleration (TSA), using the Parallel Block-Jacobi (PBJ) algorithm. The results for the un-accelerated algorithm show that convergence of PBJ can degrade, leading in particular to stagnation of GMRES(m) in problems containing optically thin sub-domains. The results for the accelerated algorithm indicate that TSA can be used to efficiently precondition an iterative method in the optically thin case when implemented in the 'modified' version MTSA, in which only the scattering in the low order equations is reduced by some non-negative factor β<1. (authors)
Hyperbaric oxygen preconditioning protects against traumatic brain injury at high altitude.
Hu, S L; Hu, R; Li, F; Liu, Z; Xia, Y Z; Cui, G Y; Feng, H
2008-01-01
Recent studies have shown that preconditioning with hyperbaric oxygen (HBO) can reduce ischemic and hemorrhagic brain injury. We investigated effects of HBO preconditioning on traumatic brain injury (TBI) at high altitude and examined the role of matrix metalloproteinase-9 (MMP-9) in such protection. Rats were randomly divided into 3 groups: HBO preconditioning group (HBOP; n = 13), high-altitude group (HA; n = 13), and high-altitude sham operation group (HASO; n = 13). All groups were subjected to head trauma by weight-drop device, except for HASO group. HBOP rats received 5 sessions of HBO preconditioning (2.5 ATA, 100% oxygen, 1 h daily) and then were kept in hypobaric chamber at 0.6 ATA (to simulate pressure at 4000m altitude) for 3 days before operation. HA rats received control pretreatment (1 ATA, room air, 1 h daily), then followed the same procedures as HBOP group. HASO rats were subjected to skull opening only without brain injury. Twenty-four hours after TBI, 7 rats from each group were examined for neurological function and brain water content; 6 rats from each group were killed for analysis by H&E staining and immunohistochemistry. Neurological outcome in HBOP group (0.71 +/- 0.49) was better than HA group (1.57 +/- 0.53; p < 0.05). Preconditioning with HBO significantly reduced percentage of brain water content (86.24 +/- 0.52 vs. 84.60 +/- 0.37; p < 0.01). Brain morphology and structure seen by light microscopy was diminished in HA group, while fewer pathological injuries occurred in HBOP group. Compared to HA group, pretreatment with HBO significantly reduced the number of MMP-9-positive cells (92.25 +/- 8.85 vs. 74.42 +/- 6.27; p < 0.01). HBO preconditioning attenuates TBI in rats at high altitude. Decline in MMP-9 expression may contribute to HBO preconditioning-induced protection of brain tissue against TBI.
International Nuclear Information System (INIS)
Chen, G.S.; Yang, D.Y.
1998-01-01
We apply and compare the preconditioned generalized conjugate gradient methods to solve the linear system equation that arises in the two-dimensional neutron and photon transport equation in this paper. Several subroutines are developed on the basis of preconditioned generalized conjugate gradient methods for time-independent, two-dimensional neutron and photon transport equation in the transport theory. These generalized conjugate gradient methods are used: TFQMR (transpose free quasi-minimal residual algorithm) CGS (conjugate gradient square algorithm), Bi-CGSTAB (bi-conjugate gradient stabilized algorithm) and QMRCGSTAB (quasi-minimal residual variant of bi-conjugate gradient stabilized algorithm). These subroutines are connected to computer program DORT. Several problems are tested on a personal computer with Intel Pentium CPU. The reasons to choose the generalized conjugate gradient methods are that the methods have better residual (equivalent to error) control procedures in the computation and have better convergent rate. The pointwise incomplete LU factorization ILU, modified pointwise incomplete LU factorization MILU, block incomplete factorization BILU and modified blockwise incomplete LU factorization MBILU are the preconditioning techniques used in the several testing problems. In Bi-CGSTAB, CGS, TFQMR and QMRCGSTAB method, we find that either CGS or Bi-CGSTAB method combined with preconditioner MBILU is the most efficient algorithm in these methods in the several testing problems. The numerical solution of flux by preconditioned CGS and Bi-CGSTAB methods has the same result as those from Cray computer, obtained by either the point successive relaxation method or the line successive relaxation method combined with Gaussian elimination
Preconditioned alternating direction method of multipliers for inverse problems with constraints
International Nuclear Information System (INIS)
Jiao, Yuling; Jin, Qinian; Lu, Xiliang; Wang, Weijie
2017-01-01
We propose a preconditioned alternating direction method of multipliers (ADMM) to solve linear inverse problems in Hilbert spaces with constraints, where the feature of the sought solution under a linear transformation is captured by a possibly non-smooth convex function. During each iteration step, our method avoids solving large linear systems by choosing a suitable preconditioning operator. In case the data is given exactly, we prove the convergence of our preconditioned ADMM without assuming the existence of a Lagrange multiplier. In case the data is corrupted by noise, we propose a stopping rule using information on noise level and show that our preconditioned ADMM is a regularization method; we also propose a heuristic rule when the information on noise level is unavailable or unreliable and give its detailed analysis. Numerical examples are presented to test the performance of the proposed method. (paper)
Rapamycin preconditioning attenuates transient focal cerebral ischemia/reperfusion injury in mice.
Yin, Lele; Ye, Shasha; Chen, Zhen; Zeng, Yaoying
2012-12-01
Rapamycin, an mTOR inhibitor and immunosuppressive agent in clinic, has protective effects on traumatic brain injury and neurodegenerative diseases. But, its effects on transient focal ischemia/reperfusion disease are not very clear. In this study, we examined the effects of rapamycin preconditioning on mice treated with middle cerebral artery occlusion/reperfusion operation (MCAO/R). We found that the rapamycin preconditioning by intrahippocampal injection 20 hr before MCAO/R significantly improved the survival rate and longevity of mice. It also decreased the neurological deficit score, infracted areas and brain edema. In addition, rapamycin preconditioning decreased the production of NF-κB, TNF-α, and Bax, but not Bcl-2, an antiapoptotic protein in the ischemic area. From these results, we may conclude that rapamycin preconditioning attenuate transient focal cerebral ischemia/reperfusion injury and inhibits apoptosis induced by MCAO/R in mice.
Sprick, Justin D; Rickards, Caroline A
2017-11-01
Remote ischemic preconditioning (RIPC) is characterized by the cyclical application of limb blood flow restriction and reperfusion and has been shown to protect vital organs during a subsequent ischemic insult. Blood flow restriction exercise (BFRE) similarly combines bouts of blood flow restriction with low-intensity exercise and thus could potentially emulate the protection demonstrated by RIPC. One concern with BFRE, however, is the potential for an augmented rise in sympathetic outflow due to greater activation of the exercise pressor reflex. Because of the use of lower workloads, however, we hypothesized that BFRE would elicit an attenuated increase in sympathetic outflow [assessed via plasma norepinephrine (NE) and mean arterial pressure (MAP)] and middle cerebral artery velocity (MCAv) when compared with conventional exercise (CE). Fifteen subjects underwent two leg press exercise interventions: 1 ) BFRE-220 mmHg bilateral thigh occlusion at 20% 1 rep-max (1RM), and 2 ) CE-65% 1RM without occlusion. Each condition consisted of 4 × 5-min cycles of exercise, with 3 × 10-reps in each cycle. Five minutes of rest and reperfusion (for BFRE) followed each cycle. MAP increased with exercise ( P exercise ( P exercise only ( P = 0.07). Plasma NE concentration increased with CE only ( P exercise ( P ≤ 0.02). The attenuated sympathetic response, combined with similar cerebrovascular responses, suggest that cyclical BFRE could be explored as an alternative to CE in the clinical setting. Copyright © 2017 the American Physiological Society.
Fast implementations of 3D PET reconstruction using vector and parallel programming techniques
International Nuclear Information System (INIS)
Guerrero, T.M.; Cherry, S.R.; Dahlbom, M.; Ricci, A.R.; Hoffman, E.J.
1993-01-01
Computationally intensive techniques that offer potential clinical use have arisen in nuclear medicine. Examples include iterative reconstruction, 3D PET data acquisition and reconstruction, and 3D image volume manipulation including image registration. One obstacle in achieving clinical acceptance of these techniques is the computational time required. This study focuses on methods to reduce the computation time for 3D PET reconstruction through the use of fast computer hardware, vector and parallel programming techniques, and algorithm optimization. The strengths and weaknesses of i860 microprocessor based workstation accelerator boards are investigated in implementations of 3D PET reconstruction
The Role of Ionospheric Outflow Preconditioning in Determining Storm Geoeffectiveness
Welling, D. T.; Liemohn, M. W.; Ridley, A. J.
2012-12-01
It is now well accepted that ionospheric outflow plays an important role in the development of the plasma sheet and ring current during geomagnetic storms. Furthermore, even during quiet times, ionospheric plasma populates the magnetospheric lobes, producing a reservoir of hydrogen and oxygen ions. When the Interplanetary Magnetic Field (IMF) turns southward, this reservoir is connected to the plasma sheet and ring current through magnetospheric convection. Hence, the conditions of the ionosphere and magnetospheric lobes leading up to magnetospheric storm onset have important implications for storm development. Despite this, there has been little research on this preconditioning; most global simulations begin just before storm onset, neglecting preconditioning altogether. This work explores the role of preconditioning in determining the geoeffectiveness of storms using a coupled global model system. A model of ionospheric outflow (the Polar Wind Outflow Model, PWOM) is two-way coupled to a global magnetohydrodynamic model (the Block-Adaptive Tree Solar wind Roe-type Upwind Scheme, BATS-R-US), which in turn drives a ring current model (the Ring current Atmosphere interactions Model, RAM). This unique setup is used to simulate an idealized storm. The model is started at many different times, from 1 hour before storm onset to 12 hours before. The effects of storm preconditioning are examined by investigating the total ionospheric plasma content in the lobes just before onset, the total ionospheric contribution in the ring current just after onset, and the effects on Dst, magnetic elevation angle at geosynchronous, and total ring current energy density. This experiment is repeated for different solar activity levels as set by F10.7 flux. Finally, a synthetic double-dip storm is constructed to see how two closely spaced storms affect each other by changing the preconditioning environment. It is found that preconditioning of the magnetospheric lobes via ionospheric
Warner, Dennis B.
1984-02-01
Recognition of the socioeconomic preconditions for successful rural water-supply and sanitation projects in developing countries is the key to identifying a new project. Preconditions are the social, economic and technical characteristics defining the project environment. There are two basic types of preconditions: those existing at the time of the initial investigation and those induced by subsequent project activities. Successful project identification is dependent upon an accurate recognition of existing constraints and a carefully tailored package of complementary investments intended to overcome the constraints. This paper discusses the socioeconomic aspects of preconditions in the context of a five-step procedure for project identification. The procedure includes: (1) problem identification; (2) determination of socioeconomic status; (3) technology selection; (4) utilization of support conditions; and (5) benefit estimation. Although the establishment of specific preconditions should be based upon the types of projects likely to be implemented, the paper outlines a number of general relationships regarding favourable preconditions in water and sanitation planning. These relationships are used within the above five-step procedure to develop a set of general guidelines for the application of preconditions in the identification of rural water-supply and sanitation projects.
PIXIE3D: An efficient, fully implicit, parallel, 3D extended MHD code for fusion plasma modeling
International Nuclear Information System (INIS)
Chacon, L.
2007-01-01
PIXIE3D is a modern, parallel, state-of-the-art extended MHD code that employs fully implicit methods for efficiency and accuracy. It features a general geometry formulation, and is therefore suitable for the study of many magnetic fusion configurations of interest. PIXIE3D advances the state of the art in extended MHD modeling in two fundamental ways. Firstly, it employs a novel conservative finite volume scheme which is remarkably robust and stable, and demands very small physical and/or numerical dissipation. This is a fundamental requirement when one wants to study fusion plasmas with realistic conductivities. Secondly, PIXIE3D features fully-implicit time stepping, employing Newton-Krylov methods for inverting the associated nonlinear systems. These methods have been shown to be scalable and efficient when preconditioned properly. Novel preconditioned ideas (so-called physics based), which were prototypes in the context of reduced MHD, have been adapted for 3D primitive-variable resistive MHD in PIXIE3D, and are currently being extended to Hall MHD. PIXIE3D is fully parallel, employing PETSc for parallelism. PIXIE3D has been thoroughly benchmarked against linear theory and against other available extended MHD codes on nonlinear test problems (such as the GEM reconnection challenge). We are currently in the process of extending such comparisons to fusion-relevant problems in realistic geometries. In this talk, we will describe both the spatial discretization approach and the preconditioning strategy employed for extended MHD in PIXIE3D. We will report on recent benchmarking studies between PIXIE3D and other 3D extended MHD codes, and will demonstrate its usefulness in a variety of fusion-relevant configurations such as Tokamaks and Reversed Field Pinches. (Author)
Logical inference techniques for loop parallelization
DEFF Research Database (Denmark)
Oancea, Cosmin Eugen; Rauchwerger, Lawrence
2012-01-01
the parallelization transformation by verifying the independence of the loop's memory references. To this end it represents array references using the USR (uniform set representation) language and expresses the independence condition as an equation, S={}, where S is a set expression representing array indexes. Using...... of their estimated complexities. We evaluate our automated solution on 26 benchmarks from PERFECT-CLUB and SPEC suites and show that our approach is effective in parallelizing large, complex loops and obtains much better full program speedups than the Intel and IBM Fortran compilers....
Murni, Bustamam, A.; Ernastuti, Handhika, T.; Kerami, D.
2017-07-01
Calculation of the matrix-vector multiplication in the real-world problems often involves large matrix with arbitrary size. Therefore, parallelization is needed to speed up the calculation process that usually takes a long time. Graph partitioning techniques that have been discussed in the previous studies cannot be used to complete the parallelized calculation of matrix-vector multiplication with arbitrary size. This is due to the assumption of graph partitioning techniques that can only solve the square and symmetric matrix. Hypergraph partitioning techniques will overcome the shortcomings of the graph partitioning technique. This paper addresses the efficient parallelization of matrix-vector multiplication through hypergraph partitioning techniques using CUDA GPU-based parallel computing. CUDA (compute unified device architecture) is a parallel computing platform and programming model that was created by NVIDIA and implemented by the GPU (graphics processing unit).
Blokhin, I O; Galagudza, M M; Vlasov, T D; Nifontov, E M; Petrishchev, N N
2008-07-01
Traditionally infarction size reduction by ischemic preconditioning is estimated in duration of test ischemia. This approach limits the understanding of real antiischemic efficacy of ischemic preconditioning. Present study was performed in the in vivo rat model of regional myocardial ischemia-reperfusion and showed that protective effect afforded by ischemic preconditioning progressively decreased with prolongation of test ischemia. There were no statistically significant differences in infarction size between control and preconditioned animals when the duration of test ischemia was increased up to 1 hour. Preconditioning ensured maximal infarction-limiting effect in duration of test ischemia varying from 20 to 40 minutes.
Fourier analysis of finite element preconditioned collocation schemes
Deville, Michel O.; Mund, Ernest H.
1990-01-01
The spectrum of the iteration operator of some finite element preconditioned Fourier collocation schemes is investigated. The first part of the paper analyses one-dimensional elliptic and hyperbolic model problems and the advection-diffusion equation. Analytical expressions of the eigenvalues are obtained with use of symbolic computation. The second part of the paper considers the set of one-dimensional differential equations resulting from Fourier analysis (in the tranverse direction) of the 2-D Stokes problem. All results agree with previous conclusions on the numerical efficiency of finite element preconditioning schemes.
Parallel Programming with Intel Parallel Studio XE
Blair-Chappell , Stephen
2012-01-01
Optimize code for multi-core processors with Intel's Parallel Studio Parallel programming is rapidly becoming a "must-know" skill for developers. Yet, where to start? This teach-yourself tutorial is an ideal starting point for developers who already know Windows C and C++ and are eager to add parallelism to their code. With a focus on applying tools, techniques, and language extensions to implement parallelism, this essential resource teaches you how to write programs for multicore and leverage the power of multicore in your programs. Sharing hands-on case studies and real-world examples, the
Soman, S; Liu, Z; Kim, G; Nemec, U; Holdsworth, S J; Main, K; Lee, B; Kolakowsky-Hayner, S; Selim, M; Furst, A J; Massaband, P; Yesavage, J; Adamson, M M; Spincemallie, P; Moseley, M; Wang, Y
2018-04-01
Identifying cerebral microhemorrhage burden can aid in the diagnosis and management of traumatic brain injury, stroke, hypertension, and cerebral amyloid angiopathy. MR imaging susceptibility-based methods are more sensitive than CT for detecting cerebral microhemorrhage, but methods other than quantitative susceptibility mapping provide results that vary with field strength and TE, require additional phase maps to distinguish blood from calcification, and depict cerebral microhemorrhages as bloom artifacts. Quantitative susceptibility mapping provides universal quantification of tissue magnetic property without these constraints but traditionally requires a mask generated by skull-stripping, which can pose challenges at tissue interphases. We evaluated the preconditioned quantitative susceptibility mapping MR imaging method, which does not require skull-stripping, for improved depiction of brain parenchyma and pathology. Fifty-six subjects underwent brain MR imaging with a 3D multiecho gradient recalled echo acquisition. Mask-based quantitative susceptibility mapping images were created using a commonly used mask-based quantitative susceptibility mapping method, and preconditioned quantitative susceptibility images were made using precondition-based total field inversion. All images were reviewed by a neuroradiologist and a radiology resident. Ten subjects (18%), all with traumatic brain injury, demonstrated blood products on 3D gradient recalled echo imaging. All lesions were visible on preconditioned quantitative susceptibility mapping, while 6 were not visible on mask-based quantitative susceptibility mapping. Thirty-one subjects (55%) demonstrated brain parenchyma and/or lesions that were visible on preconditioned quantitative susceptibility mapping but not on mask-based quantitative susceptibility mapping. Six subjects (11%) demonstrated pons artifacts on preconditioned quantitative susceptibility mapping and mask-based quantitative susceptibility mapping
International Nuclear Information System (INIS)
Romaneehsen, B.; Oberholzer, K.; Kreitner, K.-F.; Mueller, L.P.
2003-01-01
Purpose: To investigate the feasibility of using multiple receiver coil elements for time saving integrated parallel imaging techniques (iPAT) in traumatic musculoskeletal disorders. Material and methods: 6 patients with traumatic derangements of the knee, ankle and hip underwent MR imaging at 1.5 T. For signal detection of the knee and ankle, we used a 6-channel body array coil that was placed around the joints, for hip imaging two 4-channel body array coils and two elements of the spine array coil were combined for signal detection. All patients were investigated with a standard imaging protocol that mainly consisted of different turbo spin-echo sequences (PD-, T 2 -weighted TSE with and without fat suppression, STIR). All sequences were repeated with an integrated parallel acquisition technique (iPAT) using a modified sensitivity encoding (mSENSE) technique with an acceleration factor of 2. Overall image quality was subjectively assessed using a five-point scale as well as the ability for detection of pathologic findings. Results: Regarding overall image quality, there were no significant differences between standard imaging and imaging using mSENSE. All pathologies (occult fracture, meniscal tear, torn and interpositioned Hoffa's cleft, cartilage damage) were detected by both techniques. iPAT led to a 48% reduction of acquisition time compared with standard technique. Additionally, time savings with iPAT led to a decrease of pain-induced motion artifacts in two cases. Conclusion: In times of increasing cost pressure, iPAT using multiple coil elements seems to be an efficient and economic tool for fast musculoskeletal imaging with diagnostic performance comparable to conventional techniques. (orig.) [de
Application of parallel computing techniques to a large-scale reservoir simulation
International Nuclear Information System (INIS)
Zhang, Keni; Wu, Yu-Shu; Ding, Chris; Pruess, Karsten
2001-01-01
Even with the continual advances made in both computational algorithms and computer hardware used in reservoir modeling studies, large-scale simulation of fluid and heat flow in heterogeneous reservoirs remains a challenge. The problem commonly arises from intensive computational requirement for detailed modeling investigations of real-world reservoirs. This paper presents the application of a massive parallel-computing version of the TOUGH2 code developed for performing large-scale field simulations. As an application example, the parallelized TOUGH2 code is applied to develop a three-dimensional unsaturated-zone numerical model simulating flow of moisture, gas, and heat in the unsaturated zone of Yucca Mountain, Nevada, a potential repository for high-level radioactive waste. The modeling approach employs refined spatial discretization to represent the heterogeneous fractured tuffs of the system, using more than a million 3-D gridblocks. The problem of two-phase flow and heat transfer within the model domain leads to a total of 3,226,566 linear equations to be solved per Newton iteration. The simulation is conducted on a Cray T3E-900, a distributed-memory massively parallel computer. Simulation results indicate that the parallel computing technique, as implemented in the TOUGH2 code, is very efficient. The reliability and accuracy of the model results have been demonstrated by comparing them to those of small-scale (coarse-grid) models. These comparisons show that simulation results obtained with the refined grid provide more detailed predictions of the future flow conditions at the site, aiding in the assessment of proposed repository performance
A finite element solution method for quadrics parallel computer
International Nuclear Information System (INIS)
Zucchini, A.
1996-08-01
A distributed preconditioned conjugate gradient method for finite element analysis has been developed and implemented on a parallel SIMD Quadrics computer. The main characteristic of the method is that it does not require any actual assembling of all element equations in a global system. The physical domain of the problem is partitioned in cells of n p finite elements and each cell element is assigned to a different node of an n p -processors machine. Element stiffness matrices are stored in the data memory of the assigned processing node and the solution process is completely executed in parallel at element level. Inter-element and therefore inter-processor communications are required once per iteration to perform local sums of vector quantities between neighbouring elements. A prototype implementation has been tested on an 8-nodes Quadrics machine in a simple 2D benchmark problem
Parallel Reservoir Simulations with Sparse Grid Techniques and Applications to Wormhole Propagation
Wu, Yuanqing
2015-09-08
In this work, two topics of reservoir simulations are discussed. The first topic is the two-phase compositional flow simulation in hydrocarbon reservoir. The major obstacle that impedes the applicability of the simulation code is the long run time of the simulation procedure, and thus speeding up the simulation code is necessary. Two means are demonstrated to address the problem: parallelism in physical space and the application of sparse grids in parameter space. The parallel code can gain satisfactory scalability, and the sparse grids can remove the bottleneck of flash calculations. Instead of carrying out the flash calculation in each time step of the simulation, a sparse grid approximation of all possible results of the flash calculation is generated before the simulation. Then the constructed surrogate model is evaluated to approximate the flash calculation results during the simulation. The second topic is the wormhole propagation simulation in carbonate reservoir. In this work, different from the traditional simulation technique relying on the Darcy framework, we propose a new framework called Darcy-Brinkman-Forchheimer framework to simulate wormhole propagation. Furthermore, to process the large quantity of cells in the simulation grid and shorten the long simulation time of the traditional serial code, standard domain-based parallelism is employed, using the Hypre multigrid library. In addition to that, a new technique called “experimenting field approach” to set coefficients in the model equations is introduced. In the 2D dissolution experiments, different configurations of wormholes and a series of properties simulated by both frameworks are compared. We conclude that the numerical results of the DBF framework are more like wormholes and more stable than the Darcy framework, which is a demonstration of the advantages of the DBF framework. The scalability of the parallel code is also evaluated, and good scalability can be achieved. Finally, a mixed
Introduction to parallel programming
Brawer, Steven
1989-01-01
Introduction to Parallel Programming focuses on the techniques, processes, methodologies, and approaches involved in parallel programming. The book first offers information on Fortran, hardware and operating system models, and processes, shared memory, and simple parallel programs. Discussions focus on processes and processors, joining processes, shared memory, time-sharing with multiple processors, hardware, loops, passing arguments in function/subroutine calls, program structure, and arithmetic expressions. The text then elaborates on basic parallel programming techniques, barriers and race
Use of a preconditioned Bi-conjugate gradient method for hybrid plasma stability analysis
International Nuclear Information System (INIS)
Mikic, Z.; Morse, E.C.
1985-01-01
The numerical stability analysis of compact toroidal plasmas using implicit time differencing requires the solution of a set of coupled, 2-dimensional, elliptic partial differential equations for the field quantities at every timestep. When the equations are spatially finite-differenced and written in matrix form, the resulting matrix is large, sparse, complex, non-Hermitian, and indefinite. The use of the preconditioned bi-conjugate gradient method for solving these equations is discussed. The effect of block-diagonal preconditioning and incomplete block-LU preconditionig on the convergence of the method is investigated. For typical matrices arising in our studies, the eigenvalue spectra of the original and preconditioned matrices are calculated as an illustration of the effectiveness of the preconditioning. We show that the preconditioned bi-conjugate gradient method coverages more rapidly than the conjugate gradient method applied to the normal equations, and that it is an effective iterative method for the class of non-Hermitian, indefinite problems of interest
Remote ischaemic preconditioning and prevention of cerebral injury.
Rehni, Ashish K; Shri, Richa; Singh, Manjeet
2007-03-01
Bilateral carotid artery occlusion of 10 min followed by reperfusion for 24 hr was employed in present study to produce ischaemia and reperfusion induced cerebral injury in mice. Cerebral infarct size was measured using triphenyltetrazolium chloride staining. Short-term memory was evaluated using elevated plus maze. Inclined beam walking test was employed to assess motor incoordination. Bilateral carotid artery occlusion followed by reperfusion produced cerebral infarction and impaired short-term memory, motor co-ordination and lateral push response. A preceding episode of mesenteric artery occlusion for 15 min and reperfusion of 15 min (remote mesenteric ischaemic preconditioning) prevented markedly ischaemia-reperfusion-induced cerebral injury measured in terms of infarct size, loss of short-term memory, motor coordination and lateral push response. Glibenclamide (5 mg/kg, iv) a KATP channel blocker and caffeine (7 mg/kg, iv) an adenosine receptor blocker attenuated the neuroprotective effect of remote mesenteric ischaemic preconditioning. It may be concluded that neuroprotective effect of remote mesenteric ischaemic preconditioning may be due to activation of adenosine receptors and consequent activation of KATP channels in mice.
Parallel conjugate gradient algorithms for manipulator dynamic simulation
Fijany, Amir; Scheld, Robert E.
1989-01-01
Parallel conjugate gradient algorithms for the computation of multibody dynamics are developed for the specialized case of a robot manipulator. For an n-dimensional positive-definite linear system, the Classical Conjugate Gradient (CCG) algorithms are guaranteed to converge in n iterations, each with a computation cost of O(n); this leads to a total computational cost of O(n sq) on a serial processor. A conjugate gradient algorithms is presented that provide greater efficiency using a preconditioner, which reduces the number of iterations required, and by exploiting parallelism, which reduces the cost of each iteration. Two Preconditioned Conjugate Gradient (PCG) algorithms are proposed which respectively use a diagonal and a tridiagonal matrix, composed of the diagonal and tridiagonal elements of the mass matrix, as preconditioners. Parallel algorithms are developed to compute the preconditioners and their inversions in O(log sub 2 n) steps using n processors. A parallel algorithm is also presented which, on the same architecture, achieves the computational time of O(log sub 2 n) for each iteration. Simulation results for a seven degree-of-freedom manipulator are presented. Variants of the proposed algorithms are also developed which can be efficiently implemented on the Robot Mathematics Processor (RMP).
Directory of Open Access Journals (Sweden)
Sushama R Galgali
2011-01-01
Full Text Available Background: Maintenance of gingival health is a key factor for longevity of the teeth as well as of restorations. The physiologic dentogingival unit (DGU, which is composed of the epithelial and connective tissue attachments of the gingiva, functions as a barrier against microbial entry into the periodontium. Invasion of this space triggers inflammation and causes periodontal destruction. Despite the clinical relevance of the determination of the length and width of the DGU, there is no standardized technique. The length of the DGU can be either determined by histologic preparations or by transgingival probing. Although width can also be assessed by transgingival probing or with an ultrasound device, they are either invasive or expensive Aims: This study sought to evaluate an innovative radiographic exploration technique - parallel profile radiography - for measuring the dimensions of the DGU on the labial surfaces of anterior teeth. Materials and Methods: Two radiographs were made using the long-cone parallel technique in ten individuals, one in frontal projection, while the second radiograph was a parallel profile radiograph obtained from a lateral position. The length and width of the DGU was measured using computer software. Transgingival probing (trans-sulcular was done for these same patients and length of the DGU was measured. The values obtained by the two methods were compared. Pearson product correlation coefficient was calculated to examine the agreement between the values obtained by PPRx and transgingival probing. Results: The mean biologic width by the parallel profile radiography (PPRx technique was 1.72 mm (range 0.94-2.11 mm, while the mean thickness of the gingiva was 1.38 mm (range 0.92-1.77 mm. The mean biologic width by trans-gingival probing was 1.6 mm (range 0.8-2.2mm. Pearson product correlation coefficient (r for the above values was 0.914; thus, a high degree of agreement exists between the PPRx and TGP techniques
Energy Technology Data Exchange (ETDEWEB)
Romaneehsen, B.; Oberholzer, K.; Kreitner, K.-F. [Johannes Gutenberg-Univ. Mainz (Germany). Klinik und Poliklinik fuer Radiologie; Mueller, L.P. [Johannes Gutenberg-Univ. Mainz (Germany). Klinik und Poliklinik fuer Unfallchirurgie
2003-09-01
Purpose: To investigate the feasibility of using multiple receiver coil elements for time saving integrated parallel imaging techniques (iPAT) in traumatic musculoskeletal disorders. Material and methods: 6 patients with traumatic derangements of the knee, ankle and hip underwent MR imaging at 1.5 T. For signal detection of the knee and ankle, we used a 6-channel body array coil that was placed around the joints, for hip imaging two 4-channel body array coils and two elements of the spine array coil were combined for signal detection. All patients were investigated with a standard imaging protocol that mainly consisted of different turbo spin-echo sequences (PD-, T{sub 2}-weighted TSE with and without fat suppression, STIR). All sequences were repeated with an integrated parallel acquisition technique (iPAT) using a modified sensitivity encoding (mSENSE) technique with an acceleration factor of 2. Overall image quality was subjectively assessed using a five-point scale as well as the ability for detection of pathologic findings. Results: Regarding overall image quality, there were no significant differences between standard imaging and imaging using mSENSE. All pathologies (occult fracture, meniscal tear, torn and interpositioned Hoffa's cleft, cartilage damage) were detected by both techniques. iPAT led to a 48% reduction of acquisition time compared with standard technique. Additionally, time savings with iPAT led to a decrease of pain-induced motion artifacts in two cases. Conclusion: In times of increasing cost pressure, iPAT using multiple coil elements seems to be an efficient and economic tool for fast musculoskeletal imaging with diagnostic performance comparable to conventional techniques. (orig.) [German] Ziel: Einsatz integrierter paralleler Akquisitionstechniken (iPAT) zur Verkuerzung der Untersuchungszeit bei muskuloskelettalen Verletzungen. Material und Methoden: 6 Patienten mit einem Knie, Sprunggelenks- oder Huefttrauma wurden bei 1,5 T
Sensory Preconditioning in Newborn Rabbits: From Common to Distinct Odor Memories
Coureaud, Gerard; Tourat, Audrey; Ferreira, Guillaume
2013-01-01
This study evaluated whether olfactory preconditioning is functional in newborn rabbits and based on joined or independent memory of odorants. First, after exposure to odorants A+B, the conditioning of A led to high responsiveness to odorant B. Second, responsiveness to B persisted after amnesia of A. Third, preconditioning was also functional…
Directory of Open Access Journals (Sweden)
Daniel Marcsa
2015-01-01
Full Text Available The analysis and design of electromechanical devices involve the solution of large sparse linear systems, and require therefore high performance algorithms. In this paper, the primal Domain Decomposition Method (DDM with parallel forward-backward and with parallel Preconditioned Conjugate Gradient (PCG solvers are introduced in two-dimensional parallel time-stepping finite element formulation to analyze rotating machine considering the electromagnetic field, external circuit and rotor movement. The proposed parallel direct and the iterative solver with two preconditioners are analyzed concerning its computational efficiency and number of iterations of the solver with different preconditioners. Simulation results of a rotating machine is also presented.
Techniques applied in design optimization of parallel manipulators
CSIR Research Space (South Africa)
Modungwa, D
2011-11-01
Full Text Available the desired dexterous workspace " Robot.Comput.Integrated Manuf., vol. 23, pp. 38 - 46, 2007. [12] A.P. Murray, F. Pierrot, P. Dauchez and J.M. McCarthy, "A planar quaternion approach to the kinematic synthesis of a parallel manipulator " Robotica, vol... design of a three translational DoFs parallel manipulator " Robotica, vol. 24, pp. 239, 2005. [15] J. Angeles, "The robust design of parallel manipulators," in 1st Int. Colloquium, Collaborative Research Centre 562, 2002. [16] S. Bhattacharya, H...
Two-level preconditioned conjugate gradient methods with applications to bubbly flow problems
Tang, J.M.
2008-01-01
The Preconditioned Conjugate Gradient (PCG) method is one of the most popular iterative methods for solving large linear systems with a symmetric and positive semi-definite coefficient matrix. However, if the preconditioned coefficient matrix is ill-conditioned, the convergence of the PCG method
Nitroglycerine and sodium trioxodinitrate: from the discovery to the preconditioning effect.
Pagliaro, Pasquale; Gattullo, Donatella; Penna, Claudia
2013-10-01
The history began in the 19th century with Ascanio Sobrero (1812-1888), the discoverer of glycerol trinitrate (nitroglycerine, NTG), and with Angelo Angeli (1864-1931), the discoverer of sodium trioxodinitrate (Angeli's salt). It is likely that Angeli and Sobrero never met, but their two histories will join each other more than a century later. In fact, it has been discovered that both NTG and Angeli's salt are able to induce a preconditioning effect. As NTG has a long history as an antianginal drug its newly discovered property as a preconditioning agent has also been tested in humans. Angeli's salt properties as a preconditioning and inotropic agent have only been tested in animals so far.
Automatic Parallelization An Overview of Fundamental Compiler Techniques
Midkiff, Samuel P
2012-01-01
Compiling for parallelism is a longstanding topic of compiler research. This book describes the fundamental principles of compiling "regular" numerical programs for parallelism. We begin with an explanation of analyses that allow a compiler to understand the interaction of data reads and writes in different statements and loop iterations during program execution. These analyses include dependence analysis, use-def analysis and pointer analysis. Next, we describe how the results of these analyses are used to enable transformations that make loops more amenable to parallelization, and
Priming of the Cells: Hypoxic Preconditioning for Stem Cell Therapy.
Wei, Zheng Z; Zhu, Yan-Bing; Zhang, James Y; McCrary, Myles R; Wang, Song; Zhang, Yong-Bo; Yu, Shan-Ping; Wei, Ling
2017-10-05
Stem cell-based therapies are promising in regenerative medicine for protecting and repairing damaged brain tissues after injury or in the context of chronic diseases. Hypoxia can induce physiological and pathological responses. A hypoxic insult might act as a double-edged sword, it induces cell death and brain damage, but on the other hand, sublethal hypoxia can trigger an adaptation response called hypoxic preconditioning or hypoxic tolerance that is of immense importance for the survival of cells and tissues. This review was based on articles published in PubMed databases up to August 16, 2017, with the following keywords: "stem cells," "hypoxic preconditioning," "ischemic preconditioning," and "cell transplantation." Original articles and critical reviews on the topics were selected. Hypoxic preconditioning has been investigated as a primary endogenous protective mechanism and possible treatment against ischemic injuries. Many cellular and molecular mechanisms underlying the protective effects of hypoxic preconditioning have been identified. In cell transplantation therapy, hypoxic pretreatment of stem cells and neural progenitors markedly increases the survival and regenerative capabilities of these cells in the host environment, leading to enhanced therapeutic effects in various disease models. Regenerative treatments can mobilize endogenous stem cells for neurogenesis and angiogenesis in the adult brain. Furthermore, transplantation of stem cells/neural progenitors achieves therapeutic benefits via cell replacement and/or increased trophic support. Combinatorial approaches of cell-based therapy with additional strategies such as neuroprotective protocols, anti-inflammatory treatment, and rehabilitation therapy can significantly improve therapeutic benefits. In this review, we will discuss the recent progress regarding cell types and applications in regenerative medicine as well as future applications.
Pharmacological preconditioning with GYKI 52466: a prophylactic approach to neuroprotection
Directory of Open Access Journals (Sweden)
Chelsea S Goulton
2010-08-01
Full Text Available Some toxins and drugs can trigger lasting neuroprotective mechanisms that enable neurons to resist a subsequent severe insult. This ‘pharmacological preconditioning’ has far-reaching implications for conditions in which blood flow to the brain is interrupted. We have previously shown that in vitro preconditioning with the AMPA receptor antagonist GYKI 52466 induces tolerance to kainic acid (KA toxicity in hippocampus. This effect persists well after washout of the drug and may be mediated via inverse agonism of G protein linked receptors. Given the amplifying nature of metabotropic modulation, we hypothesised that GYKI 52466 may be effective in reducing seizure severity at doses well below those normally associated with adverse side effects. Here we report that pharmacological preconditioning with low-dose GYKI imparts a significant protection against KA-induced seizures in vivo. GYKI (3 mg/kg, s.c., 90 to 180 min. prior to high-dose KA, markedly reduced seizure scores, virtually abolished all level 3 and level 4 seizures, and completely suppressed KA-induced hippocampal cFOS expression. In addition, preconditioned animals exhibited significant reductions in high frequency/high amplitude spiking and ECoG power in the delta, theta, alpha and beta bands during KA. Adverse behaviours often associated with higher doses of GYKI were not evident during preconditioning. The fact that GYKI is effective at doses well-below, and at pre-administration intervals well-beyond previous studies, suggests that a classical blockade of ionotropic AMPA receptors does not underlie anticonvulsant effects. Low-dose GYKI preconditioning may represent a novel, prophylactic strategy for neuroprotection in a field almost completely devoid of effective pharmaceuticals.
Effect of ozone oxidative preconditioning in preventing early radiation-induced lung injury in rats
Energy Technology Data Exchange (ETDEWEB)
Bakkal, B.H. [Department of Radiation Oncology, School of Medicine, Bulent Ecevit University, Kozlu, Zonguldak (Turkey); Gultekin, F.A. [Department of General Surgery, School of Medicine, Bulent Ecevit University, Kozlu, Zonguldak (Turkey); Guven, B. [Department of Biochemistry, School of Medicine, Bulent Ecevit University, Kozlu, Zonguldak (Turkey); Turkcu, U.O. [Mugla School of Health Sciences, Mugla Sitki Kocman University, Mugla (Turkey); Bektas, S. [Department of Pathology, School of Medicine, Bulent Ecevit University, Kozlu, Zonguldak (Turkey); Can, M. [Department of Biochemistry, School of Medicine, Bulent Ecevit University, Kozlu, Zonguldak (Turkey)
2013-09-27
Ionizing radiation causes its biological effects mainly through oxidative damage induced by reactive oxygen species. Previous studies showed that ozone oxidative preconditioning attenuated pathophysiological events mediated by reactive oxygen species. As inhalation of ozone induces lung injury, the aim of this study was to examine whether ozone oxidative preconditioning potentiates or attenuates the effects of irradiation on the lung. Rats were subjected to total body irradiation, with or without treatment with ozone oxidative preconditioning (0.72 mg/kg). Serum proinflammatory cytokine levels, oxidative damage markers, and histopathological analysis were compared at 6 and 72 h after total body irradiation. Irradiation significantly increased lung malondialdehyde levels as an end-product of lipoperoxidation. Irradiation also significantly decreased lung superoxide dismutase activity, which is an indicator of the generation of oxidative stress and an early protective response to oxidative damage. Ozone oxidative preconditioning plus irradiation significantly decreased malondialdehyde levels and increased the activity of superoxide dismutase, which might indicate protection of the lung from radiation-induced lung injury. Serum tumor necrosis factor alpha and interleukin-1 beta levels, which increased significantly following total body irradiation, were decreased with ozone oxidative preconditioning. Moreover, ozone oxidative preconditioning was able to ameliorate radiation-induced lung injury assessed by histopathological evaluation. In conclusion, ozone oxidative preconditioning, repeated low-dose intraperitoneal administration of ozone, did not exacerbate radiation-induced lung injury, and, on the contrary, it provided protection against radiation-induced lung damage.
Effect of ozone oxidative preconditioning in preventing early radiation-induced lung injury in rats
International Nuclear Information System (INIS)
Bakkal, B.H.; Gultekin, F.A.; Guven, B.; Turkcu, U.O.; Bektas, S.; Can, M.
2013-01-01
Ionizing radiation causes its biological effects mainly through oxidative damage induced by reactive oxygen species. Previous studies showed that ozone oxidative preconditioning attenuated pathophysiological events mediated by reactive oxygen species. As inhalation of ozone induces lung injury, the aim of this study was to examine whether ozone oxidative preconditioning potentiates or attenuates the effects of irradiation on the lung. Rats were subjected to total body irradiation, with or without treatment with ozone oxidative preconditioning (0.72 mg/kg). Serum proinflammatory cytokine levels, oxidative damage markers, and histopathological analysis were compared at 6 and 72 h after total body irradiation. Irradiation significantly increased lung malondialdehyde levels as an end-product of lipoperoxidation. Irradiation also significantly decreased lung superoxide dismutase activity, which is an indicator of the generation of oxidative stress and an early protective response to oxidative damage. Ozone oxidative preconditioning plus irradiation significantly decreased malondialdehyde levels and increased the activity of superoxide dismutase, which might indicate protection of the lung from radiation-induced lung injury. Serum tumor necrosis factor alpha and interleukin-1 beta levels, which increased significantly following total body irradiation, were decreased with ozone oxidative preconditioning. Moreover, ozone oxidative preconditioning was able to ameliorate radiation-induced lung injury assessed by histopathological evaluation. In conclusion, ozone oxidative preconditioning, repeated low-dose intraperitoneal administration of ozone, did not exacerbate radiation-induced lung injury, and, on the contrary, it provided protection against radiation-induced lung damage
A fast, preconditioned conjugate gradient Toeplitz solver
Pan, Victor; Schrieber, Robert
1989-01-01
A simple factorization is given of an arbitrary hermitian, positive definite matrix in which the factors are well-conditioned, hermitian, and positive definite. In fact, given knowledge of the extreme eigenvalues of the original matrix A, an optimal improvement can be achieved, making the condition numbers of each of the two factors equal to the square root of the condition number of A. This technique is to applied to the solution of hermitian, positive definite Toeplitz systems. Large linear systems with hermitian, positive definite Toeplitz matrices arise in some signal processing applications. A stable fast algorithm is given for solving these systems that is based on the preconditioned conjugate gradient method. The algorithm exploits Toeplitz structure to reduce the cost of an iteration to O(n log n) by applying the fast Fourier Transform to compute matrix-vector products. Matrix factorization is used as a preconditioner.
High-energy physics software parallelization using database techniques
International Nuclear Information System (INIS)
Argante, E.; Van der Stok, P.D.V.; Willers, I.
1997-01-01
A programming model for software parallelization, called CoCa, is introduced that copes with problems caused by typical features of high-energy physics software. By basing CoCa on the database transaction paradigm, the complexity induced by the parallelization is for a large part transparent to the programmer, resulting in a higher level of abstraction than the native message passing software. CoCa is implemented on a Meiko CS-2 and on a SUN SPARCcenter 2000 parallel computer. On the CS-2, the performance is comparable with the performance of native PVM and MPI. (orig.)
Zhang, Xiao-bo
2017-06-01
The gradient preconditioning approach based on seismic wave energy can effectively avoid the huge storage consumption in the gradient preconditioning algorithms based on Hessian matrices in time-domain full waveform inversion (FWI), but the accuracy is affected by the energy of reflected waves when strong reflectors are present in velocity model. To address this problem, we propose a gradient preconditioning method, which scales the gradient based on the energy of the “approximated transmitted wavefield” simulated by the nonreflecting acoustic wave equation. The method does not require computing or storing the Hessian matrix or its inverse. Furthermore, it can effectively eliminate the effects caused by geometric diffusion and non-uniformity illumination on gradient. The results of model experiments confirm that the time-domain FWI using the gradient preconditioning based on transmitted waves energy can achieve higher inversion precision for high-velocity body and the deep strata below when compared with using the gradient preconditioning based on seismic waves energy.
Equivalent operator preconditioning for elliptic problems
Czech Academy of Sciences Publication Activity Database
Axelsson, Owe; Karátson, J.
2009-01-01
Roč. 50, č. 3 (2009), s. 297-380 ISSN 1017-1398 Institutional research plan: CEZ:AV0Z30860518 Keywords : Elliptic problem * Conjugate gradient method * preconditioning * equivalent operators * compact operators Subject RIV: BA - General Mathematics Impact factor: 0.716, year: 2009 http://en.scientificcommons.org/42514649
Block Preconditioning to Enable Physics-Compatible Implicit Multifluid Plasma Simulations
Phillips, Edward; Shadid, John; Cyr, Eric; Miller, Sean
2017-10-01
Multifluid plasma simulations involve large systems of partial differential equations in which many time-scales ranging over many orders of magnitude arise. Since the fastest of these time-scales may set a restrictively small time-step limit for explicit methods, the use of implicit or implicit-explicit time integrators can be more tractable for obtaining dynamics at time-scales of interest. Furthermore, to enforce properties such as charge conservation and divergence-free magnetic field, mixed discretizations using volume, nodal, edge-based, and face-based degrees of freedom are often employed in some form. Together with the presence of stiff modes due to integrating over fast time-scales, the mixed discretization makes the required linear solves for implicit methods particularly difficult for black box and monolithic solvers. This work presents a block preconditioning strategy for multifluid plasma systems that segregates the linear system based on discretization type and approximates off-diagonal coupling in block diagonal Schur complement operators. By employing multilevel methods for the block diagonal subsolves, this strategy yields algorithmic and parallel scalability which we demonstrate on a range of problems.
Preconditioning the modified conjugate gradient method ...
African Journals Online (AJOL)
In this paper, the convergence analysis of the conventional conjugate Gradient method was reviewed. And the convergence analysis of the modified conjugate Gradient method was analysed with our extension on preconditioning the algorithm. Convergence of the algorithm is a function of the condition number of M-1A.
The role of adenosine in preconditioning by brief pressure overload in rats.
Huang, Cheng-Hsiung; Tsai, Shen-Kou; Chiang, Shu-Chiung; Lai, Chang-Chi; Weng, Zen-Chung
2015-08-01
Brief pressure overload of the left ventricle reduced myocardial infarct (MI) size in rabbits has been previously reported. Its effects in other species are not known. This study investigates effects of pressure overload and the role of adenosine in rats in this study. MI was induced by 40-minute occlusion of the left anterior descending coronary artery followed by 3-hour reperfusion. MI size was determined by triphenyl tetrazolium chloride staining. Brief pressure overload was induced by two 10-minute episodes of partial snaring of the ascending aorta. Systolic left ventricular pressure was raised 50% above the baseline value. Ischemic preconditioning was elicited by two 10-minute coronary artery occlusions. The MI size (mean ± standard deviation), expressed as percentage of area at risk, was significantly reduced in the pressure overload group as well as in the ischemic preconditioning group (17.4 ± 3.0% and 18.2 ± 1.5% vs. 26.6 ± 2.4% in the control group, p overload and ischemic preconditioning (18.3 ± 1.5% and 18.2 ± 2.0%, respectively, p overload of the left ventricle preconditioned rat myocardium against infarction. Because SPT did not significantly alter MI size reduction, our results did not support a role of adenosine in preconditioning by pressure overload in rats. Copyright © 2013. Published by Elsevier B.V.
Ketamine, but not S(+)-ketamine, blocks ischemic preconditioning in rabbit hearts in vivo
Müllenheim, J.; Frässdorf, J.; Preckel, B.; Thämer, V.; Schlack, W.
2001-01-01
BACKGROUND: Ketamine blocks KATP channels in isolated cells and abolishes the cardioprotective effect of ischemic preconditioning in vitro. The authors investigated the effects of ketamine and S(+)-ketamine on ischemic preconditioning in the rabbit heart in vivo. METHODS: In 46
Combined incomplete LU and strongly implicit procedure preconditioning
Energy Technology Data Exchange (ETDEWEB)
Meese, E.A. [Univ. of Trondheim (Norway)
1996-12-31
For the solution of large sparse linear systems of equations, the Krylov-subspace methods have gained great merit. Their efficiency are, however, largely dependent upon preconditioning of the equation-system. A family of matrix factorisations often used for preconditioning, is obtained from a truncated Gaussian elimination, ILU(p). Less common, supposedly due to it`s restriction to certain sparsity patterns, is factorisations generated by the strongly implicit procedure (SIP). The ideas from ILU(p) and SIP are used in this paper to construct a generalized strongly implicit procedure, applicable to matrices with any sparsity pattern. The new algorithm has been run on some test equations, and efficiency improvements over ILU(p) was found.
S2SA preconditioning for the Sn equations with strictly non negative spatial discretization
International Nuclear Information System (INIS)
Bruss, D. E.; Morel, J. E.; Ragusa, J. C.
2013-01-01
Preconditioners based upon sweeps and diffusion-synthetic acceleration have been constructed and applied to the zeroth and first spatial moments of the 1-D S n transport equation using a strictly non negative nonlinear spatial closure. Linear and nonlinear preconditioners have been analyzed. The effectiveness of various combinations of these preconditioners are compared. In one dimension, nonlinear sweep preconditioning is shown to be superior to linear sweep preconditioning, and DSA preconditioning using nonlinear sweeps in conjunction with a linear diffusion equation is found to be essentially equivalent to nonlinear sweeps in conjunction with a nonlinear diffusion equation. The ability to use a linear diffusion equation has important implications for preconditioning the S n equations with a strictly non negative spatial discretization in multiple dimensions. (authors)
Scalable multi-grid preconditioning techniques for the even-parity S_N solver in UNIC
International Nuclear Information System (INIS)
Mahadevan, Vijay S.; Smith, Michael A.
2011-01-01
The Even-parity neutron transport equation with FE-S_N discretization is solved traditionally using SOR preconditioned CG method at the lowest level of iterations in order to compute the criticality in reactor analysis problems. The use of high order isoparametric finite elements prohibits the formation of the discrete operator explicitly due to memory constraints in peta scale architectures. Hence, a h-p multi-grid preconditioner based on linear tessellation of the higher order mesh is introduced here for the space-angle system and compared against SOR and Algebraic MG black-box solvers. The performance and scalability of the multi-grid scheme was determined for two test problems and found to be competitive in terms of both computational time and memory requirements. The implementation of this preconditioner in an even-parity solver like UNIC from ANL can further enable high fidelity calculations in a scalable manner on peta flop machines. (author)
International Nuclear Information System (INIS)
Wang Shuxia
2001-01-01
Ischemic preconditioning is the intrinsic and most potently myocardial protection. Its mechanism is the foundation of rational therapeutic application. Nowadays there are some theories about delayed phase of preconditioning such as nitric oxide hypothesis, free radical mechanisms, protective protein synthesis and opening of ATP-sensitive potassium channels. By incorporation 3 H-leucine, using liquid scintillation counter, the authors know there was protective protein synthesis during preconditioning. SPECT could study the characteristics of preconditioned myocardium in vivo, and PET might further show the metabolism, energy consumption and its relationship to myocardium dysfunction
Iterative solution of general sparse linear systems on clusters of workstations
Energy Technology Data Exchange (ETDEWEB)
Lo, Gen-Ching; Saad, Y. [Univ. of Minnesota, Minneapolis, MN (United States)
1996-12-31
Solving sparse irregularly structured linear systems on parallel platforms poses several challenges. First, sparsity makes it difficult to exploit data locality, whether in a distributed or shared memory environment. A second, perhaps more serious challenge, is to find efficient ways to precondition the system. Preconditioning techniques which have a large degree of parallelism, such as multicolor SSOR, often have a slower rate of convergence than their sequential counterparts. Finally, a number of other computational kernels such as inner products could ruin any gains gained from parallel speed-ups, and this is especially true on workstation clusters where start-up times may be high. In this paper we discuss these issues and report on our experience with PSPARSLIB, an on-going project for building a library of parallel iterative sparse matrix solvers.
Zhang, Xiao-bo; Tan, Jun; Song, Peng; Li, Jin-shan; Xia, Dong-ming; Liu, Zhao-lun
2017-01-01
The gradient preconditioning approach based on seismic wave energy can effectively avoid the huge storage consumption in the gradient preconditioning algorithms based on Hessian matrices in time-domain full waveform inversion (FWI), but the accuracy
Directory of Open Access Journals (Sweden)
Yuhei Harada
2016-02-01
Full Text Available A taste sensor that uses lipid/polymer membranes can evaluate aftertastes felt by humans using Change in membrane Potential caused by Adsorption (CPA measurements. The sensor membrane for evaluating bitterness, which is caused by acidic bitter substances such as iso-alpha acid contained in beer, needs an immersion process in monosodium glutamate (MSG solution, called “MSG preconditioning”. However, what happens to the lipid/polymer membrane during MSG preconditioning is not clear. Therefore, we carried out three experiments to investigate the changes in the lipid/polymer membrane caused by the MSG preconditioning, i.e., measurements of the taste sensor, measurements of the amount of the bitterness substance adsorbed onto the membrane and measurements of the contact angle of the membrane surface. The CPA values increased as the preconditioning process progressed, and became stable after 3 d of preconditioning. The response potentials to the reference solution showed the same tendency of the CPA value change during the preconditioning period. The contact angle of the lipid/polymer membrane surface decreased after 7 d of MSG preconditioning; in short, the surface of the lipid/polymer membrane became hydrophilic during MSG preconditioning. The amount of adsorbed iso-alpha acid was increased until 5 d preconditioning, and then it decreased. In this study, we revealed that the CPA values increased with the progress of MSG preconditioning in spite of the decrease of the amount of iso-alpha acid adsorbed onto the lipid/polymer membrane, and it was indicated that the CPA values increase because the sensor sensitivity was improved by the MSG preconditioning.
International Nuclear Information System (INIS)
Alleon, G.; Carpentieri, B.; Du, I.S.; Giraud, L.; Langou, J.; Martin, E.
2003-01-01
The boundary element method has become a popular tool for the solution of Maxwell's equations in electromagnetism. It discretizes only the surface of the radiating object and gives rise to linear systems that are smaller in size compared to those arising from finite element or finite difference discretizations. However, these systems are prohibitively demanding in terms of memory for direct methods and challenging to solve by iterative methods. In this paper we address the iterative solution via preconditioned Krylov methods of electromagnetic scattering problems expressed in an integral formulation, with main focus on the design of the pre-conditioner. We consider an approximate inverse method based on the Frobenius-norm minimization with a pattern prescribed in advance. The pre-conditioner is constructed from a sparse approximation of the dense coefficient matrix, and the patterns both for the pre-conditioner and for the coefficient matrix are computed a priori using geometric information from the mesh. We describe the implementation of the approximate inverse in an out-of-core parallel code that uses multipole techniques for the matrix-vector products, and show results on the numerical scalability of our method on systems of size up to one million unknowns. We propose an embedded iterative scheme based on the GMRES method and combined with multipole techniques, aimed at improving the robustness of the approximate inverse for large problems. We prove by numerical experiments that the proposed scheme enables the solution of very large and difficult problems efficiently at reduced computational and memory cost. Finally we perform a preliminary study on a spectral two-level pre-conditioner to enhance the robustness of our method. This numerical technique exploits spectral information of the preconditioned systems to build a low rank-update of the pre-conditioner. (authors)
Energy Technology Data Exchange (ETDEWEB)
Alleon, G. [EADS-CCR, 31 - Blagnac (France); Carpentieri, B.; Du, I.S.; Giraud, L.; Langou, J.; Martin, E. [Cerfacs, 31 - Toulouse (France)
2003-07-01
The boundary element method has become a popular tool for the solution of Maxwell's equations in electromagnetism. It discretizes only the surface of the radiating object and gives rise to linear systems that are smaller in size compared to those arising from finite element or finite difference discretizations. However, these systems are prohibitively demanding in terms of memory for direct methods and challenging to solve by iterative methods. In this paper we address the iterative solution via preconditioned Krylov methods of electromagnetic scattering problems expressed in an integral formulation, with main focus on the design of the pre-conditioner. We consider an approximate inverse method based on the Frobenius-norm minimization with a pattern prescribed in advance. The pre-conditioner is constructed from a sparse approximation of the dense coefficient matrix, and the patterns both for the pre-conditioner and for the coefficient matrix are computed a priori using geometric information from the mesh. We describe the implementation of the approximate inverse in an out-of-core parallel code that uses multipole techniques for the matrix-vector products, and show results on the numerical scalability of our method on systems of size up to one million unknowns. We propose an embedded iterative scheme based on the GMRES method and combined with multipole techniques, aimed at improving the robustness of the approximate inverse for large problems. We prove by numerical experiments that the proposed scheme enables the solution of very large and difficult problems efficiently at reduced computational and memory cost. Finally we perform a preliminary study on a spectral two-level pre-conditioner to enhance the robustness of our method. This numerical technique exploits spectral information of the preconditioned systems to build a low rank-update of the pre-conditioner. (authors)
Kolb, Alexander L; Corridon, Peter R; Zhang, Shijun; Xu, Weimin; Witzmann, Frank A; Collett, Jason A; Rhodes, George J; Winfree, Seth; Bready, Devin; Pfeffenberger, Zechariah J; Pomerantz, Jeremy M; Hato, Takashi; Nagami, Glenn T; Molitoris, Bruce A; Basile, David P; Atkinson, Simon J; Bacallao, Robert L
2018-04-01
Ischemic preconditioning confers organ-wide protection against subsequent ischemic stress. A substantial body of evidence underscores the importance of mitochondria adaptation as a critical component of cell protection from ischemia. To identify changes in mitochondria protein expression in response to ischemic preconditioning, we isolated mitochondria from ischemic preconditioned kidneys and sham-treated kidneys as a basis for comparison. The proteomic screen identified highly upregulated proteins, including NADP+-dependent isocitrate dehydrogenase 2 (IDH2), and we confirmed the ability of this protein to confer cellular protection from injury in murine S3 proximal tubule cells subjected to hypoxia. To further evaluate the role of IDH2 in cell protection, we performed detailed analysis of the effects of Idh2 gene delivery on kidney susceptibility to ischemia-reperfusion injury. Gene delivery of IDH2 before injury attenuated the injury-induced rise in serum creatinine ( P <0.05) observed in controls and increased the mitochondria membrane potential ( P <0.05), maximal respiratory capacity ( P <0.05), and intracellular ATP levels ( P <0.05) above those in controls. This communication shows that gene delivery of Idh2 can confer organ-wide protection against subsequent ischemia-reperfusion injury and mimics ischemic preconditioning. Copyright © 2018 by the American Society of Nephrology.
Effects of ketamine and its isomers on ischemic preconditioning in the isolated rat heart
Molojavyi, A.; Preckel, B.; Comfère, T.; Müllenheim, J.; Thämer, V.; Schlack, W.
2001-01-01
BACKGROUND: Ischemic preconditioning protects the heart against subsequent ischemia. Opening of the adenosine triphosphate-sensitive potassium (KATP) channel is a key mechanism of preconditioning. Ketamine blocks KATP channels of isolated cardiomyocytes. The authors investigated the effects of
Field-Split Preconditioned Inexact Newton Algorithms
Liu, Lulu
2015-06-02
The multiplicative Schwarz preconditioned inexact Newton (MSPIN) algorithm is presented as a complement to additive Schwarz preconditioned inexact Newton (ASPIN). At an algebraic level, ASPIN and MSPIN are variants of the same strategy to improve the convergence of systems with unbalanced nonlinearities; however, they have natural complementarity in practice. MSPIN is naturally based on partitioning of degrees of freedom in a nonlinear PDE system by field type rather than by subdomain, where a modest factor of concurrency can be sacrificed for physically motivated convergence robustness. ASPIN, originally introduced for decompositions into subdomains, is natural for high concurrency and reduction of global synchronization. We consider both types of inexact Newton algorithms in the field-split context, and we augment the classical convergence theory of ASPIN for the multiplicative case. Numerical experiments show that MSPIN can be significantly more robust than Newton methods based on global linearizations, and that MSPIN can be more robust than ASPIN and maintain fast convergence even for challenging problems, such as high Reynolds number Navier--Stokes equations.
Field-Split Preconditioned Inexact Newton Algorithms
Liu, Lulu; Keyes, David E.
2015-01-01
The multiplicative Schwarz preconditioned inexact Newton (MSPIN) algorithm is presented as a complement to additive Schwarz preconditioned inexact Newton (ASPIN). At an algebraic level, ASPIN and MSPIN are variants of the same strategy to improve the convergence of systems with unbalanced nonlinearities; however, they have natural complementarity in practice. MSPIN is naturally based on partitioning of degrees of freedom in a nonlinear PDE system by field type rather than by subdomain, where a modest factor of concurrency can be sacrificed for physically motivated convergence robustness. ASPIN, originally introduced for decompositions into subdomains, is natural for high concurrency and reduction of global synchronization. We consider both types of inexact Newton algorithms in the field-split context, and we augment the classical convergence theory of ASPIN for the multiplicative case. Numerical experiments show that MSPIN can be significantly more robust than Newton methods based on global linearizations, and that MSPIN can be more robust than ASPIN and maintain fast convergence even for challenging problems, such as high Reynolds number Navier--Stokes equations.
Preconditioning of iterative methods - theory and applications
Czech Academy of Sciences Publication Activity Database
Axelsson, Owe; Blaheta, Radim; Neytcheva, M.; Pultarová, I.
2015-01-01
Roč. 22, č. 6 (2015), s. 901-902 ISSN 1070-5325 Institutional support: RVO:68145535 Keywords : preconditioning * iterative methods * applications Subject RIV: BA - General Mathematics Impact factor: 1.431, year: 2015 http://onlinelibrary.wiley.com/doi/10.1002/nla.2016/epdf
Directory of Open Access Journals (Sweden)
Norio Saga
2008-03-01
Full Text Available The purpose of this study was to clarify whether heat preconditioning results in less eccentric exercise-induced muscle damage and muscle soreness, and whether the repeated bout effect is enhanced by heat preconditioning prior to eccentric exercise. Nine untrained male volunteers aged 23 ± 3 years participated in this study. Heat preconditioning included treatment with a microwave hyperthermia unit (150 W, 20 min that was randomly applied to one of the subject's arms (MW; the other arm was used as a control (CON. One day after heat preconditioning, the subjects performed 24 maximal isokinetic eccentric contractions of the elbow flexors at 30°·s-1 (ECC1. One week after ECC1, the subjects repeated the procedure (ECC2. After each bout of exercise, maximal voluntary contraction (MVC, range of motion (ROM of the elbow joint, upper arm circumference, blood creatine kinase (CK activity and muscle soreness were measured. The subjects experienced both conditions at an interval of 3 weeks. MVC and ROM in the MW were significantly higher than those in the CON (p < 0.05 for ECC1; however, the heat preconditioning had no significant effect on upper arm circumference, blood CK activity, or muscle soreness following ECC1 and ECC2. Heat preconditioning may protect human skeletal muscle from eccentric exercise-induced muscle damage after a single bout of eccentric exercise but does not appear to promote the repeated bout effect after a second bout of eccentric exercise
Advanced parallel processing with supercomputer architectures
International Nuclear Information System (INIS)
Hwang, K.
1987-01-01
This paper investigates advanced parallel processing techniques and innovative hardware/software architectures that can be applied to boost the performance of supercomputers. Critical issues on architectural choices, parallel languages, compiling techniques, resource management, concurrency control, programming environment, parallel algorithms, and performance enhancement methods are examined and the best answers are presented. The authors cover advanced processing techniques suitable for supercomputers, high-end mainframes, minisupers, and array processors. The coverage emphasizes vectorization, multitasking, multiprocessing, and distributed computing. In order to achieve these operation modes, parallel languages, smart compilers, synchronization mechanisms, load balancing methods, mapping parallel algorithms, operating system functions, application library, and multidiscipline interactions are investigated to ensure high performance. At the end, they assess the potentials of optical and neural technologies for developing future supercomputers
Impact of remote ischemic preconditioning on wound healing in small bowel anastomoses
Holzner, Philipp Anton; Kulemann, Birte; Kuesters, Simon; Timme, Sylvia; Hoeppner, Jens; Hopt, Ulrich Theodor; Marjanovic, Goran
2011-01-01
AIM: To investigate the influence of remote ischemic preconditioning (RIPC) on anastomotic integrity. METHODS: Sixty male Wistar rats were randomized to six groups. The control group (n = 10) had an end-to-end ileal anastomosis without RIPC. The preconditioned groups (n = 34) varied in time of ischemia and time of reperfusion. One group received the amino acid L-arginine before constructing the anastomosis (n = 9). On postoperative day 4, the rats were re-laparotomized, and bursting pressure, hydroxyproline concentration, intra-abdominal adhesions, and a histological score concerning the mucosal ischemic injury were collected. The data are given as median (range). RESULTS: On postoperative day 4, median bursting pressure was 124 mmHg (60-146 mmHg) in the control group. The experimental groups did not show a statistically significant difference (P > 0.05). Regarding the hydroxyproline concentration, we did not find any significant variation in the experimental groups. We detected significantly less mucosal injury in the RIPC groups. Furthermore, we assessed more extensive intra-abdominal adhesions in the preconditioned groups than in the control group. CONCLUSION: RIPC directly before performing small bowel anastomosis does not affect anastomotic stability in the early period, as seen in ischemic preconditioning. PMID:21455330
Deja, Marek A; Wiaderkiewicz, Ryszard; Czekaj, Piotr; Czech, Ewa; Malinowski, Marcin; Machej, Leszek; Węglarzy, Andrzej; Kowalówka, Adam; Piekarska, Magda; Szurlej, Bartosz; Latusek, Tomasz
2018-01-01
Remote preconditioning has been shown to be a potent protective phenomenon in many animals. Several studies aimed to demonstrate it was feasible in humans by trying to show its protective effect during cardiac surgery. Of these, some small studies and one larger trial were positive while two other bigger studies showed no effectiveness of remote preconditioning as assessed by levels of postoperatively released cardiac markers. Recently, two large clinical trials also failed to prove the benefit of remote preconditioning in cardiac surgery. No study showed that remote preconditioning actually increases resistance of human myocardium to standardised ischaemic and reperfusion stimulus in experimental settings. In animal studies, remote preconditioning was shown to improve mitochondrial function and structure, but such data on human myocardium are scarce. The aim of the study is to determine whether remote preconditioning protects human myocardium against ischaemia-reperfusion injury in both in vivo and in vitro conditions. The trial is designed as a single-centre, double-blinded, sham-controlled trial of 120 patients. We randomise (1:1) patients referred for coronary artery bypass grafting for stable coronary artery disease to remote preconditioning or "sham" intervention. The remote preconditioning is obtained by three cycles of 5 min inflation and 5 min deflation of a blood pressure cuff on the right arm. Postoperative course including myocardial enzymes profile will be analysed. Moreover, in the in-vitro arm the clinically preconditioned myocardium will be assessed for function, mitochondria structure, and mitochondria-dependent apoptosis. The informed consent of all patients is obtained before enrolment into the study by the investigator. The study conforms to the spirit and the letter of the declaration of Helsinki. In case the effect of remote preconditioning is not measurable in ex-vivo assessment, any future attempt at implementing this phenomenon in clinical
Jönsthövel, T.B.; Van Gijzen, M.B.; MacLachlan, S.; Vuik, C.; Scarpas, A.
2011-01-01
The demand for large FE meshes increases as parallel computing becomes the standard in FE simulations. Direct and iterative solution methods are used to solve the resulting linear systems. Many applications concern composite materials, which are characterized by large discontinuities in the material
V. V. Likhvantsev; O. A. Grebenchikov; R. A. Cherpakov; Yu. V. Skripkin; K. Yu. Borisov
2016-01-01
The purpose of this study is to determine and evaluate if the preconditioning with desflurane depends on level of phosphoGSK3β.Material and methods. White outbred male rats (56) were randomly allocated to 6 groups. Ischemia/reperfusion modeling was performed using V. G.Korpachev's technique. The reference group consisted of sham (falselyoperated) animals. The second group underwent global ischemia/reperfusion after anesthesia with chloral hydrate. The next two groups were treated with either ...
Impact of pre-conditioning on the qualification of safety-related equipment
International Nuclear Information System (INIS)
Isgro, J.R.
1982-01-01
This paper shares some recent experiences on the effects of preconditioning on the qualification of safety-related equipment not located in a harsh environment. Environmental and seismic qualification testing programs were conducted following the guidelines of IEEE 323-1974, IEEE 344-1975 and appropriate IEEE daughter standards, where available. The examples that follow will illustrate the degree of pre-conditioning of safety-related equipment qualified to the requirements of IEEE-323-1974, and its effect on the outcome of the qualification program
Directory of Open Access Journals (Sweden)
Eugene V. Golanov
2017-09-01
Full Text Available Excitation of intrinsic neurons of cerebellar fastigial nucleus (FN renders brain tolerant to local and global ischemia. This effect reaches a maximum 72 h after the stimulation and lasts over 10 days. Comparable neuroprotection is observed following sublethal global brain ischemia, a phenomenon known as preconditioning. We hypothesized that FN may participate in the mechanisms of ischemic preconditioning as a part of the intrinsic neuroprotective mechanism. To explore potential significance of FN neurons in brain ischemic tolerance we lesioned intrinsic FN neurons with excitotoxin ibotenic acid five days before exposure to 20 min four-vessel occlusion (4-VO global ischemia while analyzing neuronal damage in Cornu Ammoni area 1 (CA1 hippocampal area one week later. In FN-lesioned animals, loss of CA1 cells was higher by 22% compared to control (phosphate buffered saline (PBS-injected animals. Moreover, lesion of FN neurons increased morbidity following global ischemia by 50%. Ablation of FN neurons also reversed salvaging effects of five-minute ischemic preconditioning on CA1 neurons and morbidity, while ablation of cerebellar dentate nucleus neurons did not change effect of ischemic preconditioning. We conclude that FN is an important part of intrinsic neuroprotective system, which participates in ischemic preconditioning and may participate in naturally occurring neuroprotection, such as “diving response”.
Rethinking The Going Concern Assumption As A Pre-Condition For Accounting Measurement
Saratiel Wedzerai Musvoto; Daan G Gouws
2011-01-01
This study compares the principles of the going concern concept against the principles of representational measurement to determine if it is possible to establish foundations of accounting measurement with the going concern concept as a precondition. Representational measurement theory is a theory that establishes measurement in social scientific disciplines such as accounting. The going concern assumption is prescribed as one of the preconditions for measuring the attributes of the elements ...
Exploiting Symmetry on Parallel Architectures.
Stiller, Lewis Benjamin
1995-01-01
This thesis describes techniques for the design of parallel programs that solve well-structured problems with inherent symmetry. Part I demonstrates the reduction of such problems to generalized matrix multiplication by a group-equivariant matrix. Fast techniques for this multiplication are described, including factorization, orbit decomposition, and Fourier transforms over finite groups. Our algorithms entail interaction between two symmetry groups: one arising at the software level from the problem's symmetry and the other arising at the hardware level from the processors' communication network. Part II illustrates the applicability of our symmetry -exploitation techniques by presenting a series of case studies of the design and implementation of parallel programs. First, a parallel program that solves chess endgames by factorization of an associated dihedral group-equivariant matrix is described. This code runs faster than previous serial programs, and discovered it a number of results. Second, parallel algorithms for Fourier transforms for finite groups are developed, and preliminary parallel implementations for group transforms of dihedral and of symmetric groups are described. Applications in learning, vision, pattern recognition, and statistics are proposed. Third, parallel implementations solving several computational science problems are described, including the direct n-body problem, convolutions arising from molecular biology, and some communication primitives such as broadcast and reduce. Some of our implementations ran orders of magnitude faster than previous techniques, and were used in the investigation of various physical phenomena.
Energy Technology Data Exchange (ETDEWEB)
2017-04-04
A parallelization of the k-means++ seed selection algorithm on three distinct hardware platforms: GPU, multicore CPU, and multithreaded architecture. K-means++ was developed by David Arthur and Sergei Vassilvitskii in 2007 as an extension of the k-means data clustering technique. These algorithms allow people to cluster multidimensional data, by attempting to minimize the mean distance of data points within a cluster. K-means++ improved upon traditional k-means by using a more intelligent approach to selecting the initial seeds for the clustering process. While k-means++ has become a popular alternative to traditional k-means clustering, little work has been done to parallelize this technique. We have developed original C++ code for parallelizing the algorithm on three unique hardware architectures: GPU using NVidia's CUDA/Thrust framework, multicore CPU using OpenMP, and the Cray XMT multithreaded architecture. By parallelizing the process for these platforms, we are able to perform k-means++ clustering much more quickly than it could be done before.
Parallel sparse direct solver for integrated circuit simulation
Chen, Xiaoming; Yang, Huazhong
2017-01-01
This book describes algorithmic methods and parallelization techniques to design a parallel sparse direct solver which is specifically targeted at integrated circuit simulation problems. The authors describe a complete flow and detailed parallel algorithms of the sparse direct solver. They also show how to improve the performance by simple but effective numerical techniques. The sparse direct solver techniques described can be applied to any SPICE-like integrated circuit simulator and have been proven to be high-performance in actual circuit simulation. Readers will benefit from the state-of-the-art parallel integrated circuit simulation techniques described in this book, especially the latest parallel sparse matrix solution techniques. · Introduces complicated algorithms of sparse linear solvers, using concise principles and simple examples, without complex theory or lengthy derivations; · Describes a parallel sparse direct solver that can be adopted to accelerate any SPICE-like integrated circuit simulato...
Improving image quality of parallel phase-shifting digital holography
International Nuclear Information System (INIS)
Awatsuji, Yasuhiro; Tahara, Tatsuki; Kaneko, Atsushi; Koyama, Takamasa; Nishio, Kenzo; Ura, Shogo; Kubota, Toshihiro; Matoba, Osamu
2008-01-01
The authors propose parallel two-step phase-shifting digital holography to improve the image quality of parallel phase-shifting digital holography. The proposed technique can increase the effective number of pixels of hologram twice in comparison to the conventional parallel four-step technique. The increase of the number of pixels makes it possible to improve the image quality of the reconstructed image of the parallel phase-shifting digital holography. Numerical simulation and preliminary experiment of the proposed technique were conducted and the effectiveness of the technique was confirmed. The proposed technique is more practical than the conventional parallel phase-shifting digital holography, because the composition of the digital holographic system based on the proposed technique is simpler.
The effect of preconditioning cells under osmotic stress on high alcohol production
Directory of Open Access Journals (Sweden)
Logotetis Stilijanos
2013-01-01
Full Text Available This paper focuses on the research into the influence of salt on physiology of the yeast, Saccharomyces cerevisiae. Specifically, the work focused on how NaCl affected the growth, viability and fermentation performance of this yeast in laboratory-scale experiments. One of the main findings of the research presented involved the influence of salt “preconditioning” of yeasts which represents a method of pre-culturing of cells in the presence of salt in an attempt to improve subsequent fermentation performance. Such an approach resulted in preconditioned yeasts having an improved capability to ferment high-sugar containing media (up to 60% w/v of glucose with increased cell viability and with increased levels of produced ethanol (higher than 20% in vol.. Salt-preconditioning was most likely influencing the stress-tolerance of yeasts by inducing the synthesis of key metabolites such as trehalose and glycerol which act to improve cells’ ability to withstand osmostress and ethanol toxicity. The industrial-scale trials using salt-preconditioned yeasts verified the benefit of the physiological engineering approach to practical fermentations. Overall, this research has demonstrated that a relatively simple method designed to adapt yeast cells physiologically - by salt-preconditioning - can have distinct advantages for alcohol fermentation processes.
Hypoxic preconditioning induces neuroprotective stanniocalcin-1 in brain via IL-6 signaling
DEFF Research Database (Denmark)
Westberg, Johan A; Serlachius, Martina; Lankila, Petri
2007-01-01
BACKGROUND AND PURPOSE: Exposure of animals for a few hours to moderate hypoxia confers relative protection against subsequent ischemic brain damage. This phenomenon, known as hypoxic preconditioning, depends on new RNA and protein synthesis, but its molecular mechanisms are poorly understood...... originally reported expression of mammalian STC-1 in brain neurons and showed that STC-1 guards neurons against hypercalcemic and hypoxic damage. METHODS: We treated neural Paju cells with IL-6 and measured the induction of STC-1 mRNA. In addition, we quantified the effect of hypoxic preconditioning on Stc-1...... mRNA levels in brains of wild-type and IL-6 deficient mice. Furthermore, we monitored the Stc-1 response in brains of wild-type and transgenic mice, overexpressing IL-6 in the astroglia, before and after induced brain injury. RESULTS: Hypoxic preconditioning induced an upregulated expression of Stc...
40 CFR 86.232-94 - Vehicle preconditioning.
2010-07-01
... 40 Protection of Environment 18 2010-07-01 2010-07-01 false Vehicle preconditioning. 86.232-94... (CONTINUED) CONTROL OF EMISSIONS FROM NEW AND IN-USE HIGHWAY VEHICLES AND ENGINES Emission Regulations for 1994 and Later Model Year Gasoline-Fueled New Light-Duty Vehicles, New Light-Duty Trucks and New Medium...
Hajabdollahi, Farzaneh; Premnath, Kannan N.
2018-05-01
Lattice Boltzmann (LB) models used for the computation of fluid flows represented by the Navier-Stokes (NS) equations on standard lattices can lead to non-Galilean-invariant (GI) viscous stress involving cubic velocity errors. This arises from the dependence of their third-order diagonal moments on the first-order moments for standard lattices, and strategies have recently been introduced to restore Galilean invariance without such errors using a modified collision operator involving corrections to either the relaxation times or the moment equilibria. Convergence acceleration in the simulation of steady flows can be achieved by solving the preconditioned NS equations, which contain a preconditioning parameter that can be used to tune the effective sound speed, and thereby alleviating the numerical stiffness. In the present paper, we present a GI formulation of the preconditioned cascaded central-moment LB method used to solve the preconditioned NS equations, which is free of cubic velocity errors on a standard lattice, for steady flows. A Chapman-Enskog analysis reveals the structure of the spurious non-GI defect terms and it is demonstrated that the anisotropy of the resulting viscous stress is dependent on the preconditioning parameter, in addition to the fluid velocity. It is shown that partial correction to eliminate the cubic velocity defects is achieved by scaling the cubic velocity terms in the off-diagonal third-order moment equilibria with the square of the preconditioning parameter. Furthermore, we develop additional corrections based on the extended moment equilibria involving gradient terms with coefficients dependent locally on the fluid velocity and the preconditioning parameter. Such parameter dependent corrections eliminate the remaining truncation errors arising from the degeneracy of the diagonal third-order moments and fully restore Galilean invariance without cubic defects for the preconditioned LB scheme on a standard lattice. Several
Error Estimation in Preconditioned Conjugate Gradients
Czech Academy of Sciences Publication Activity Database
Strakoš, Zdeněk; Tichý, Petr
2005-01-01
Roč. 45, - (2005), s. 789-817 ISSN 0006-3835 R&D Projects: GA AV ČR 1ET400300415; GA AV ČR KJB1030306 Institutional research plan: CEZ:AV0Z10300504 Keywords : preconditioned conjugate gradient method * error bounds * stopping criteria * evaluation of convergence * numerical stability * finite precision arithmetic * rounding errors Subject RIV: BA - General Mathematics Impact factor: 0.509, year: 2005
M-step preconditioned conjugate gradient methods
Adams, L.
1983-01-01
Preconditioned conjugate gradient methods for solving sparse symmetric and positive finite systems of linear equations are described. Necessary and sufficient conditions are given for when these preconditioners can be used and an analysis of their effectiveness is given. Efficient computer implementations of these methods are discussed and results on the CYBER 203 and the Finite Element Machine under construction at NASA Langley Research Center are included.
A Linguistic Technique for Marking and Analyzing Syntactic Parallelism.
Sackler, Jessie Brome
Sentences in rhetoric texts were used in this study to determine a way in which thetorical syntactic parallelism can be analyzed. A tagmemic analysis determined tagmas which were parallel or identical or similar to one another. These were distinguished from tagmas which were identical because of the syntactic constraints of the language…
40 CFR 86.132-00 - Vehicle preconditioning.
2010-07-01
... 40 Protection of Environment 18 2010-07-01 2010-07-01 false Vehicle preconditioning. 86.132-00... (CONTINUED) CONTROL OF EMISSIONS FROM NEW AND IN-USE HIGHWAY VEHICLES AND ENGINES Emission Regulations for 1977 and Later Model Year New Light-Duty Vehicles and New Light-Duty Trucks and New Otto-Cycle Complete...
High-Order Calderón Preconditioned Time Domain Integral Equation Solvers
Valdes, Felipe; Ghaffari-Miab, Mohsen; Andriulli, Francesco P.; Cools, Kristof; Michielssen,
2013-01-01
Two high-order accurate Calderón preconditioned time domain electric field integral equation (TDEFIE) solvers are presented. In contrast to existing Calderón preconditioned time domain solvers, the proposed preconditioner allows for high-order surface representations and current expansions by using a novel set of fully-localized high-order div-and quasi curl-conforming (DQCC) basis functions. Numerical results demonstrate that the linear systems of equations obtained using the proposed basis functions converge rapidly, regardless of the mesh density and of the order of the current expansion. © 1963-2012 IEEE.
High-Order Calderón Preconditioned Time Domain Integral Equation Solvers
Valdes, Felipe
2013-05-01
Two high-order accurate Calderón preconditioned time domain electric field integral equation (TDEFIE) solvers are presented. In contrast to existing Calderón preconditioned time domain solvers, the proposed preconditioner allows for high-order surface representations and current expansions by using a novel set of fully-localized high-order div-and quasi curl-conforming (DQCC) basis functions. Numerical results demonstrate that the linear systems of equations obtained using the proposed basis functions converge rapidly, regardless of the mesh density and of the order of the current expansion. © 1963-2012 IEEE.
PRECONDITIONED BI-CONJUGATE GRADIENT METHOD FOR RADIATIVE TRANSFER IN SPHERICAL MEDIA
International Nuclear Information System (INIS)
Anusha, L. S.; Nagendra, K. N.; Paletou, F.; Leger, L.
2009-01-01
A robust numerical method called the Preconditioned Bi-Conjugate Gradient (Pre-BiCG) method is proposed for the solution of the radiative transfer equation in spherical geometry. A variant of this method called Stabilized Preconditioned Bi-Conjugate Gradient (Pre-BiCG-STAB) is also presented. These are iterative methods based on the construction of a set of bi-orthogonal vectors. The application of the Pre-BiCG method in some benchmark tests shows that the method is quite versatile, and can handle difficult problems that may arise in astrophysical radiative transfer theory.
International Nuclear Information System (INIS)
Habermann, C.R.; Cramer, M.C.; Aldefeld, D.; Weiss, F.; Kaul, M.G.; Adam, G.; Graessner, J.; Reitmeier, F.; Jaehne, M.; Petersen, K.U.
2005-01-01
Purpose: To optimise a fast sequence for MR-sialography and to compare a parallel and non-parallel acquisition technique. Additionally, the effect of oral stimulation regarding the image quality was evaluated. Material and Methods: All examinations were performed by using a 1.5-T superconducting system. After developing a sufficient sequence for MR-sialography, a single-shot turbo-spin-echo sequence (ss-TSE) with an acquisition time of 2.8 sec was used in transverse and oblique sagittal orientation in 27 healthy volunteers. All images were performed with and without parallel imaging technique. The assessment of the ductal system of the submandibular and parotid gland was performed using a 1 to 5 visual scale for each side separately. Images were evaluated by four independent experienced radiologists. For statistical evaluation, an ANOVA with post-hoc comparisons was used with an overall two-tailed significance level of P=.05. For evaluation of interobserver variability, an intraclass correlation was computed and correlation >.08 was determined to indicate a high correlation. Results: All parts of salivary excretal ducts could be visualised in all volunteers, with an overall rating for all ducts of 2.26 (SD±1.09). Between the four observers a high correlation could be obtained with an intraclass correlation of 0.9475. A significant influence regarding the slice angulations could not be obtained (p=0.74). In all healthy volunteers the visibility of excretory ducts improved significantly after oral application of a Sialogogum (p 2 =0.049). The use of a parallel imaging technique did not lead to an improvement of visualisation, showing a significant loss of image quality compared to an acquistion technique without parallel imaging (p 2 =0.013). Conclusion: The optimised ss-TSE MR-sialography seems to be a fast and sufficient technique for visualisation of excretory ducts of the main salivary glands, with no elaborate post-processing needed. To improve results of MR
Energy Technology Data Exchange (ETDEWEB)
Habermann, C.R.; Cramer, M.C.; Aldefeld, D.; Weiss, F.; Kaul, M.G.; Adam, G. [Radiologisches Zentrum, Klinik und Poliklinik fuer Diagnostische und Interventionelle Radiologie, Universitaetsklinikum Hamburg-Eppendorf (Germany); Graessner, J. [Siemens Medical Systems, Hamburg (Germany); Reitmeier, F.; Jaehne, M. [Kopf- und Hautzentrum, Klinik und Poliklinik fuer Hals-, Nasen- und Ohrenheilkunde, Universitaetsklinikum Hamburg-Eppendorf (Germany); Petersen, K.U. [Zentrum fuer Psychosoziale Medizin, Klinik und Poliklinik fuer Psychiatrie und Psychotherapie, Universitaetsklinikum Hamburg-Eppendorf (Germany)
2005-04-01
Purpose: To optimise a fast sequence for MR-sialography and to compare a parallel and non-parallel acquisition technique. Additionally, the effect of oral stimulation regarding the image quality was evaluated. Material and Methods: All examinations were performed by using a 1.5-T superconducting system. After developing a sufficient sequence for MR-sialography, a single-shot turbo-spin-echo sequence (ss-TSE) with an acquisition time of 2.8 sec was used in transverse and oblique sagittal orientation in 27 healthy volunteers. All images were performed with and without parallel imaging technique. The assessment of the ductal system of the submandibular and parotid gland was performed using a 1 to 5 visual scale for each side separately. Images were evaluated by four independent experienced radiologists. For statistical evaluation, an ANOVA with post-hoc comparisons was used with an overall two-tailed significance level of P=.05. For evaluation of interobserver variability, an intraclass correlation was computed and correlation >.08 was determined to indicate a high correlation. Results: All parts of salivary excretal ducts could be visualised in all volunteers, with an overall rating for all ducts of 2.26 (SD{+-}1.09). Between the four observers a high correlation could be obtained with an intraclass correlation of 0.9475. A significant influence regarding the slice angulations could not be obtained (p=0.74). In all healthy volunteers the visibility of excretory ducts improved significantly after oral application of a Sialogogum (p<0.001; {eta}{sup 2}=0.049). The use of a parallel imaging technique did not lead to an improvement of visualisation, showing a significant loss of image quality compared to an acquistion technique without parallel imaging (p<0.001; {eta}{sup 2}=0.013). Conclusion: The optimised ss-TSE MR-sialography seems to be a fast and sufficient technique for visualisation of excretory ducts of the main salivary glands, with no elaborate post
Codd, A. L.; Gross, L.
2018-03-01
We present a new inversion method for Electrical Resistivity Tomography which, in contrast to established approaches, minimizes the cost function prior to finite element discretization for the unknown electric conductivity and electric potential. Minimization is performed with the Broyden-Fletcher-Goldfarb-Shanno method (BFGS) in an appropriate function space. BFGS is self-preconditioning and avoids construction of the dense Hessian which is the major obstacle to solving large 3-D problems using parallel computers. In addition to the forward problem predicting the measurement from the injected current, the so-called adjoint problem also needs to be solved. For this problem a virtual current is injected through the measurement electrodes and an adjoint electric potential is obtained. The magnitude of the injected virtual current is equal to the misfit at the measurement electrodes. This new approach has the advantage that the solution process of the optimization problem remains independent to the meshes used for discretization and allows for mesh adaptation during inversion. Computation time is reduced by using superposition of pole loads for the forward and adjoint problems. A smoothed aggregation algebraic multigrid (AMG) preconditioned conjugate gradient is applied to construct the potentials for a given electric conductivity estimate and for constructing a first level BFGS preconditioner. Through the additional reuse of AMG operators and coarse grid solvers inversion time for large 3-D problems can be reduced further. We apply our new inversion method to synthetic survey data created by the resistivity profile representing the characteristics of subsurface fluid injection. We further test it on data obtained from a 2-D surface electrode survey on Heron Island, a small tropical island off the east coast of central Queensland, Australia.
Hill, Mary C.
1990-01-01
This report documents PCG2 : a numerical code to be used with the U.S. Geological Survey modular three-dimensional, finite-difference, ground-water flow model . PCG2 uses the preconditioned conjugate-gradient method to solve the equations produced by the model for hydraulic head. Linear or nonlinear flow conditions may be simulated. PCG2 includes two reconditioning options : modified incomplete Cholesky preconditioning, which is efficient on scalar computers; and polynomial preconditioning, which requires less computer storage and, with modifications that depend on the computer used, is most efficient on vector computers . Convergence of the solver is determined using both head-change and residual criteria. Nonlinear problems are solved using Picard iterations. This documentation provides a description of the preconditioned conjugate gradient method and the two preconditioners, detailed instructions for linking PCG2 to the modular model, sample data inputs, a brief description of PCG2, and a FORTRAN listing.
Zaripov, D. I.; Renfu, Li
2018-05-01
The implementation of high-efficiency digital image correlation methods based on a zero-normalized cross-correlation (ZNCC) procedure for high-speed, time-resolved measurements using a high-resolution digital camera is associated with big data processing and is often time consuming. In order to speed-up ZNCC computation, a high-speed technique based on a parallel projection correlation procedure is proposed. The proposed technique involves the use of interrogation window projections instead of its two-dimensional field of luminous intensity. This simplification allows acceleration of ZNCC computation up to 28.8 times compared to ZNCC calculated directly, depending on the size of interrogation window and region of interest. The results of three synthetic test cases, such as a one-dimensional uniform flow, a linear shear flow and a turbulent boundary-layer flow, are discussed in terms of accuracy. In the latter case, the proposed technique is implemented together with an iterative window-deformation technique. On the basis of the results of the present work, the proposed technique is recommended to be used for initial velocity field calculation, with further correction using more accurate techniques.
Tsuruta, S; Misztal, I; Strandén, I
2001-05-01
Utility of the preconditioned conjugate gradient algorithm with a diagonal preconditioner for solving mixed-model equations in animal breeding applications was evaluated with 16 test problems. The problems included single- and multiple-trait analyses, with data on beef, dairy, and swine ranging from small examples to national data sets. Multiple-trait models considered low and high genetic correlations. Convergence was based on relative differences between left- and right-hand sides. The ordering of equations was fixed effects followed by random effects, with no special ordering within random effects. The preconditioned conjugate gradient program implemented with double precision converged for all models. However, when implemented in single precision, the preconditioned conjugate gradient algorithm did not converge for seven large models. The preconditioned conjugate gradient and successive overrelaxation algorithms were subsequently compared for 13 of the test problems. The preconditioned conjugate gradient algorithm was easy to implement with the iteration on data for general models. However, successive overrelaxation requires specific programming for each set of models. On average, the preconditioned conjugate gradient algorithm converged in three times fewer rounds of iteration than successive overrelaxation. With straightforward implementations, programs using the preconditioned conjugate gradient algorithm may be two or more times faster than those using successive overrelaxation. However, programs using the preconditioned conjugate gradient algorithm would use more memory than would comparable implementations using successive overrelaxation. Extensive optimization of either algorithm can influence rankings. The preconditioned conjugate gradient implemented with iteration on data, a diagonal preconditioner, and in double precision may be the algorithm of choice for solving mixed-model equations when sufficient memory is available and ease of implementation is
Comments on “Techniques and Architectures for Hazard-Free Semi-Parallel Decoding of LDPC Codes”
Directory of Open Access Journals (Sweden)
Mark B. Yeary
2009-01-01
Full Text Available This is a comment article on the publication “Techniques and Architectures for Hazard-Free Semi-Parallel Decoding of LDPC Codes” Rovini et al. (2009. We mention that there has been similar work reported in the literature before, and the previous work has not been cited correctly, for example Gunnam et al. (2006, 2007. This brief note serves to clarify these issues.
Ischemic preconditioning enhances integrity of coronary endothelial tight junctions
International Nuclear Information System (INIS)
Li, Zhao; Jin, Zhu-Qiu
2012-01-01
Highlights: ► Cardiac tight junctions are present between coronary endothelial cells. ► Ischemic preconditioning preserves the structural and functional integrity of tight junctions. ► Myocardial edema is prevented in hearts subjected to ischemic preconditioning. ► Ischemic preconditioning enhances translocation of ZO-2 from cytosol to cytoskeleton. -- Abstract: Ischemic preconditioning (IPC) is one of the most effective procedures known to protect hearts against ischemia/reperfusion (IR) injury. Tight junction (TJ) barriers occur between coronary endothelial cells. TJs provide barrier function to maintain the homeostasis of the inner environment of tissues. However, the effect of IPC on the structure and function of cardiac TJs remains unknown. We tested the hypothesis that myocardial IR injury ruptures the structure of TJs and impairs endothelial permeability whereas IPC preserves the structural and functional integrity of TJs in the blood–heart barrier. Langendorff hearts from C57BL/6J mice were prepared and perfused with Krebs–Henseleit buffer. Cardiac function, creatine kinase release, and myocardial edema were measured. Cardiac TJ function was evaluated by measuring Evans blue-conjugated albumin (EBA) content in the extravascular compartment of hearts. Expression and translocation of zonula occludens (ZO)-2 in IR and IPC hearts were detected with Western blot. A subset of hearts was processed for the observation of ultra-structure of cardiac TJs with transmission electron microscopy. There were clear TJs between coronary endothelial cells of mouse hearts. IR caused the collapse of TJs whereas IPC sustained the structure of TJs. IR increased extravascular EBA content in the heart and myocardial edema but decreased the expression of ZO-2 in the cytoskeleton. IPC maintained the structure of TJs. Cardiac EBA content and edema were reduced in IPC hearts. IPC enhanced the translocation of ZO-2 from cytosol to cytoskeleton. In conclusion, TJs occur in
Ischemic preconditioning enhances integrity of coronary endothelial tight junctions
Energy Technology Data Exchange (ETDEWEB)
Li, Zhao [Department of Pharmaceutical Sciences, College of Pharmacy, South Dakota State University, Brookings, SD 57007 (United States); Jin, Zhu-Qiu, E-mail: zhu-qiu.jin@sdstate.edu [Department of Pharmaceutical Sciences, College of Pharmacy, South Dakota State University, Brookings, SD 57007 (United States)
2012-08-31
Highlights: Black-Right-Pointing-Pointer Cardiac tight junctions are present between coronary endothelial cells. Black-Right-Pointing-Pointer Ischemic preconditioning preserves the structural and functional integrity of tight junctions. Black-Right-Pointing-Pointer Myocardial edema is prevented in hearts subjected to ischemic preconditioning. Black-Right-Pointing-Pointer Ischemic preconditioning enhances translocation of ZO-2 from cytosol to cytoskeleton. -- Abstract: Ischemic preconditioning (IPC) is one of the most effective procedures known to protect hearts against ischemia/reperfusion (IR) injury. Tight junction (TJ) barriers occur between coronary endothelial cells. TJs provide barrier function to maintain the homeostasis of the inner environment of tissues. However, the effect of IPC on the structure and function of cardiac TJs remains unknown. We tested the hypothesis that myocardial IR injury ruptures the structure of TJs and impairs endothelial permeability whereas IPC preserves the structural and functional integrity of TJs in the blood-heart barrier. Langendorff hearts from C57BL/6J mice were prepared and perfused with Krebs-Henseleit buffer. Cardiac function, creatine kinase release, and myocardial edema were measured. Cardiac TJ function was evaluated by measuring Evans blue-conjugated albumin (EBA) content in the extravascular compartment of hearts. Expression and translocation of zonula occludens (ZO)-2 in IR and IPC hearts were detected with Western blot. A subset of hearts was processed for the observation of ultra-structure of cardiac TJs with transmission electron microscopy. There were clear TJs between coronary endothelial cells of mouse hearts. IR caused the collapse of TJs whereas IPC sustained the structure of TJs. IR increased extravascular EBA content in the heart and myocardial edema but decreased the expression of ZO-2 in the cytoskeleton. IPC maintained the structure of TJs. Cardiac EBA content and edema were reduced in IPC hearts. IPC
Fourier domain preconditioned conjugate gradient algorithm for atmospheric tomography.
Yang, Qiang; Vogel, Curtis R; Ellerbroek, Brent L
2006-07-20
By 'atmospheric tomography' we mean the estimation of a layered atmospheric turbulence profile from measurements of the pupil-plane phase (or phase gradients) corresponding to several different guide star directions. We introduce what we believe to be a new Fourier domain preconditioned conjugate gradient (FD-PCG) algorithm for atmospheric tomography, and we compare its performance against an existing multigrid preconditioned conjugate gradient (MG-PCG) approach. Numerical results indicate that on conventional serial computers, FD-PCG is as accurate and robust as MG-PCG, but it is from one to two orders of magnitude faster for atmospheric tomography on 30 m class telescopes. Simulations are carried out for both natural guide stars and for a combination of finite-altitude laser guide stars and natural guide stars to resolve tip-tilt uncertainty.
PRECONDITIONS AND DETERMINING CAUSES OF THE SHADOW ECONOMY IN UKRAINE
Directory of Open Access Journals (Sweden)
Z. Varnalii
2014-03-01
Full Text Available The article analyzes the main processes that led to the high level of the economy shadowing. The historical aspects of the formation of the shadow economy in Ukraine are highlighted. The socio-economic aspects of the shadow economy of Ukraine causality are discussed. The theoretical contribution of foreign and domestic researchers on the preconditions of formation of the shadow economy in transition economies is studied. Theoretical perspective on the factors of the shadowing processes in the economy of Ukraine from the standpoint of modern scientific researches is analyzed. The paper also provides scientific vectors for further development of researches aimed at studying the causes and preconditions of the shadow economy.
DEFF Research Database (Denmark)
Vlassaks, Evi; Brudek, Tomasz; Pakkenberg, Bente
2014-01-01
the effects of perinatal asphyxia and fetal asphyctic preconditioning on the inflammatory cytokine response in the cerebellum. Fetal asphyxia was induced at embryonic day 17 by clamping the uterine vasculature for 30 min. At term birth, global perinatal asphyxia was induced by placing the uterine horns...... was decreased 96 h postfetal asphyxia. When applied as preconditioning stimulus, fetal asphyxia attenuates the cerebellar cytokine response. These results indicate that sublethal fetal asphyxia may protect the cerebellum from perinatal asphyxia-induced damage via inhibition of inflammation.......Asphyctic brain injury is a major cause of neuronal inflammation in the perinatal period. Fetal asphyctic preconditioning has been shown to modulate the cerebral inflammatory cytokine response, hereby protecting the brain against asphyctic injury at birth. This study was designated to examine...
Nonlinear Preconditioning and its Application in Multicomponent Problems
Liu, Lulu
2015-12-07
The Multiplicative Schwarz Preconditioned Inexact Newton (MSPIN) algorithm is presented as a complement to Additive Schwarz Preconditioned Inexact Newton (ASPIN). At an algebraic level, ASPIN and MSPIN are variants of the same strategy to improve the convergence of systems with unbalanced nonlinearities; however, they have natural complementarity in practice. MSPIN is naturally based on partitioning of degrees of freedom in a nonlinear PDE system by field type rather than by subdomain, where a modest factor of concurrency can be sacrificed for physically motivated convergence robustness. ASPIN, originally introduced for decompositions into subdomains, is natural for high concurrency and reduction of global synchronization. The ASPIN framework, as an option for the outermost solver, successfully handles strong nonlinearities in computational fluid dynamics, but is barely explored for the highly nonlinear models of complex multiphase flow with capillarity, heterogeneity, and complex geometry. In this dissertation, the fully implicit ASPIN method is demonstrated for a finite volume discretization based on incompressible two-phase reservoir simulators in the presence of capillary forces and gravity. Numerical experiments show that the number of global nonlinear iterations is not only scalable with respect to the number of processors, but also significantly reduced compared with the standard inexact Newton method with a backtracking technique. Moreover, the ASPIN method, in contrast with the IMPES method, saves overall execution time because of the savings in timestep size. We consider the additive and multiplicative types of inexact Newton algorithms in the field-split context, and we augment the classical convergence theory of ASPIN for the multiplicative case. Moreover, we provide the convergence analysis of the MSPIN algorithm. Under suitable assumptions, it is shown that MSPIN is locally convergent, and desired superlinear or even quadratic convergence can be
A SPECT reconstruction method for extending parallel to non-parallel geometries
International Nuclear Information System (INIS)
Wen Junhai; Liang Zhengrong
2010-01-01
Due to its simplicity, parallel-beam geometry is usually assumed for the development of image reconstruction algorithms. The established reconstruction methodologies are then extended to fan-beam, cone-beam and other non-parallel geometries for practical application. This situation occurs for quantitative SPECT (single photon emission computed tomography) imaging in inverting the attenuated Radon transform. Novikov reported an explicit parallel-beam formula for the inversion of the attenuated Radon transform in 2000. Thereafter, a formula for fan-beam geometry was reported by Bukhgeim and Kazantsev (2002 Preprint N. 99 Sobolev Institute of Mathematics). At the same time, we presented a formula for varying focal-length fan-beam geometry. Sometimes, the reconstruction formula is so implicit that we cannot obtain the explicit reconstruction formula in the non-parallel geometries. In this work, we propose a unified reconstruction framework for extending parallel-beam geometry to any non-parallel geometry using ray-driven techniques. Studies by computer simulations demonstrated the accuracy of the presented unified reconstruction framework for extending parallel-beam to non-parallel geometries in inverting the attenuated Radon transform.
Parallel multiphysics algorithms and software for computational nuclear engineering
International Nuclear Information System (INIS)
Gaston, D; Hansen, G; Kadioglu, S; Knoll, D A; Newman, C; Park, H; Permann, C; Taitano, W
2009-01-01
There is a growing trend in nuclear reactor simulation to consider multiphysics problems. This can be seen in reactor analysis where analysts are interested in coupled flow, heat transfer and neutronics, and in fuel performance simulation where analysts are interested in thermomechanics with contact coupled to species transport and chemistry. These more ambitious simulations usually motivate some level of parallel computing. Many of the coupling efforts to date utilize simple code coupling or first-order operator splitting, often referred to as loose coupling. While these approaches can produce answers, they usually leave questions of accuracy and stability unanswered. Additionally, the different physics often reside on separate grids which are coupled via simple interpolation, again leaving open questions of stability and accuracy. Utilizing state of the art mathematics and software development techniques we are deploying next generation tools for nuclear engineering applications. The Jacobian-free Newton-Krylov (JFNK) method combined with physics-based preconditioning provide the underlying mathematical structure for our tools. JFNK is understood to be a modern multiphysics algorithm, but we are also utilizing its unique properties as a scale bridging algorithm. To facilitate rapid development of multiphysics applications we have developed the Multiphysics Object-Oriented Simulation Environment (MOOSE). Examples from two MOOSE-based applications: PRONGHORN, our multiphysics gas cooled reactor simulation tool and BISON, our multiphysics, multiscale fuel performance simulation tool will be presented.
Parallel S/sub n/ iteration schemes
International Nuclear Information System (INIS)
Wienke, B.R.; Hiromoto, R.E.
1986-01-01
The iterative, multigroup, discrete ordinates (S/sub n/) technique for solving the linear transport equation enjoys widespread usage and appeal. Serial iteration schemes and numerical algorithms developed over the years provide a timely framework for parallel extension. On the Denelcor HEP, the authors investigate three parallel iteration schemes for solving the one-dimensional S/sub n/ transport equation. The multigroup representation and serial iteration methods are also reviewed. This analysis represents a first attempt to extend serial S/sub n/ algorithms to parallel environments and provides good baseline estimates on ease of parallel implementation, relative algorithm efficiency, comparative speedup, and some future directions. The authors examine ordered and chaotic versions of these strategies, with and without concurrent rebalance and diffusion acceleration. Two strategies efficiently support high degrees of parallelization and appear to be robust parallel iteration techniques. The third strategy is a weaker parallel algorithm. Chaotic iteration, difficult to simulate on serial machines, holds promise and converges faster than ordered versions of the schemes. Actual parallel speedup and efficiency are high and payoff appears substantial
Association of Exercise Preconditioning With Immediate Cardioprotection: A Review.
Thijssen, D.H.J.; Redington, A.; George, K.P.; Hopman, M.T.E.; Jones, H.
2018-01-01
Importance: Exercise reduces the risk of cardiovascular events, including through an underrecognized, clinically useful form of acute cardioprotection accessible after a single episode of exercise, which is called cardiovascular preconditioning. Observations: Preclinical evidence shows that 1 to 3
Comparison of the mass preconditioned HMC and the DD-HMC algorithm for two-flavour QCD
Marinkovic, Marina
2010-01-01
Mass preconditioned HMC and DD-HMC are among the most popular algorithms to simulate Wilson fermions. We present a comparison of the performance of the two algorithms for realistic quark masses and lattice sizes. In particular, we use the locally deflated solver of the DD-HMC environment also for the mass preconditioned simulations.
International Nuclear Information System (INIS)
Yamazaki, Takao; Fujisaki, Masahide; Okuda, Motoi; Takano, Makoto; Masukawa, Fumihiro; Naito, Yoshitaka
1993-01-01
The general purpose Monte Carlo code MCNP4 has been implemented on the Fujitsu AP1000 distributed memory highly parallel computer. Parallelization techniques developed and studied are reported. A shielding analysis function of the MCNP4 code is parallelized in this study. A technique to map a history to each processor dynamically and to map control process to a certain processor was applied. The efficiency of parallelized code is up to 80% for a typical practical problem with 512 processors. These results demonstrate the advantages of a highly parallel computer to the conventional computers in the field of shielding analysis by Monte Carlo method. (orig.)
Manipulation in political stock markets: Preconditions and evidence
Hansen, Jan; Schmidt, Carsten; Strobel, Martin
2001-01-01
Political stock markets (PSM) are sometimes seen as substitutes for opinion polls. On the bases of a behavioral model, specific preconditions were drawn out under which manipulation in PSM can weaken this argument. Evidence for manipulation is reported from the data of two separate PSM during the Berlin 99 state elections.
HMC algorithm with multiple time scale integration and mass preconditioning
Urbach, C.; Jansen, K.; Shindler, A.; Wenger, U.
2006-01-01
We present a variant of the HMC algorithm with mass preconditioning (Hasenbusch acceleration) and multiple time scale integration. We have tested this variant for standard Wilson fermions at β=5.6 and at pion masses ranging from 380 to 680 MeV. We show that in this situation its performance is comparable to the recently proposed HMC variant with domain decomposition as preconditioner. We give an update of the "Berlin Wall" figure, comparing the performance of our variant of the HMC algorithm to other published performance data. Advantages of the HMC algorithm with mass preconditioning and multiple time scale integration are that it is straightforward to implement and can be used in combination with a wide variety of lattice Dirac operators.
Load-balancing techniques for a parallel electromagnetic particle-in-cell code
Energy Technology Data Exchange (ETDEWEB)
PLIMPTON,STEVEN J.; SEIDEL,DAVID B.; PASIK,MICHAEL F.; COATS,REBECCA S.
2000-01-01
QUICKSILVER is a 3-d electromagnetic particle-in-cell simulation code developed and used at Sandia to model relativistic charged particle transport. It models the time-response of electromagnetic fields and low-density-plasmas in a self-consistent manner: the fields push the plasma particles and the plasma current modifies the fields. Through an LDRD project a new parallel version of QUICKSILVER was created to enable large-scale plasma simulations to be run on massively-parallel distributed-memory supercomputers with thousands of processors, such as the Intel Tflops and DEC CPlant machines at Sandia. The new parallel code implements nearly all the features of the original serial QUICKSILVER and can be run on any platform which supports the message-passing interface (MPI) standard as well as on single-processor workstations. This report describes basic strategies useful for parallelizing and load-balancing particle-in-cell codes, outlines the parallel algorithms used in this implementation, and provides a summary of the modifications made to QUICKSILVER. It also highlights a series of benchmark simulations which have been run with the new code that illustrate its performance and parallel efficiency. These calculations have up to a billion grid cells and particles and were run on thousands of processors. This report also serves as a user manual for people wishing to run parallel QUICKSILVER.
Load-balancing techniques for a parallel electromagnetic particle-in-cell code
International Nuclear Information System (INIS)
Plimpton, Steven J.; Seidel, David B.; Pasik, Michael F.; Coats, Rebecca S.
2000-01-01
QUICKSILVER is a 3-d electromagnetic particle-in-cell simulation code developed and used at Sandia to model relativistic charged particle transport. It models the time-response of electromagnetic fields and low-density-plasmas in a self-consistent manner: the fields push the plasma particles and the plasma current modifies the fields. Through an LDRD project a new parallel version of QUICKSILVER was created to enable large-scale plasma simulations to be run on massively-parallel distributed-memory supercomputers with thousands of processors, such as the Intel Tflops and DEC CPlant machines at Sandia. The new parallel code implements nearly all the features of the original serial QUICKSILVER and can be run on any platform which supports the message-passing interface (MPI) standard as well as on single-processor workstations. This report describes basic strategies useful for parallelizing and load-balancing particle-in-cell codes, outlines the parallel algorithms used in this implementation, and provides a summary of the modifications made to QUICKSILVER. It also highlights a series of benchmark simulations which have been run with the new code that illustrate its performance and parallel efficiency. These calculations have up to a billion grid cells and particles and were run on thousands of processors. This report also serves as a user manual for people wishing to run parallel QUICKSILVER
Zapata, M. A. Uh; Van Bang, D. Pham; Nguyen, K. D.
2016-05-01
This paper presents a parallel algorithm for the finite-volume discretisation of the Poisson equation on three-dimensional arbitrary geometries. The proposed method is formulated by using a 2D horizontal block domain decomposition and interprocessor data communication techniques with message passing interface. The horizontal unstructured-grid cells are reordered according to the neighbouring relations and decomposed into blocks using a load-balanced distribution to give all processors an equal amount of elements. In this algorithm, two parallel successive over-relaxation methods are presented: a multi-colour ordering technique for unstructured grids based on distributed memory and a block method using reordering index following similar ideas of the partitioning for structured grids. In all cases, the parallel algorithms are implemented with a combination of an acceleration iterative solver. This solver is based on a parabolic-diffusion equation introduced to obtain faster solutions of the linear systems arising from the discretisation. Numerical results are given to evaluate the performances of the methods showing speedups better than linear.
International Nuclear Information System (INIS)
Ito, Satoshi; Kawawa, Yasuhiro; Yamada, Yoshifumi
2010-01-01
We propose an image reconstruction technique in which parallel image reconstruction is performed based on the sensitivity encoding (SENSE) algorithm using only a single set of signals. The signal obtained in the phase-scrambling Fourier transform (PSFT) imaging technique can be transformed to the signal described by the Fresnel transform of the objects, which is known as the diffracted wave-front equation of the object in acoustics or optics. Since the Fresnel transform is a convolution integral on the object space, the space where the PSFT signal exists can be considered as both in the Fourier domain and in the object domain. This notable feature indicates that weighting functions corresponding to the sensitivity of radiofrequency (RF) coils can be approximately given in the PSFT signal space. Therefore, we can obtain two folded images from a single set of signals with different weighting functions, and image reconstruction based on the SENSE parallel imaging algorithm is possible using a series of folded images. Simulation and experimental studies showed that almost alias-free images can be synthesized using a single signal that does not satisfy the sampling theorem. (author)
Meng, Fanjun; Li, Yan; Chi, Wenying; Li, Junfa
2016-07-01
Brain protection by narcotics such as morphine is clinically relevant due to the extensive use of narcotics in the perioperative period. Morphine preconditioning induces neuroprotection in neurons, but it remains uncertain whether microRNA-134 (miR-134) is involved in morphine preconditioning against oxygen-glucose deprivation-induced injuries in primary cortical neurons of mice. The present study examined this issue. After cortical neurons of mice were cultured in vitro for 6 days, the neurons were transfected by respective virus vector, such as lentiviral vector (LV)-miR-control-GFP, LV-pre-miR-134-GFP, LV-pre-miR-134-inhibitor-GFP for 24 hours; after being normally cultured for 3 days again, morphine preconditioning was performed by incubating the transfected primary neurons with morphine (3 μM) for 1 hour, and then neuronal cells were exposed to oxygen-glucose deprivation (OGD) for 1 hour and oxygen-glucose recovery for 12 hours. The neuronal cells survival rate and the amount of apoptotic neurons were determined by MTT assay or TUNEL staining at designated time; and the expression levels of miR-134 were detected using real-time reverse transcription polymerase chain reaction at the same time. The neuronal cell survival rate was significantly higher, and the amount of apoptotic neurons was significantly decreased in neurons preconditioned with morphine before OGD than that of OGD alone. The neuroprotection induced by morphine preconditioning was partially blocked by upregulating miR-134 expression, and was enhanced by downregulating miR-134 expression. The expression of miR-134 was significantly decreased in morphine-preconditioned neurons alone without transfection. By downregulating miR-134 expression, morphine preconditioning protects primary cortical neurons of mice against injuries induced by OGD.
Psychological preconditions of game activity development in the early childhood
Valeriya Spitsyna; Ekaterina Saraykina
2013-01-01
The article is devoted for detection the psychological preconditions of game activity development at early age and interrelation of game formation with the development of subject actions, informative activity and procedural game.
McArdle, F; Spiers, S; Aldemir, H; Vasilaki, A; Beaver, A; Iwanejko, L; McArdle, A; Jackson, M J
2004-11-15
Adaptations of skeletal muscle following exercise are accompanied by changes in gene expression, which can result in protection against subsequent potentially damaging exercise. One cellular signal activating these adaptations may be an increased production of reactive oxygen and nitrogen species (ROS). The aim of this study was to examine the effect of a short period of non-damaging contractions on the subsequent susceptibility of muscle to contraction-induced damage and to examine the changes in gene expression that occur following the initial contraction protocol. Comparisons with changes in gene expression in cultured myotubes following treatment with a non-damaging concentration of hydrogen peroxide (H(2)O(2)) were used to identify redox-sensitive genes whose expression may be modified by the increased ROS production during contractions. Hindlimb muscles of mice were subjected to a preconditioning, non-damaging isometric contraction protocol in vivo. After 4 or 12 h, extensor digitorum longus (EDL) and soleus muscles were removed and subjected to a (normally) damaging contraction protocol in vitro. Muscles were also analysed for changes in gene expression induced by the preconditioning protocol using cDNA expression techniques. In a parallel study, C(2)C(12) myotubes were treated with a non-damaging concentration (100 microM) of H(2)O(2) and, at 4 and 12 h following treatment, myotubes were treated with a damaging concentration of H(2)O(2) (2 mM). Myotubes were analysed for changes in gene expression at 4 h following treatment with 100 microM H(2)O(2) alone. Data demonstrate that a prior period of non-damaging contractile activity resulted in significant protection of EDL and soleus muscles against a normally damaging contraction protocol 4 h later. This protection was associated with significant changes in gene expression. Prior treatment of myotubes with a non-damaging concentration of H(2)O(2) also resulted in significant protection against a damaging
Analysis of a Lipid/Polymer Membrane for Bitterness Sensing with a Preconditioning Process
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Rui Yatabe
2015-09-01
Full Text Available It is possible to evaluate the taste of foods or medicines using a taste sensor. The taste sensor converts information on taste into an electrical signal using several lipid/polymer membranes. A lipid/polymer membrane for bitterness sensing can evaluate aftertaste after immersion in monosodium glutamate (MSG, which is called “preconditioning”. However, we have not yet analyzed the change in the surface structure of the membrane as a result of preconditioning. Thus, we analyzed the change in the surface by performing contact angle and surface zeta potential measurements, Fourier transform infrared spectroscopy (FTIR, X-ray photon spectroscopy (XPS and gas cluster ion beam time-of-flight secondary ion mass spectrometry (GCIB-TOF-SIMS. After preconditioning, the concentrations of MSG and tetradodecylammonium bromide (TDAB, contained in the lipid membrane were found to be higher in the surface region than in the bulk region. The effect of preconditioning was revealed by the above analysis methods.
Preconditions for Emergence of Lithuanian Clusters: from Informal Cooperation to Its Legitimation
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Grumadaitė Kristina
2017-06-01
Full Text Available This paper reveals preconditions for the emergence of clusters as self-organisation based industrial systems in a context, in which cooperation traditions are insufficiently developed. These preconditions reflect the principles of the emergence of self-organising complex adaptive systems that are analysed in the complexity theory. Those principles are based on the initiation of non-equilibrium and its purposeful direction into the creation of a new order. This paper highlights the main external and internal tensions that influence informal or formal clustering of enterprises, while various change agents perform different roles making self-organising processes to occur.
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Esther M Verhaag
Full Text Available Cholestasis is characterized by accumulation of bile acids and inflammation, causing hepatocellular damage. Still, liver damage markers are highest in acute cholestasis and drop when this condition becomes chronic, indicating that hepatocytes adapt towards the hostile environment. This may be explained by a hormetic response in hepatocytes that limits cell death during cholestasis.To investigate the mechanisms that underlie the hormetic response that protect hepatocytes against experimental cholestatic conditions.HepG2.rNtcp cells were preconditioned (24 h with sub-apoptotic concentrations (0.1-50 μM of various bile acids, the superoxide donor menadione, TNF-α or the Farsenoid X Receptor agonist GW4064, followed by a challenge with the apoptosis-inducing bile acid glycochenodeoxycholic acid (GCDCA; 200 μM for 4 h, menadione (50 μM, 6 h or cytokine mixture (CM; 6 h. Levels of apoptotic and necrotic cell death, mRNA expression of the bile salt export pump (ABCB11 and bile acid sensors, as well as intracellular GCDCA levels were analyzed.Preconditioning with the pro-apoptotic bile acids GCDCA, taurocholic acid, or the protective bile acids (tauroursodeoxycholic acid reduced GCDCA-induced caspase-3/7 activity in HepG2.rNtcp cells. Bile acid preconditioning did not induce significant levels of necrosis in GCDCA-challenged HepG2.rNtcp cells. In contrast, preconditioning with cholic acid, menadione or TNF-α potentiated GCDCA-induced apoptosis. GCDCA preconditioning specifically reduced GCDCA-induced cell death and not CM- or menadione-induced apoptosis. The hormetic effect of GCDCA preconditioning was concentration- and time-dependent. GCDCA-, CDCA- and GW4064- preconditioning enhanced ABCB11 mRNA levels, but in contrast to the bile acids, GW4064 did not significantly reduce GCDCA-induced caspase-3/7 activity. The GCDCA challenge strongly increased intracellular levels of this bile acid, which was not lowered by GCDCA-preconditioning
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Jianhua Rao
Full Text Available BACKGROUND: Low-dose lipopolysaccharide (LPS preconditioning-induced liver protection has been demonstrated during ischemia-reperfusion injury (IRI in several organs but has not been sufficiently elucidated underlying causal mechanism. This study investigated the role of low-dose LPS preconditioning on ATF4-CHOP pathway as well as the effects of the pathway on tissue injury and inflammation in a mouse model of liver partial-warm IRI. METHODS: LPS (100 µg/kg/d was injected intraperitoneally two days before ischemia. Hepatic injury was evaluated based on serum alanine aminotransferase levels, histopathology, and caspase-3 activity. The ATF4-CHOP pathway and its related apoptotic molecules were investigated after reperfusion. The role of LPS preconditioning on apoptosis and ATF4-CHOP pathway was examined in vitro. Moreover, the effects of the ATF4-CHOP pathway on apoptosis, Caspase-12, and Caspase-3 were determined with ATF4 small interfering RNA (siRNA. Inflammatory cytokine expression was also checked after reperfusion. Inflammatory cytokines and related signaling pathways were analyzed in vitro in macrophages treated by LPS preconditioning or ATF4 siRNA. RESULTS: LPS preconditioning significantly attenuated liver injury after IRI. As demonstrated by in vitro experiments, LPS preconditioning significantly reduced the upregulation of the ATF4-CHOP pathway and inhibited Caspase-12 and Caspase-3 activation after IRI. Later experiments showed that ATF4 knockdown significantly suppressed CHOP, cleaved caspase-12 and caspase-3 expression, as well as inhibited hepatocellular apoptosis. In addition, in mice pretreated with LPS, TNF-α and IL-6 were inhibited after reperfusion, whereas IL-10 was upregulated. Similarly, low-dose LPS significantly inhibited TNF-α, IL-6, ATF4-CHOP pathway, NF-κB pathway, and ERK1/2 in high-dose LPS-stimulated macrophages, whereas IL-10 and cytokine signaling (SOCS-3 suppressor were induced. Importantly, ATF4 siRNA is
Evaluation of onboard hyperspectral-image compression techniques for a parallel push-broom sensor
Energy Technology Data Exchange (ETDEWEB)
Briles, S.
1996-04-01
A single hyperspectral imaging sensor can produce frames with spatially-continuous rows of differing, but adjacent, spectral wavelength. If the frame sample-rate of the sensor is such that subsequent hyperspectral frames are spatially shifted by one row, then the sensor can be thought of as a parallel (in wavelength) push-broom sensor. An examination of data compression techniques for such a sensor is presented. The compression techniques are intended to be implemented onboard a space-based platform and to have implementation speeds that match the date rate of the sensor. Data partitions examined extend from individually operating on a single hyperspectral frame to operating on a data cube comprising the two spatial axes and the spectral axis. Compression algorithms investigated utilize JPEG-based image compression, wavelet-based compression and differential pulse code modulation. Algorithm performance is quantitatively presented in terms of root-mean-squared error and root-mean-squared correlation coefficient error. Implementation issues are considered in algorithm development.
Preconditioned stochastic gradient descent optimisation for monomodal image registration
Klein, S.; Staring, M.; Andersson, J.P.; Pluim, J.P.W.; Fichtinger, G.; Martel, A.; Peters, T.
2011-01-01
We present a stochastic optimisation method for intensity-based monomodal image registration. The method is based on a Robbins-Monro stochastic gradient descent method with adaptive step size estimation, and adds a preconditioning matrix. The derivation of the pre-conditioner is based on the
Massively parallel mathematical sieves
Energy Technology Data Exchange (ETDEWEB)
Montry, G.R.
1989-01-01
The Sieve of Eratosthenes is a well-known algorithm for finding all prime numbers in a given subset of integers. A parallel version of the Sieve is described that produces computational speedups over 800 on a hypercube with 1,024 processing elements for problems of fixed size. Computational speedups as high as 980 are achieved when the problem size per processor is fixed. The method of parallelization generalizes to other sieves and will be efficient on any ensemble architecture. We investigate two highly parallel sieves using scattered decomposition and compare their performance on a hypercube multiprocessor. A comparison of different parallelization techniques for the sieve illustrates the trade-offs necessary in the design and implementation of massively parallel algorithms for large ensemble computers.
Preconditions for Citizen Journalism: A Sociological Assessment
Hayley Watson
2011-01-01
The rise of the citizen journalist and increased attention to this phenomenon requires a sociological assessment that seeks to develop an understanding of how citizen journalism has emerged in contemporary society. This article makes a distinction between two different subcategories of citizen journalism, that is independent and dependent citizen journalism. The purpose of this article is to present four preconditions for citizen journalism to emerge in contemporary society: advanced technolo...
Linares, Gabriel R; Chiu, Chi-Tso; Scheuing, Lisa; Leng, Yan; Liao, Hsiao-Mei; Maric, Dragan; Chuang, De-Maw
2016-07-01
Huntington's disease (HD) is a fatal neurodegenerative disorder caused by CAG repeat expansions in the huntingtin gene. Although, stem cell-based therapy has emerged as a potential treatment for neurodegenerative diseases, limitations remain, including optimizing delivery to the brain and donor cell loss after transplantation. One strategy to boost cell survival and efficacy is to precondition cells before transplantation. Because the neuroprotective actions of the mood stabilizers lithium and valproic acid (VPA) induce multiple pro-survival signaling pathways, we hypothesized that preconditioning bone marrow-derived mesenchymal stem cells (MSCs) with lithium and VPA prior to intranasal delivery to the brain would enhance their therapeutic efficacy, and thereby facilitate functional recovery in N171-82Q HD transgenic mice. MSCs were treated in the presence or absence of combined lithium and VPA, and were then delivered by brain-targeted single intranasal administration to eight-week old HD mice. Histological analysis confirmed the presence of MSCs in the brain. Open-field test revealed that ambulatory distance and mean velocity were significantly improved in HD mice that received preconditioned MSCs, compared to HD vehicle-control and HD mice transplanted with non-preconditioned MSCs. Greater benefits on motor function were observed in HD mice given preconditioned MSCs, while HD mice treated with non-preconditioned MSCs showed no functional benefits. Moreover, preconditioned MSCs reduced striatal neuronal loss and huntingtin aggregates in HD mice. Gene expression profiling of preconditioned MSCs revealed a robust increase in expression of genes involved in trophic effects, antioxidant, anti-apoptosis, cytokine/chemokine receptor, migration, mitochondrial energy metabolism, and stress response signaling pathways. Consistent with this finding, preconditioned MSCs demonstrated increased survival after transplantation into the brain compared to non-preconditioned cells
Weber, Nina C.; Toma, Octavian; Awan, Saqib; Frässdorf, Jan; Preckel, Benedikt; Schlack, Wolfgang
2005-01-01
BACKGROUND: For nitrous oxide, a preconditioning effect on the heart has yet not been investigated. This is important because nitrous oxide is commonly used in combination with volatile anesthetics, which are known to precondition the heart. The authors aimed to clarify (1) whether nitrous oxide
Sbarouni, Eftihia; Iliodromitis, Efstathios K; Zoga, Anastasia; Vlachou, Georgia; Andreadou, Ioanna; Kremastinos, Dimitrios Th
2006-08-01
We have previously shown that estrogen administered in ovariectomized female rabbits significantly reduce myocardial infarct size. We now investigated whether the phytoestrogen genistein similarly protects ischemic myocardium and whether this is associated with its antioxidant properties. In addition, we examined whether genistein abolishes preconditioning, since at high doses, it inhibits tyrosine kinase. We studied five groups of New Zealand white female rabbits. Group A (n = 12) were normal controls, group B (n = 14) were ovariectomized 4 weeks prior to the experiment, group C (n = 10) were ovariectomized and treated with genistein (0.2 mg kg(-1) day(-1) subcutaneously) for 4 weeks before the experiment, group D (n = 12) had intact gonads and were treated with genistein (0.2 mg kg(-1) day(-1) subcutaneously) for 4 weeks before the experiment and group E (n = 8) were ovariectomized 4 weeks prior to the experiment and treated with a single dose of genistein (0.2 mg kg(-1) day(-1) subcutaneously) just prior to the experiment. All animals underwent 30 min of heart ischemia and 120 min of reperfusion, with (subgroup I) or without (subgroup II) preconditioning. Malondialdehyde (MDA) concentration just before the experiment was determined. We found significant differences between the groups-p protect ischemic myocardium in either ovariectomized or non-ovariectomized animals-BII vs CII and AII vs DII, p = NS. There was no significant difference between the preconditioned animals, with intact gonads or ovariectomized (AI vs BI, p = NS), ovariectomized with or without genistein (BI vs CI, p = NS) and non-ovariectomized whether treated with genistein or not (AI vs DI, p = NS). A single dose of genistein did not offer any protection (EII vs BII, p = NS), nor did it modify the preconditioning effect (EI vs BI, p = NS). We found no significant difference in MDA plasma levels between the groups. Genistein, at this dose, does not reduce infarct size per se nor abolishes the
Solving large test-day models by iteration on data and preconditioned conjugate gradient.
Lidauer, M; Strandén, I; Mäntysaari, E A; Pösö, J; Kettunen, A
1999-12-01
A preconditioned conjugate gradient method was implemented into an iteration on a program for data estimation of breeding values, and its convergence characteristics were studied. An algorithm was used as a reference in which one fixed effect was solved by Gauss-Seidel method, and other effects were solved by a second-order Jacobi method. Implementation of the preconditioned conjugate gradient required storing four vectors (size equal to number of unknowns in the mixed model equations) in random access memory and reading the data at each round of iteration. The preconditioner comprised diagonal blocks of the coefficient matrix. Comparison of algorithms was based on solutions of mixed model equations obtained by a single-trait animal model and a single-trait, random regression test-day model. Data sets for both models used milk yield records of primiparous Finnish dairy cows. Animal model data comprised 665,629 lactation milk yields and random regression test-day model data of 6,732,765 test-day milk yields. Both models included pedigree information of 1,099,622 animals. The animal model ¿random regression test-day model¿ required 122 ¿305¿ rounds of iteration to converge with the reference algorithm, but only 88 ¿149¿ were required with the preconditioned conjugate gradient. To solve the random regression test-day model with the preconditioned conjugate gradient required 237 megabytes of random access memory and took 14% of the computation time needed by the reference algorithm.
Wang, Peng-Fei; Xiong, Xiao-Yi; Chen, Jing; Wang, Yan-Chun; Duan, Wei; Yang, Qing-Wu
2015-01-01
Increasing evidence suggests that toll-like receptors (TLRs) play an important role in cerebral ischemia-reperfusion injury. The endogenous ligands released from ischemic neurons activate the TLR signaling pathway, resulting in the production of a large number of inflammatory cytokines, thereby causing secondary inflammation damage following cerebral ischemia. However, the preconditioning for minor cerebral ischemia or the preconditioning with TLR ligands can reduce cerebral ischemic injury b...
MOOSE: A parallel computational framework for coupled systems of nonlinear equations
International Nuclear Information System (INIS)
Gaston, Derek; Newman, Chris; Hansen, Glen; Lebrun-Grandie, Damien
2009-01-01
Systems of coupled, nonlinear partial differential equations (PDEs) often arise in simulation of nuclear processes. MOOSE: Multiphysics Object Oriented Simulation Environment, a parallel computational framework targeted at the solution of such systems, is presented. As opposed to traditional data-flow oriented computational frameworks, MOOSE is instead founded on the mathematical principle of Jacobian-free Newton-Krylov (JFNK). Utilizing the mathematical structure present in JFNK, physics expressions are modularized into 'Kernels,' allowing for rapid production of new simulation tools. In addition, systems are solved implicitly and fully coupled, employing physics-based preconditioning, which provides great flexibility even with large variance in time scales. A summary of the mathematics, an overview of the structure of MOOSE, and several representative solutions from applications built on the framework are presented.
Chitu, Zenaida; Bogaard, Thom; Busuioc, Aristita; Burcea, Sorin; Adler, Mary-Jeanne; Sandric, Ionut
2015-04-01
Like in many parts of the world, in Romania, landslides represent recurrent phenomena that produce numerous damages to infrastructure every few years. Various studies on landslide occurrence in the Curvature Subcarpathians reveal that rainfall represents the most important triggering factor for landslides. Depending on rainfall characteristics and environmental factors different types of landslides were recorded in the Ialomita Subcarpathians: slumps, earthflows and complex landslides. This area, located in the western part of Curvature Subcarpathians, is characterized by a very complex geology whose main features are represented by the nappes system, the post tectonic covers, the diapirism phenomena and vertical faults. This work aims to investigate hydrological pre-conditions and rainfall characteristics which triggered slope failures in 2014 in the Ialomita Subcarpathians, Romania. Hydrological pre-conditions were investigated by means of water balance analysis and low flow techniques, while spatial and temporal patterns of rainfalls were estimated using radar data and six rain gauges. Additionally, six soil moisture stations that are fitted with volumetric soil moisture sensors and temperature soil sensors were used to estimate the antecedent soil moisture conditions.
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Yi ZHANG
2014-12-01
Full Text Available Objective To evaluate the protective effects of endoplasmic reticulum stress preconditioning induced by 2-deoxyglucose (2-DG on hippocampal neurons of rats with status epilepticus (SE and the possible mechanism. Methods Ninety Sprague-Dawley (SD rats were randomly enrolled into preconditioning group (N = 30, SE group (N = 30 and control group (N = 30. Each group was divided into 6 subsets (N = 5 according to six time points (before seizure, 6 h, 12 h, 1 d, 2 d and 7 d after seizure. The preconditioning group was administered 2-DG intraperitoneally with a dose of 150 mg/kg for 7 days, and the lithium-pilocarpine induced SE rat model was established on both preconditioning group and SE group. The rats were sacrificed at the above six time points, and the brains were removed to make paraffin sections. Nissl staining was performed by toluidine blue to evaluate the hippocampal neuronal damage after seizure, and the number of survival neurons in hippocampal CA1 and CA3 regions of the rats were counted. Immunohistochemical staining was performed to detect the expressions of glucose regulated protein 78 (GRP78 and X-box binding protein 1 (XBP-1 in hippocampal CA3 region of the rats. Results The number of survival neurons in preconditioning group was much more than that in SE group at 7 d after seizure (t = 5.353, P = 0.000, and was more obvious in CA1 region. There was no significant hippocampal neuronal damage in control group. The expressions of GRP78 and XBP-1 in CA3 region of hippocampus in SE group at 6 h after seizure were significantly higher than that in control group (P = 0.000, and then kept increasing until reaching the peak at 2 d (P = 0.000, for all. The expressions of GRP78 and XBP-1 in hippocampal CA3 region in preconditioning group were significantly higher than that in control group before seizure (P = 0.000, for all. The level of GRP78 maintained the highest at 24 h and 2 d after seizure (P = 0.000, for all, while the XBP-1 level
Experiments and Recommendations for Partitioning Systems of Equations
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Mafteiu-Scai Liviu Octavian
2014-06-01
Full Text Available Partitioning the systems of equations is a very important process when solving it on a parallel computer. This paper presents some criteria which leads to more efficient parallelization, that must be taken into consideration. New criteria added to preconditioning process by reducing average bandwidth are pro- posed in this paper. These new criteria lead to a combination between preconditioning and partitioning of systems equations, so no need two distinct algorithms/processes. In our proposed methods - where the preconditioning is done by reducing the average bandwidth- two directions were followed in terms of partitioning: for a given preconditioned system determining the best partitioning (or one as close and the second consist in achieving an adequate preconditioning, depending on a given/desired partitioning. A mixed method it is also proposed. Experimental results, conclusions and recommendations, obtained after parallel implementation of conjugate gradient on IBM BlueGene /P supercomputer- based on a synchronous model of parallelization- are also presented in this paper.
Preconditioned alternating projection algorithms for maximum a posteriori ECT reconstruction
International Nuclear Information System (INIS)
Krol, Andrzej; Li, Si; Shen, Lixin; Xu, Yuesheng
2012-01-01
We propose a preconditioned alternating projection algorithm (PAPA) for solving the maximum a posteriori (MAP) emission computed tomography (ECT) reconstruction problem. Specifically, we formulate the reconstruction problem as a constrained convex optimization problem with the total variation (TV) regularization. We then characterize the solution of the constrained convex optimization problem and show that it satisfies a system of fixed-point equations defined in terms of two proximity operators raised from the convex functions that define the TV-norm and the constraint involved in the problem. The characterization (of the solution) via the proximity operators that define two projection operators naturally leads to an alternating projection algorithm for finding the solution. For efficient numerical computation, we introduce to the alternating projection algorithm a preconditioning matrix (the EM-preconditioner) for the dense system matrix involved in the optimization problem. We prove theoretically convergence of the PAPA. In numerical experiments, performance of our algorithms, with an appropriately selected preconditioning matrix, is compared with performance of the conventional MAP expectation-maximization (MAP-EM) algorithm with TV regularizer (EM-TV) and that of the recently developed nested EM-TV algorithm for ECT reconstruction. Based on the numerical experiments performed in this work, we observe that the alternating projection algorithm with the EM-preconditioner outperforms significantly the EM-TV in all aspects including the convergence speed, the noise in the reconstructed images and the image quality. It also outperforms the nested EM-TV in the convergence speed while providing comparable image quality. (paper)
Parallel RFSAI-BFGS Preconditioners for Large Symmetric Eigenproblems
Directory of Open Access Journals (Sweden)
L. Bergamaschi
2013-01-01
the linearized Newton system to solve Au=q(uu, q(u being the Rayleigh quotient. In a previous work (Bergamaschi and Martínez, 2013 the sequence of preconditioned Jacobians is proven to remain close to the identity matrix if the initial preconditioned Jacobian is so. Numerical results onto matrices arising from various realistic problems with size up to 1.5 million unknowns account for the efficiency and the scalability of the proposed low rank update of the RFSAI preconditioner. The overall RFSAI-BFGS preconditioned Newton algorithm has shown comparable efficiencies with a well-established eigenvalue solver on all the test problems.
Directory of Open Access Journals (Sweden)
Patrick C. Baer
2018-06-01
Full Text Available Stem cell-based therapies require cells with a maximum regenerative capacity in order to support regeneration after tissue injury and organ failure. Optimization of this regenerative potential of mesenchymal stromal/stem cells (MSC or their conditioned medium by in vitro preconditioning regimens are considered to be a promising strategy to improve the release of regenerative factors. In the present study, MSC were isolated from inguinal adipose tissue (mASC from C57BL/6 mice, cultured, and characterized. Then, mASC were either preconditioned by incubation in a hypoxic environment (0.5% O2, or in normoxia in the presence of murine epidermal growth factor (EGF or tumor necrosis factor α (TNFα for 48 h. Protein expression was measured by a commercially available array. Selected factors were verified by PCR analysis. The expression of 83 out of 308 proteins (26.9% assayed was found to be increased after preconditioning with TNFα, whereas the expression of 61 (19.8% and 70 (22.7% proteins was increased after incubation with EGF or in hypoxia, respectively. Furthermore, we showed the proliferation-promoting effects of the preconditioned culture supernatants on injured epithelial cells in vitro. Our findings indicate that each preconditioning regimen tested induced an individual expression profile with a wide variety of factors, including several growth factors and cytokines, and therefore may enhance the regenerative potential of mASC for cell-based therapies.
An Adaptive Multilevel Factorized Sparse Approximate Inverse Preconditioning
Czech Academy of Sciences Publication Activity Database
Kopal, Jiří; Rozložník, Miroslav; Tůma, Miroslav
2017-01-01
Roč. 113, November (2017), s. 19-24 ISSN 0965-9978 R&D Projects: GA ČR GA13-06684S Grant - others:GA MŠk(CZ) LL1202 Institutional support: RVO:67985807 Keywords : approximate inverse * Gram–Schmidt orthogonalization * incomplete factorization * multilevel methods * preconditioned conjugate gradient method Subject RIV: BA - General Mathematics OBOR OECD: Applied mathematics Impact factor: 3.000, year: 2016
Preconditioned Iterative Methods for Solving Weighted Linear Least Squares Problems
Czech Academy of Sciences Publication Activity Database
Bru, R.; Marín, J.; Mas, J.; Tůma, Miroslav
2014-01-01
Roč. 36, č. 4 (2014), A2002-A2022 ISSN 1064-8275 Institutional support: RVO:67985807 Keywords : preconditioned iterative methods * incomplete decompositions * approximate inverses * linear least squares Subject RIV: BA - General Mathematics Impact factor: 1.854, year: 2014
Parallel Monte Carlo reactor neutronics
International Nuclear Information System (INIS)
Blomquist, R.N.; Brown, F.B.
1994-01-01
The issues affecting implementation of parallel algorithms for large-scale engineering Monte Carlo neutron transport simulations are discussed. For nuclear reactor calculations, these include load balancing, recoding effort, reproducibility, domain decomposition techniques, I/O minimization, and strategies for different parallel architectures. Two codes were parallelized and tested for performance. The architectures employed include SIMD, MIMD-distributed memory, and workstation network with uneven interactive load. Speedups linear with the number of nodes were achieved
Simulation of neutron transport equation using parallel Monte Carlo for deep penetration problems
International Nuclear Information System (INIS)
Bekar, K. K.; Tombakoglu, M.; Soekmen, C. N.
2001-01-01
Neutron transport equation is simulated using parallel Monte Carlo method for deep penetration neutron transport problem. Monte Carlo simulation is parallelized by using three different techniques; direct parallelization, domain decomposition and domain decomposition with load balancing, which are used with PVM (Parallel Virtual Machine) software on LAN (Local Area Network). The results of parallel simulation are given for various model problems. The performances of the parallelization techniques are compared with each other. Moreover, the effects of variance reduction techniques on parallelization are discussed
Linear multifrequency-grey acceleration recast for preconditioned Krylov iterations
International Nuclear Information System (INIS)
Morel, Jim E.; Brian Yang, T.-Y.; Warsa, James S.
2007-01-01
The linear multifrequency-grey acceleration (LMFGA) technique is used to accelerate the iterative convergence of multigroup thermal radiation diffusion calculations in high energy density simulations. Although it is effective and efficient in one-dimensional calculations, the LMFGA method has recently been observed to significantly degrade under certain conditions in multidimensional calculations with large discontinuities in material properties. To address this deficiency, we recast the LMFGA method in terms of a preconditioned system that is solved with a Krylov method (LMFGK). Results are presented demonstrating that the new LMFGK method always requires fewer iterations than the original LMFGA method. The reduction in iteration count increases with both the size of the time step and the inhomogeneity of the problem. However, for reasons later explained, the LMFGK method can cost more per iteration than the LMFGA method, resulting in lower but comparable efficiency in problems with small time steps and weak inhomogeneities. In problems with large time steps and strong inhomogeneities, the LMFGK method is significantly more efficient than the LMFGA method
Veres, Tünde Gyöngyvér; Takács, Ildikó; Nagy, Tibor; Jancsó, Gábor; Kondor, Ariella; Pótó, László; Vereczkei, András
2018-04-13
Laparoscopy is more beneficial than the conventional open technique, however the pneumoperitoneum created may have an ischemic side effect. Our aim was to evaluate the protective effects of preconditioning during laparoscopic cholecystectomies (LC). 30 patients were randomized into 2 groups: I. PreC (preconditioning: 5 min. inflation, 5 min. deflation, followed by conventional LC), II: LC (conventional LC). Blood samples were taken before hospitalization (C = control), before surgery, after anaesthesia (B.S.), after surgery (A.S.) and 24 hours after the procedure (24 h). Measured parameters were: malondialdehyde (MDA), reduced glutathione (GSH), sulfhydril groups (-SH), superoxide-dismutase (SOD), catalase (CAT), myeloperoxidase (MPO), length of hospitalization and pain (VAS = visual analogue scale). Compared to the BS levels, no significant changes were detected in SOD's activity and MDA levels. GSH concentrations were significantly increased in the PreC group after operation. SH-, MPO, CAT and liver function enzymes were not significantly different. Hospitalization was shorter in the PreC group. Based on the VAS score patients had less pain in the PreC group. Significant differences concerning PreC group were found in GSH values. In the PreC group pain decreased by 2-2.5 units following the procedure, 24 h after surgery, and hospitalisation was also significantly shorter. In our pilot study the potential protective effect of preconditioning could be defined.
Material pre-conditioning effects on the creep behaviour of 316H stainless steel
International Nuclear Information System (INIS)
Mehmanparast, A.; Davies, C.M.; Dean, D.W.; Nikbin, K.
2013-01-01
Material pre-conditioning by, for example, pre-strain through component bending and welding is known to alter the creep deformation and creep crack growth (CCG) behaviour of 316H stainless steel. Experimental test data on the creep deformation and crack growth behaviour of 316H weldment compact tension specimens at 550 °C, where the starter defect was introduced into the heat affected zone (HAZ), have been compared to those of obtained from similar specimens manufactured from parent material, which had been subjected to 8% compressive plastic pre-strain at room temperature. Similar degrees of accelerated cracking behaviour compared to parent material, for given values of C*, were exhibited in both 316H HAZ and pre-compressed parent materials. This acceleration has been attributed to the influence of material hardening effects and the reduction of creep ductility in the pre-conditioned materials. These results are discussed in terms of the potential for using material pre-conditioning to assist in predicting the long term cracking behaviour of high temperature 316H stainless steel plant components from shorter term laboratory CCG tests
Microwave tomography global optimization, parallelization and performance evaluation
Noghanian, Sima; Desell, Travis; Ashtari, Ali
2014-01-01
This book provides a detailed overview on the use of global optimization and parallel computing in microwave tomography techniques. The book focuses on techniques that are based on global optimization and electromagnetic numerical methods. The authors provide parallelization techniques on homogeneous and heterogeneous computing architectures on high performance and general purpose futuristic computers. The book also discusses the multi-level optimization technique, hybrid genetic algorithm and its application in breast cancer imaging.
Decomposition based parallel processing technique for efficient collaborative optimization
International Nuclear Information System (INIS)
Park, Hyung Wook; Kim, Sung Chan; Kim, Min Soo; Choi, Dong Hoon
2000-01-01
In practical design studies, most of designers solve multidisciplinary problems with complex design structure. These multidisciplinary problems have hundreds of analysis and thousands of variables. The sequence of process to solve these problems affects the speed of total design cycle. Thus it is very important for designer to reorder original design processes to minimize total cost and time. This is accomplished by decomposing large multidisciplinary problem into several MultiDisciplinary Analysis SubSystem (MDASS) and processing it in parallel. This paper proposes new strategy for parallel decomposition of multidisciplinary problem to raise design efficiency by using genetic algorithm and shows the relationship between decomposition and Multidisciplinary Design Optimization(MDO) methodology
Bredeweg, Steef W.; Zijlstra, Sjouke; Bessem, Bram; Buist, Ida
Objectives There is no consensus on the aetiology and prevention of running-related injuries in runners. Preconditioning studies among different athlete populations show positive effects on the incidence of sports injuries. Hypothesis A 4-week preconditioning programme in novice runners will reduce
Vartanian, Keri B; Mitchell, Hugh D; Stevens, Susan L; Conrad, Valerie K; McDermott, Jason E; Stenzel-Poore, Mary P
2015-01-01
Cytosine-phosphate-guanine (CpG) preconditioning reprograms the genomic response to stroke to protect the brain against ischemic injury. The mechanisms underlying genomic reprogramming are incompletely understood. MicroRNAs (miRNAs) regulate gene expression; however, their role in modulating gene responses produced by CpG preconditioning is unknown. We evaluated brain miRNA expression in response to CpG preconditioning before and after stroke using microarray. Importantly, we have data from previous gene microarrays under the same conditions, which allowed integration of miRNA and gene expression data to specifically identify regulated miRNA gene targets. CpG preconditioning did not significantly alter miRNA expression before stroke, indicating that miRNA regulation is not critical for the initiation of preconditioning-induced neuroprotection. However, after stroke, differentially regulated miRNAs between CpG- and saline-treated animals associated with the upregulation of several neuroprotective genes, implicating these miRNAs in genomic reprogramming that increases neuroprotection. Statistical analysis revealed that the miRNA targets were enriched in the gene population regulated in the setting of stroke, implying that miRNAs likely orchestrate this gene expression. These data suggest that miRNAs regulate endogenous responses to stroke and that manipulation of these miRNAs may have the potential to acutely activate novel neuroprotective processes that reduce damage. PMID:25388675
Arctic atmospheric preconditioning: do not rule out shortwave radiation just yet
Sedlar, J.
2017-12-01
Springtime atmospheric preconditioning of Arctic sea ice for enhanced or buffered sea ice melt during the subsequent melt year has received considerable research focus in recent years. A general consensus points to enhanced poleward atmospheric transport of moisture and heat during spring, effectively increasing the emission of longwave radiation to the surface. Studies have essentially ruled out the role of shortwave radiation as an effective preconditioning mechanism because of the relatively weak incident solar radiation and high surface albedo from sea ice and snow during spring. These conclusions, however, are derived primarily from atmospheric reanalysis data, which may not always represent an accurate depiction of the Arctic climate system. Here, observations of top of atmosphere radiation from state of the art satellite sensors are examined and compared with reanalysis and climate model data to examine the differences in the spring radiative budget over the Arctic Ocean for years with extreme low/high ice extent at the end of the ice melt season (September). Distinct biases are observed between satellite-based measurements and reanalysis/models, particularly for the amount of shortwave radiation trapped (warming effect) within the Arctic climate system during spring months. A connection between the differences in reanalysis/model surface albedo representation and the albedo observed by satellite is discussed. These results suggest that shortwave radiation should not be overlooked as a significant contributing mechanism to springtime Arctic atmospheric preconditioning.
Improving the making ready process - Exploring the preconditions to work tasks in construction
DEFF Research Database (Denmark)
Lindhard, Søren; Wandahl, Søren
2012-01-01
preconditions have been revealed. The seven first is basically corresponding to the ones presented by Koskela (1999), while the last two are new and extends the existing knowledge. The preconditions are as follows: 1) Construction design and management. 2) Components and materials are present. 3) Workers...... are present. 4) Equipment and machinery are present. 5) Sufficient space for conduction. 6) Previous activities must be completed. 7) Climate conditions must be in order. 8) Safe working conditions in relation to national “Health and Safety at Work Act ” have to be present, 9) Known working conditions. Often...... productivity....
Giusti, Sebastián; Fiszer de Plazas, Sara
2012-02-01
The molecular pathways underlying the neuroprotective effects of preconditioning are promising, potentially drugable targets to promote cell survival. However, these pathways are complex and are not yet fully understood. In this study we have established a paradigm of hypoxic preconditioning based on a chick embryo model of normobaric acute hypoxia previously developed by our group. With this model, we analyzed the role of hypoxia-inducible factor-1α (HIF-1α) stabilization during preconditioning in HIF-1 signaling after the hypoxic injury and in the development of a neuroprotective effect against the insult. To this end, we used a pharmacological approach, based on the in vivo administration of positive (Fe(2+), ascorbate) and negative (CoCl(2)) modulators of the activity of HIF-prolyl hydroxylases (PHDs), the main regulators of HIF-1. We have found that preconditioning has a reinforcing effect on HIF-1 accumulation during the subsequent hypoxic injury. In addition, we have also demonstrated that HIF-1 induction during hypoxic preconditioning is necessary to obtain an enhancement in HIF-1 accumulation and to develop a tolerance against a subsequent hypoxic injury. We provide in vivo evidence that administration of Fe(2+) and ascorbate modulates HIF accumulation, suggesting that PHDs might be targets for neuroprotection in the CNS. Copyright © 2011 Wiley Periodicals, Inc.
Parallel processing based decomposition technique for efficient collaborative optimization
International Nuclear Information System (INIS)
Park, Hyung Wook; Kim, Sung Chan; Kim, Min Soo; Choi, Dong Hoon
2001-01-01
In practical design studies, most of designers solve multidisciplinary problems with large sized and complex design system. These multidisciplinary problems have hundreds of analysis and thousands of variables. The sequence of process to solve these problems affects the speed of total design cycle. Thus it is very important for designer to reorder the original design processes to minimize total computational cost. This is accomplished by decomposing large multidisciplinary problem into several MultiDisciplinary Analysis SubSystem (MDASS) and processing it in parallel. This paper proposes new strategy for parallel decomposition of multidisciplinary problem to raise design efficiency by using genetic algorithm and shows the relationship between decomposition and Multidisciplinary Design Optimization(MDO) methodology
Hatazaki, S; Bellver-Estelles, C; Jimenez-Mateos, E M; Meller, R; Bonner, C; Murphy, N; Matsushima, S; Taki, W; Prehn, J H M; Simon, R P; Henshall, D C
2007-12-05
A neuroprotected state can be acquired by preconditioning brain with a stimulus that is subthreshold for damage (tolerance). Acquisition of tolerance involves coordinate, bi-directional changes to gene expression levels and the re-programmed phenotype is determined by the preconditioning stimulus. While best studied in ischemic brain there is evidence brief seizures can confer tolerance against prolonged seizures (status epilepticus). Presently, we developed a model of epileptic preconditioning in mice and used microarrays to gain insight into the transcriptional phenotype within the target hippocampus at the time tolerance had been acquired. Epileptic tolerance was induced by an episode of non-damaging seizures in adult C57Bl/6 mice using a systemic injection of kainic acid. Neuron and DNA damage-positive cell counts 24 h after status epilepticus induced by intraamygdala microinjection of kainic acid revealed preconditioning given 24 h prior reduced CA3 neuronal death by approximately 45% compared with non-tolerant seizure mice. Microarray analysis of over 39,000 transcripts (Affymetrix 430 2.0 chip) from microdissected CA3 subfields was undertaken at the point at which tolerance was acquired. Results revealed a unique profile of small numbers of equivalently up- and down-regulated genes with biological functions that included transport and localization, ubiquitin metabolism, apoptosis and cell cycle control. Select microarray findings were validated post hoc by real-time polymerase chain reaction and Western blotting. The present study defines a paradigm for inducing epileptic preconditioning in mice and first insight into the global transcriptome of the seizure-damage refractory brain.
Rehni, Ashish K; Singh, Thakur Gurjeet
2012-10-01
The present study has been designed to investigate the potential role of CCR-2 chemokine receptor in ischemic preconditioning as well as postconditioning induced reversal of ischemia-reperfusion injury in mouse brain. Bilateral carotid artery occlusion of 17 min followed by reperfusion for 24h was employed in present study to produce ischemia and reperfusion induced cerebral injury in mice. Cerebral infarct size was measured using triphenyltetrazolium chloride staining. Memory was evaluated using elevated plus-maze test and Morris water maze test. Rota rod test was employed to assess motor incoordination. Bilateral carotid artery occlusion followed by reperfusion produced cerebral infarction and impaired memory and motor co-ordination. Three preceding episodes of bilateral carotid artery occlusion for 1 min and reperfusion of 1 min were employed to elicit ischemic preconditioning of brain, while three episodes of bilateral carotid artery occlusion for 10s and reperfusion of 10s immediately after the completion of were employed to elicit ischemic postconditioning of brain. Both prior ischemic preconditioning as well as ischemic postconditioning immediately after global cerebral ischemia prevented markedly ischemia-reperfusion-induced cerebral injury as measured in terms of infarct size, loss of memory and motor coordination. RS 102895, a selective CCR-2 chemokine receptor antagonist, attenuated the neuroprotective effect of both the ischemic preconditioning as well as postconditioning. It is concluded that the neuroprotective effect of both ischemic preconditioning as well as ischemic postconditioning may involve the activation of CCR-2 chemokine receptors. Copyright © 2012 Elsevier Ltd. All rights reserved.
An, Gary C; Faeder, James R
2009-01-01
Intracellular signaling/synthetic pathways are being increasingly extensively characterized. However, while these pathways can be displayed in static diagrams, in reality they exist with a degree of dynamic complexity that is responsible for heterogeneous cellular behavior. Multiple parallel pathways exist and interact concurrently, limiting the ability to integrate the various identified mechanisms into a cohesive whole. Computational methods have been suggested as a means of concatenating this knowledge to aid in the understanding of overall system dynamics. Since the eventual goal of biomedical research is the identification and development of therapeutic modalities, computational representation must have sufficient detail to facilitate this 'engineering' process. Adding to the challenge, this type of representation must occur in a perpetual state of incomplete knowledge. We present a modeling approach to address this challenge that is both detailed and qualitative. This approach is termed 'dynamic knowledge representation,' and is intended to be an integrated component of the iterative cycle of scientific discovery. BioNetGen (BNG), a software platform for modeling intracellular signaling pathways, was used to model the toll-like receptor 4 (TLR-4) signal transduction cascade. The informational basis of the model was a series of reference papers on modulation of (TLR-4) signaling, and some specific primary research papers to aid in the characterization of specific mechanistic steps in the pathway. This model was detailed with respect to the components of the pathway represented, but qualitative with respect to the specific reaction coefficients utilized to execute the reactions. Responsiveness to simulated lipopolysaccharide (LPS) administration was measured by tumor necrosis factor (TNF) production. Simulation runs included evaluation of initial dose-dependent response to LPS administration at 10, 100, 1000 and 10,000, and a subsequent examination of
Preconditions of origin, essence and assignment of strategic managerial accounting
Boiko, I.
2010-01-01
The article is devoted to the research of preconditions and necessity of creation strategic managerial accounting in the accounting system of enterprise. There are investigated economic essence and assignment of strategic managerial accounting and substantiated its importance for making strategic decisions on an enterprise.
New preconditioned conjugate gradient algorithms for nonlinear unconstrained optimization problems
International Nuclear Information System (INIS)
Al-Bayati, A.; Al-Asadi, N.
1997-01-01
This paper presents two new predilection conjugate gradient algorithms for nonlinear unconstrained optimization problems and examines their computational performance. Computational experience shows that the new proposed algorithms generally imp lone the efficiency of Nazareth's [13] preconditioned conjugate gradient algorithm. (authors). 16 refs., 1 tab
International Nuclear Information System (INIS)
Ikuno, Soichiro; Chen, Gong; Yamamoto, Susumu; Itoh, Taku; Abe, Kuniyoshi; Nakamura, Hiroaki
2016-01-01
Krylov subspace method and the variable preconditioned Krylov subspace method with communication avoiding technique for a linear system obtained from electromagnetic analysis are numerically investigated. In the k−skip Krylov method, the inner product calculations are expanded by Krylov basis, and the inner product calculations are transformed to the scholar operations. k−skip CG method is applied for the inner-loop solver of Variable Preconditioned Krylov subspace methods, and the converged solution of electromagnetic problem is obtained using the method. (author)
Domain decomposition methods and parallel computing
International Nuclear Information System (INIS)
Meurant, G.
1991-01-01
In this paper, we show how to efficiently solve large linear systems on parallel computers. These linear systems arise from discretization of scientific computing problems described by systems of partial differential equations. We show how to get a discrete finite dimensional system from the continuous problem and the chosen conjugate gradient iterative algorithm is briefly described. Then, the different kinds of parallel architectures are reviewed and their advantages and deficiencies are emphasized. We sketch the problems found in programming the conjugate gradient method on parallel computers. For this algorithm to be efficient on parallel machines, domain decomposition techniques are introduced. We give results of numerical experiments showing that these techniques allow a good rate of convergence for the conjugate gradient algorithm as well as computational speeds in excess of a billion of floating point operations per second. (author). 5 refs., 11 figs., 2 tabs., 1 inset
Weighted SGD for ℓp Regression with Randomized Preconditioning*
Yang, Jiyan; Chow, Yin-Lam; Ré, Christopher; Mahoney, Michael W.
2018-01-01
In recent years, stochastic gradient descent (SGD) methods and randomized linear algebra (RLA) algorithms have been applied to many large-scale problems in machine learning and data analysis. SGD methods are easy to implement and applicable to a wide range of convex optimization problems. In contrast, RLA algorithms provide much stronger performance guarantees but are applicable to a narrower class of problems. We aim to bridge the gap between these two methods in solving constrained overdetermined linear regression problems—e.g., ℓ2 and ℓ1 regression problems. We propose a hybrid algorithm named pwSGD that uses RLA techniques for preconditioning and constructing an importance sampling distribution, and then performs an SGD-like iterative process with weighted sampling on the preconditioned system.By rewriting a deterministic ℓp regression problem as a stochastic optimization problem, we connect pwSGD to several existing ℓp solvers including RLA methods with algorithmic leveraging (RLA for short).We prove that pwSGD inherits faster convergence rates that only depend on the lower dimension of the linear system, while maintaining low computation complexity. Such SGD convergence rates are superior to other related SGD algorithm such as the weighted randomized Kaczmarz algorithm.Particularly, when solving ℓ1 regression with size n by d, pwSGD returns an approximate solution with ε relative error in the objective value in 𝒪(log n·nnz(A)+poly(d)/ε2) time. This complexity is uniformly better than that of RLA methods in terms of both ε and d when the problem is unconstrained. In the presence of constraints, pwSGD only has to solve a sequence of much simpler and smaller optimization problem over the same constraints. In general this is more efficient than solving the constrained subproblem required in RLA.For ℓ2 regression, pwSGD returns an approximate solution with ε relative error in the objective value and the solution vector measured in
Kalman Filter Tracking on Parallel Architectures
International Nuclear Information System (INIS)
Cerati, Giuseppe; Elmer, Peter; Krutelyov, Slava; Lantz, Steven; Lefebvre, Matthieu; McDermott, Kevin; Riley, Daniel; Tadel, Matevž; Wittich, Peter; Würthwein, Frank; Yagil, Avi
2016-01-01
Power density constraints are limiting the performance improvements of modern CPUs. To address this we have seen the introduction of lower-power, multi-core processors such as GPGPU, ARM and Intel MIC. In order to achieve the theoretical performance gains of these processors, it will be necessary to parallelize algorithms to exploit larger numbers of lightweight cores and specialized functions like large vector units. Track finding and fitting is one of the most computationally challenging problems for event reconstruction in particle physics. At the High-Luminosity Large Hadron Collider (HL-LHC), for example, this will be by far the dominant problem. The need for greater parallelism has driven investigations of very different track finding techniques such as Cellular Automata or Hough Transforms. The most common track finding techniques in use today, however, are those based on a Kalman filter approach. Significant experience has been accumulated with these techniques on real tracking detector systems, both in the trigger and offline. They are known to provide high physics performance, are robust, and are in use today at the LHC. Given the utility of the Kalman filter in track finding, we have begun to port these algorithms to parallel architectures, namely Intel Xeon and Xeon Phi. We report here on our progress towards an end-to-end track reconstruction algorithm fully exploiting vectorization and parallelization techniques in a simplified experimental environment
Unified analysis of preconditioning methods for saddle point matrices
Czech Academy of Sciences Publication Activity Database
Axelsson, Owe
2015-01-01
Roč. 22, č. 2 (2015), s. 233-253 ISSN 1070-5325 R&D Projects: GA MŠk ED1.1.00/02.0070 Institutional support: RVO:68145535 Keywords : saddle point problems * preconditioning * spectral properties Subject RIV: BA - General Mathematics Impact factor: 1.431, year: 2015 http://onlinelibrary.wiley.com/doi/10.1002/nla.1947/pdf
Kast, Brigitte; Schori, Christian; Grimm, Christian
2016-05-01
Hypoxic preconditioning protects photoreceptors against light-induced degeneration preserving retinal morphology and function. Although hypoxia inducible transcription factors 1 and 2 (HIF1, HIF2) are the main regulators of the hypoxic response, photoreceptor protection does not depend on HIF1 in rods. Here we used rod-specific Hif2a single and Hif1a;Hif2a double knockout mice to investigate the potential involvement of HIF2 in rods for protection after hypoxic preconditioning. To identify potential HIF2 target genes in rods we determined the retinal transcriptome of hypoxic control and rod-specific Hif2a knockouts by RNA sequencing. We show that rods do not need HIF2 for hypoxia-induced increased survival after light exposure. The transcriptomic analysis revealed a number of genes that are potentially regulated by HIF2 in rods; among those were Htra1, Timp3 and Hmox1, candidates that are interesting due to their connection to human degenerative diseases of the retina. We conclude that neither HIF1 nor HIF2 are required in photoreceptors for protection by hypoxic preconditioning. We hypothesize that HIF transcription factors may be needed in other cells to produce protective factors acting in a paracrine fashion on photoreceptor cells. Alternatively, hypoxic preconditioning induces a rod-intrinsic response that is independent of HIF transcription factors. Copyright © 2015 Elsevier Ltd. All rights reserved.
HATAZAKI, S.; BELLVER-ESTELLES, C.; JIMENEZ-MATEOS, E. M.; MELLER, R.; BONNER, C.; MURPHY, N.; MATSUSHIMA, S.; TAKI, W.; PREHN, J. H. M.; SIMON, R. P.; HENSHALL, D. C.
2007-01-01
A neuroprotected state can be acquired by preconditioning brain with a stimulus that is subthreshold for damage (tolerance). Acquisition of tolerance involves coordinate, bi-directional changes to gene expression levels and the re-programmed phenotype is determined by the preconditioning stimulus. While best studied in ischemic brain there is evidence brief seizures can confer tolerance against prolonged seizures (status epilepticus). Presently, we developed a model of epileptic preconditioni...
Remote Ischemic Preconditioning and Outcomes of Cardiac Surgery.
Hausenloy, DJ; Candilio, L; Evans, R; Ariti, C; Jenkins, DP; Kolvekar, S; Knight, R; Kunst, G; Laing, C; Nicholas, J; Pepper, J; Robertson, S; Xenou, M; Clayton, T; Yellon, DM
2015-01-01
: Whether remote ischemic preconditioning (transient ischemia and reperfusion of the arm) can improve clinical outcomes in patients undergoing coronary-artery bypass graft (CABG) surgery is not known. We investigated this question in a randomized trial. : We conducted a multicenter, sham-controlled trial involving adults at increased surgical risk who were undergoing on-pump CABG (with or without valve surgery) with blood cardioplegia. After anesthesia induction and before surgical incision, ...
Efficient Preconditioning of Sequences of Nonsymmetric Linear Systems
Czech Academy of Sciences Publication Activity Database
Duintjer Tebbens, Jurjen; Tůma, Miroslav
2007-01-01
Roč. 29, č. 5 (2007), s. 1918-1941 ISSN 1064-8275 R&D Projects: GA AV ČR 1ET400300415; GA AV ČR KJB100300703 Institutional research plan: CEZ:AV0Z10300504 Keywords : preconditioned iterative methods * sparse matrices * sequences of linear algebraic systems * incomplete factorizations * factorization updates * Gauss–Jordan transformations * minimum spanning tree Subject RIV: BA - General Mathematics Impact factor: 1.784, year: 2007
Professional Parallel Programming with C# Master Parallel Extensions with NET 4
Hillar, Gastón
2010-01-01
Expert guidance for those programming today's dual-core processors PCs As PC processors explode from one or two to now eight processors, there is an urgent need for programmers to master concurrent programming. This book dives deep into the latest technologies available to programmers for creating professional parallel applications using C#, .NET 4, and Visual Studio 2010. The book covers task-based programming, coordination data structures, PLINQ, thread pools, asynchronous programming model, and more. It also teaches other parallel programming techniques, such as SIMD and vectorization.Teach
Deflation in preconditioned conjugate gradient methods for Finite Element Problems
Vermolen, F.J.; Vuik, C.; Segal, A.
2002-01-01
We investigate the influence of the value of deflation vectors at interfaces on the rate of convergence of preconditioned conjugate gradient methods applied to a Finite Element discretization for an elliptic equation. Our set-up is a Poisson problem in two dimensions with continuous or discontinuous
Collins, Anne M; Quinlan, Christine S; Dolan, Roisin T; O'Neill, Shane P; Tierney, Paul; Cronin, Kevin J; Ridgway, Paul F
2015-07-01
The benefits of incorporating audiovisual materials into learning are well recognised. The outcome of integrating such a modality in to anatomical education has not been reported previously. The aim of this randomised study was to determine whether audiovisual preconditioning is a useful adjunct to learning at an upper limb dissection course. Prior to instruction participants completed a standardised pre course multiple-choice questionnaire (MCQ). The intervention group was subsequently shown a video with a pre-recorded commentary. Following initial dissection, both groups completed a second MCQ. The final MCQ was completed at the conclusion of the course. Statistical analysis confirmed a significant improvement in the performance in both groups over the duration of the three MCQs. The intervention group significantly outperformed their control group counterparts immediately following audiovisual preconditioning and in the post course MCQ. Audiovisual preconditioning is a practical and effective tool that should be incorporated in to future course curricula to optimise learning. Level of evidence This study appraises an intervention in medical education. Kirkpatrick Level 2b (modification of knowledge). Copyright © 2015 British Association of Plastic, Reconstructive and Aesthetic Surgeons. Published by Elsevier Ltd. All rights reserved.
PBMC: Pre-conditioned Backward Monte Carlo code for radiative transport in planetary atmospheres
García Muñoz, A.; Mills, F. P.
2017-08-01
PBMC (Pre-Conditioned Backward Monte Carlo) solves the vector Radiative Transport Equation (vRTE) and can be applied to planetary atmospheres irradiated from above. The code builds the solution by simulating the photon trajectories from the detector towards the radiation source, i.e. in the reverse order of the actual photon displacements. In accounting for the polarization in the sampling of photon propagation directions and pre-conditioning the scattering matrix with information from the scattering matrices of prior (in the BMC integration order) photon collisions, PBMC avoids the unstable and biased solutions of classical BMC algorithms for conservative, optically-thick, strongly-polarizing media such as Rayleigh atmospheres.
Parallel computing in genomic research: advances and applications.
Ocaña, Kary; de Oliveira, Daniel
2015-01-01
Today's genomic experiments have to process the so-called "biological big data" that is now reaching the size of Terabytes and Petabytes. To process this huge amount of data, scientists may require weeks or months if they use their own workstations. Parallelism techniques and high-performance computing (HPC) environments can be applied for reducing the total processing time and to ease the management, treatment, and analyses of this data. However, running bioinformatics experiments in HPC environments such as clouds, grids, clusters, and graphics processing unit requires the expertise from scientists to integrate computational, biological, and mathematical techniques and technologies. Several solutions have already been proposed to allow scientists for processing their genomic experiments using HPC capabilities and parallelism techniques. This article brings a systematic review of literature that surveys the most recently published research involving genomics and parallel computing. Our objective is to gather the main characteristics, benefits, and challenges that can be considered by scientists when running their genomic experiments to benefit from parallelism techniques and HPC capabilities.
Matsuzaki, Satoshi; Szweda, Pamela A; Szweda, Luke I; Humphries, Kenneth M
2009-11-30
Excessive production of free radicals by mitochondria is associated with, and likely contributes to, the progression of numerous pathological conditions. Nevertheless, the production of free radicals by the mitochondria may have important biological functions under normal or stressed conditions by activating or modulating redox-sensitive cellular signaling pathways. This raises the intriguing possibility that regulated mitochondrial free radical production occurs via mechanisms that are distinct from pathologies associated with oxidative damage. Indeed, the capacity of mitochondria to produce free radicals in a limited manner may play a role in ischemic preconditioning, the phenomenon whereby short bouts of ischemia protect from subsequent prolonged ischemia and reperfusion. Ischemic preconditioning can thus serve as an important model system for defining regulatory mechanisms that allow for transient, signal-inducing, production of free radicals by mitochondria. Defining how these mechanism(s) occur will provide insight into therapeutic approaches that minimize oxidative damage without altering normal cellular redox biology. The aim of this review is to present and discuss evidence for the regulated production of superoxide by the electron transport chain within the ischemic preconditioning paradigm of redox regulation.
Joo, Jin Deok; Kim, Mihwa; D'Agati, Vivette D; Lee, H Thomas
2006-11-01
Acute as well as delayed ischemic preconditioning (IPC) provides protection against cardiac and neuronal ischemia reperfusion (IR) injury. This study determined whether delayed preconditioning occurs in the kidney and further elucidated the mechanisms of renal IPC in mice. Mice were subjected to IPC (four cycles of 5 min of ischemia and reperfusion) and then to 30 min of renal ischemia either 15 min (acute IPC) or 24 h (delayed IPC) later. Both acute and delayed renal IPC provided powerful protection against renal IR injury. Inhibition of Akt but not extracellular signal-regulated kinase phosphorylation prevented the protection that was afforded by acute IPC. Neither extracellular signal-regulated kinase nor Akt inhibition prevented protection that was afforded by delayed renal IPC. Pretreatment with an antioxidant, N-(2-mercaptopropionyl)-glycine, to scavenge free radicals prevented the protection that was provided by acute but not delayed renal IPC. Inhibition of protein kinase C or pertussis toxin-sensitive G-proteins attenuated protection from both acute and delayed renal IPC. Delayed renal IPC increased inducible nitric oxide synthase (iNOS) as well as heat-shock protein 27 synthesis, and the renal protective effects of delayed preconditioning were attenuated by a selective inhibitor of iNOS (l-N(6)[1-iminoethyl]lysine). Moreover, delayed IPC was not observed in iNOS knockout mice. Both acute and delayed IPC were independent of A(1) adenosine receptors (AR) as a selective A(1)AR antagonist failed to block preconditioning and acute and delayed preconditioning occurred in mice that lacked A(1)AR. Therefore, this study demonstrated that acute or delayed IPC provides renal protection against IR injury in mice but involves distinct signaling pathways.
Thiersch, Markus; Lange, Christina; Joly, Sandrine; Heynen, Severin; Le, Yun Zheng; Samardzija, Marijana; Grimm, Christian
2009-06-01
Hypoxic preconditioning stabilizes hypoxia-inducible factor (HIF) 1 alpha in the retina and protects photoreceptors against light-induced cell death. HIF-1 alpha is one of the major transcription factors responding to low oxygen tension and can differentially regulate a large number of target genes. To analyse whether photoreceptor-specific expression of HIF-1 alpha is essential to protect photoreceptors by hypoxic preconditioning, we knocked down expression of HIF-1 alpha specifically in photoreceptor cells, using the cyclization recombinase (Cre)-lox system. The Cre-mediated knockdown caused a 20-fold reduced expression of Hif-1 alpha in the photoreceptor cell layer. In the total retina, RNA expression was reduced by 65%, and hypoxic preconditioning led to only a small increase in HIF-1 alpha protein levels. Accordingly, HIF-1 target gene expression after hypoxia was significantly diminished. Retinas of Hif-1 alpha knockdown animals did not show any pathological alterations, and tolerated hypoxic exposure in a comparable way to wild-type retinas. Importantly, the strong neuroprotective effect of hypoxic preconditioning against light-induced photoreceptor degeneration persisted in knockdown mice, suggesting that hypoxia-mediated survival of light exposure does not depend on an autocrine action of HIF-1 alpha in photoreceptor cells. Hypoxia-mediated stabilization of HIF-2 alpha and phosphorylation of signal transducer and activator of transcription 3 (STAT 3) were not affected in the retinas of Hif-1 alpha knockdown mice. Thus, these factors are candidates for regulating the resistance of photoreceptors to light damage after hypoxic preconditioning, along with several potentially neuroprotective genes that were similarly induced in hypoxic knockdown and control mice.
International Nuclear Information System (INIS)
Dobritz, M.; Radkow, T.; Bautz, W.; Fellner, F.A.; Nittka, M.
2002-01-01
Purpose: The VIBE (volume interpolated breath-hold examination) sequence in combination with parallel acquisition technique (iPAT: integrated parallel acquisition technique) allows dynamic contrast-enhanced MRI of the liver with high temporal and spatial resolution. The aim of this study was to obtain first clinical experience with this technique for the detection and characterization of focal liver lesions. Materials and Methods: We examined 10 consecutive patients using a 1.5 T MR system (gradient field strength 30 mT/m) with a phased-array coil combination. Following sequences- were acquired: T 2 -w TSE and T 1 -w FLASH, after administration of gadolinium, 6 VIBE sequences with iPAT (TR/TE/matrix/partition thickness/time of acquisition: 6.2 ms/ 3.2 ms/256 x 192/4 mm/13 s), as well as T 1 -weighted FLASH with fat saturation. Two observers evaluated the different sequences concerning the number of lesions and their dignity. Following lesions were found: hepatocellular carcinoma (5 patients), hemangioma (2), metastasis (1), cyst (1), adenoma (1). Results: The VIBE sequences were superior for the detection of lesions with arterial hyperperfusion with a total of 33 focal lesions. 21 lesions were found with T 2 -w TSE and 20 with plain T 1 -weighted FLASH. Diagnostic accuracy increased with the VIBE sequence in comparison to the other sequences. Conclusion: VIBE with iPAT allows MR imaging of the liver with high spatial and temporal resolution providing dynamic contrast-enhanced information about the whole liver. This may lead to improved detection of liver lesions, especially hepatocellular carcinoma. (orig.) [de
Xu, Zheng; Wang, Sheng; Li, Yeqing; Zhu, Feiyun; Huang, Junzhou
2018-02-08
The most recent history of parallel Magnetic Resonance Imaging (pMRI) has in large part been devoted to finding ways to reduce acquisition time. While joint total variation (JTV) regularized model has been demonstrated as a powerful tool in increasing sampling speed for pMRI, however, the major bottleneck is the inefficiency of the optimization method. While all present state-of-the-art optimizations for the JTV model could only reach a sublinear convergence rate, in this paper, we squeeze the performance by proposing a linear-convergent optimization method for the JTV model. The proposed method is based on the Iterative Reweighted Least Squares algorithm. Due to the complexity of the tangled JTV objective, we design a novel preconditioner to further accelerate the proposed method. Extensive experiments demonstrate the superior performance of the proposed algorithm for pMRI regarding both accuracy and efficiency compared with state-of-the-art methods.
Zerr, Robert Joseph
2011-12-01
The integral transport matrix method (ITMM) has been used as the kernel of new parallel solution methods for the discrete ordinates approximation of the within-group neutron transport equation. The ITMM abandons the repetitive mesh sweeps of the traditional source iterations (SI) scheme in favor of constructing stored operators that account for the direct coupling factors among all the cells and between the cells and boundary surfaces. The main goals of this work were to develop the algorithms that construct these operators and employ them in the solution process, determine the most suitable way to parallelize the entire procedure, and evaluate the behavior and performance of the developed methods for increasing number of processes. This project compares the effectiveness of the ITMM with the SI scheme parallelized with the Koch-Baker-Alcouffe (KBA) method. The primary parallel solution method involves a decomposition of the domain into smaller spatial sub-domains, each with their own transport matrices, and coupled together via interface boundary angular fluxes. Each sub-domain has its own set of ITMM operators and represents an independent transport problem. Multiple iterative parallel solution methods have investigated, including parallel block Jacobi (PBJ), parallel red/black Gauss-Seidel (PGS), and parallel GMRES (PGMRES). The fastest observed parallel solution method, PGS, was used in a weak scaling comparison with the PARTISN code. Compared to the state-of-the-art SI-KBA with diffusion synthetic acceleration (DSA), this new method without acceleration/preconditioning is not competitive for any problem parameters considered. The best comparisons occur for problems that are difficult for SI DSA, namely highly scattering and optically thick. SI DSA execution time curves are generally steeper than the PGS ones. However, until further testing is performed it cannot be concluded that SI DSA does not outperform the ITMM with PGS even on several thousand or tens of
Energy Technology Data Exchange (ETDEWEB)
Weston, Brian T. [Univ. of California, Davis, CA (United States)
2017-05-17
This dissertation focuses on the development of a fully-implicit, high-order compressible ow solver with phase change. The work is motivated by laser-induced phase change applications, particularly by the need to develop large-scale multi-physics simulations of the selective laser melting (SLM) process in metal additive manufacturing (3D printing). Simulations of the SLM process require precise tracking of multi-material solid-liquid-gas interfaces, due to laser-induced melting/ solidi cation and evaporation/condensation of metal powder in an ambient gas. These rapid density variations and phase change processes tightly couple the governing equations, requiring a fully compressible framework to robustly capture the rapid density variations of the ambient gas and the melting/evaporation of the metal powder. For non-isothermal phase change, the velocity is gradually suppressed through the mushy region by a variable viscosity and Darcy source term model. The governing equations are discretized up to 4th-order accuracy with our reconstructed Discontinuous Galerkin spatial discretization scheme and up to 5th-order accuracy with L-stable fully implicit time discretization schemes (BDF2 and ESDIRK3-5). The resulting set of non-linear equations is solved using a robust Newton-Krylov method, with the Jacobian-free version of the GMRES solver for linear iterations. Due to the sti nes associated with the acoustic waves and thermal and viscous/material strength e ects, preconditioning the GMRES solver is essential. A robust and scalable approximate block factorization preconditioner was developed, which utilizes the velocity-pressure (vP) and velocity-temperature (vT) Schur complement systems. This multigrid block reduction preconditioning technique converges for high CFL/Fourier numbers and exhibits excellent parallel and algorithmic scalability on classic benchmark problems in uid dynamics (lid-driven cavity ow and natural convection heat transfer) as well as for laser
Refinement of Parallel and Reactive Programs
Back, R. J. R.
1992-01-01
We show how to apply the refinement calculus to stepwise refinement of parallel and reactive programs. We use action systems as our basic program model. Action systems are sequential programs which can be implemented in a parallel fashion. Hence refinement calculus methods, originally developed for sequential programs, carry over to the derivation of parallel programs. Refinement of reactive programs is handled by data refinement techniques originally developed for the sequential refinement c...
Zhang, Qichun; Bian, Huimin; Li, Yu; Guo, Liwei; Tang, Yuping; Zhu, Huaxu
2014-06-11
Huang-Lian-Jie-Du-Tang (HLJDT) is a classical heat-clearing and detoxicating formula of traditional Chinese medicine that is widely used to treat stroke. The present study was designed to investigate the effects of HLJDT preconditioning on neurons under oxygen and glucose deprivation (OGD) and rats subjected to middle cerebral artery occlusion (MCAO). A stroke model of rats was obtained through MCAO. Following HLJDT preconditioning, the cerebral infarction volume, cerebral water content, and neurological deficient score were determined. Cerebral cortical neurons cultured in vitro were preconditioned with HLJDT and then subjected to OGD treatment. The release of lactate dehydrogenase (LDH) from neurons was detected. The levels of hypoxia-inducible factor-1α (HIF-1α) and PI3K/Akt signaling were analyzed by western blotting, and the levels of erythropoietin (EPO) and vascular endothelial growth factor (VEGF) in the supernatant of the neurons and the plasma of MCAO rats were measured through a radioimmunological assay. The apoptosis and proliferation of neurons were analyzed by immunohistochemistry. HLJDT preconditioning significantly reduced the cerebral infarction volume and cerebral water content and ameliorated the neurological deficient score of MCAO rats. In addition, HLJDT preconditioning protected neurons against OGD. Increased HIF-1α, EPO, and VEGF levels and the activation of PI3K/Akt signaling were observed as a result of HLJDT preconditioning. Furthermore, HLJDT preconditioning was found to inhibit ischemia-induced neuron apoptosis and to promote neuron proliferation under conditions of ischemia/reperfusion. Both rats and neurons subjected to HLJDT preconditioning were able to resist ischemia/reperfusion or hypoxia injury through the inhibition of apoptosis and the enhancement of proliferation, and these effects were primarily dependent on the activation of the PI3K/Akt signaling pathway and HIF-1α. Copyright © 2014 Elsevier Ireland Ltd. All rights
Parallelizing the spectral transform method: A comparison of alternative parallel algorithms
International Nuclear Information System (INIS)
Foster, I.; Worley, P.H.
1993-01-01
The spectral transform method is a standard numerical technique for solving partial differential equations on the sphere and is widely used in global climate modeling. In this paper, we outline different approaches to parallelizing the method and describe experiments that we are conducting to evaluate the efficiency of these approaches on parallel computers. The experiments are conducted using a testbed code that solves the nonlinear shallow water equations on a sphere, but are designed to permit evaluation in the context of a global model. They allow us to evaluate the relative merits of the approaches as a function of problem size and number of processors. The results of this study are guiding ongoing work on PCCM2, a parallel implementation of the Community Climate Model developed at the National Center for Atmospheric Research
Huang, Xin; Su, Kunkai; Zhou, Limin; Shen, Guofang; Dong, Qi; Lou, Yijia; Zheng, Shu
2013-12-01
Mesenchymal stromal cells (MSCs) in bone marrow may enhance tumor metastases through the secretion of chemokines. MSCs have been reported to home toward the hypoxic tumor microenvironment in vivo. In this study, we investigated prostate cancer PC3 cell behavior under the influence of hypoxia preconditioned MSCs and explored the related mechanism of prostate cancer lymphatic metastases in mice. Transwell assays revealed that VEGF-C receptor, VEGFR-3, as well as chemokine CCL21 receptor, CC chemokine receptor 7 (CCR7), were responsible for the migration of PC3 cells toward hypoxia preconditioned MSCs. Knock-in Ccr7 in PC3 cells also improved cell migration in vitro. Furthermore, when PC3 cells were labeled using the hrGfp-lentiviral vector, and were combined with hypoxia preconditioned MSCs for xenografting, it resulted in an enhancement of lymph node metastases accompanied by up-regulation of VEGFR-3 and CCR7 in primary tumors. Both PI3K/Akt/IκBα and JAK2/STAT3 signaling pathways were activated in xenografts in the presence of hypoxia-preconditioned MSCs. Unexpectedly, the p-VEGFR-2/VEGFR-2 ratio was attenuated accompanied by decreased JAK1 expression, indicating a switching-off of potential vascular signal within xenografts in the presence of hypoxia-preconditioned MSCs. Unlike results from other studies, VEGF-C maintained a stable expression in both conditions, which indicated that hypoxia preconditioning of MSCs did not influence VEGF-C secretion. Our results provide the new insights into the functional molecular events and signalings influencing prostate tumor metastases, suggesting a hopeful diagnosis and treatment in new approaches. © 2013 Wiley Periodicals, Inc.
Bayer image parallel decoding based on GPU
Hu, Rihui; Xu, Zhiyong; Wei, Yuxing; Sun, Shaohua
2012-11-01
In the photoelectrical tracking system, Bayer image is decompressed in traditional method, which is CPU-based. However, it is too slow when the images become large, for example, 2K×2K×16bit. In order to accelerate the Bayer image decoding, this paper introduces a parallel speedup method for NVIDA's Graphics Processor Unit (GPU) which supports CUDA architecture. The decoding procedure can be divided into three parts: the first is serial part, the second is task-parallelism part, and the last is data-parallelism part including inverse quantization, inverse discrete wavelet transform (IDWT) as well as image post-processing part. For reducing the execution time, the task-parallelism part is optimized by OpenMP techniques. The data-parallelism part could advance its efficiency through executing on the GPU as CUDA parallel program. The optimization techniques include instruction optimization, shared memory access optimization, the access memory coalesced optimization and texture memory optimization. In particular, it can significantly speed up the IDWT by rewriting the 2D (Tow-dimensional) serial IDWT into 1D parallel IDWT. Through experimenting with 1K×1K×16bit Bayer image, data-parallelism part is 10 more times faster than CPU-based implementation. Finally, a CPU+GPU heterogeneous decompression system was designed. The experimental result shows that it could achieve 3 to 5 times speed increase compared to the CPU serial method.
Tissier, Renaud; Souktani, Rachid; Parent de Curzon, Olivier; Lellouche, Nicolas; Henry, Patrick; Giudicelli, Jean-François; Berdeaux, Alain; Ghaleh, Bijan
2001-01-01
The goal of this study was to investigate the effects of the delayed pharmacological preconditioning produced by an adenosine A1-receptor agonist (A1-DPC) against ventricular arrhythmias induced by ischaemia and reperfusion, compared to those of ischaemia-induced delayed preconditioning (I-DPC).Eighty-nine instrumented conscious rabbits underwent a 2 consecutive days protocol. On day 1, rabbits were randomly divided into four groups: ‘Control' (saline, i.v.), ‘I-DPC' (six 4-min coronary arter...
Bilirubin nanoparticle preconditioning protects against hepatic ischemia-reperfusion injury.
Kim, Jin Yong; Lee, Dong Yun; Kang, Sukmo; Miao, Wenjun; Kim, Hyungjun; Lee, Yonghyun; Jon, Sangyong
2017-07-01
Hepatic ischemia-reperfusion injury (IRI) remains a major concern in liver transplantation and resection, despite continuing efforts to prevent it. Accumulating evidence suggests that bilirubin possesses antioxidant, anti-inflammatory and anti-apoptotic properties. However, despite obvious potential health benefits of bilirubin, its clinical applications are limited by its poor solubility. We recently developed bilirubin nanoparticles (BRNPs) consisting of polyethylene glycol (PEG)-conjugated bilirubin. Here, we sought to investigate whether BRNPs protect against IRI in the liver by preventing oxidative stress. BRNPs exerted potent antioxidant and anti-apoptotic activity in primary hepatocytes exposed to hydrogen peroxide, a precursor of reactive oxygen species (ROS). In a model of hepatic IRI in mice, BRNP preconditioning exerted profound protective effects against hepatocellular injury by reducing oxidative stress, pro-inflammatory cytokine production, and recruitment of neutrophils. They also preferentially accumulated in IRI-induced inflammatory lesions. Collectively, our findings indicate that BRNP preconditioning provides a simple and safe approach that can be easily monitored in the blood like endogenous bilirubin, and could be a promising strategy to protect against IRI in a clinical setting. Copyright © 2017 Elsevier Ltd. All rights reserved.
Energy Technology Data Exchange (ETDEWEB)
Mirrione, M.M.; Mirrione, M.M.; Konomosa, D.K.; Ioradanis, G.; Dewey, S.L.; Agzzid, A.; Heppnerd, F.L.; Tsirka, St.E.
2010-04-01
Activated microglia have been associated with neurodegeneration in patients and in animal models of Temporal Lobe Epilepsy (TLE), however their precise functions as neurotoxic or neuroprotective is a topic of significant investigation. To explore this, we examined the effects of pilocarpine-induced seizures in transgenic mice where microglia/macrophages were conditionally ablated. We found that unilateral ablation of microglia from the dorsal hippocampus did not alter acute seizure sensitivity. However, when this procedure was coupled with lipopolysaccharide (LPS) preconditioning (1 mg/kg given 24 h prior to acute seizure), we observed a significant pro-convulsant phenomenon. This effect was associated with lower metabolic activation in the ipsilateral hippocampus during acute seizures, and could be attributed to activity in the mossy fiber pathway. These findings reveal that preconditioning with LPS 24 h prior to seizure induction may have a protective effect which is abolished by unilateral hippocampal microglia/macrophage ablation.
Writing parallel programs that work
CERN. Geneva
2012-01-01
Serial algorithms typically run inefficiently on parallel machines. This may sound like an obvious statement, but it is the root cause of why parallel programming is considered to be difficult. The current state of the computer industry is still that almost all programs in existence are serial. This talk will describe the techniques used in the Intel Parallel Studio to provide a developer with the tools necessary to understand the behaviors and limitations of the existing serial programs. Once the limitations are known the developer can refactor the algorithms and reanalyze the resulting programs with the tools in the Intel Parallel Studio to create parallel programs that work. About the speaker Paul Petersen is a Sr. Principal Engineer in the Software and Solutions Group (SSG) at Intel. He received a Ph.D. degree in Computer Science from the University of Illinois in 1993. After UIUC, he was employed at Kuck and Associates, Inc. (KAI) working on auto-parallelizing compiler (KAP), and was involved in th...
Parallel computing in genomic research: advances and applications
Directory of Open Access Journals (Sweden)
Ocaña K
2015-11-01
Full Text Available Kary Ocaña,1 Daniel de Oliveira2 1National Laboratory of Scientific Computing, Petrópolis, Rio de Janeiro, 2Institute of Computing, Fluminense Federal University, Niterói, Brazil Abstract: Today's genomic experiments have to process the so-called "biological big data" that is now reaching the size of Terabytes and Petabytes. To process this huge amount of data, scientists may require weeks or months if they use their own workstations. Parallelism techniques and high-performance computing (HPC environments can be applied for reducing the total processing time and to ease the management, treatment, and analyses of this data. However, running bioinformatics experiments in HPC environments such as clouds, grids, clusters, and graphics processing unit requires the expertise from scientists to integrate computational, biological, and mathematical techniques and technologies. Several solutions have already been proposed to allow scientists for processing their genomic experiments using HPC capabilities and parallelism techniques. This article brings a systematic review of literature that surveys the most recently published research involving genomics and parallel computing. Our objective is to gather the main characteristics, benefits, and challenges that can be considered by scientists when running their genomic experiments to benefit from parallelism techniques and HPC capabilities. Keywords: high-performance computing, genomic research, cloud computing, grid computing, cluster computing, parallel computing
Shared Variable Oriented Parallel Precompiler for SPMD Model
Institute of Scientific and Technical Information of China (English)
无
1995-01-01
For the moment,commercial parallel computer systems with distributed memory architecture are usually provided with parallel FORTRAN or parallel C compliers,which are just traditional sequential FORTRAN or C compilers expanded with communication statements.Programmers suffer from writing parallel programs with communication statements. The Shared Variable Oriented Parallel Precompiler (SVOPP) proposed in this paper can automatically generate appropriate communication statements based on shared variables for SPMD(Single Program Multiple Data) computation model and greatly ease the parallel programming with high communication efficiency.The core function of parallel C precompiler has been successfully verified on a transputer-based parallel computer.Its prominent performance shows that SVOPP is probably a break-through in parallel programming technique.
Parallel Computing Strategies for Irregular Algorithms
Biswas, Rupak; Oliker, Leonid; Shan, Hongzhang; Biegel, Bryan (Technical Monitor)
2002-01-01
Parallel computing promises several orders of magnitude increase in our ability to solve realistic computationally-intensive problems, but relies on their efficient mapping and execution on large-scale multiprocessor architectures. Unfortunately, many important applications are irregular and dynamic in nature, making their effective parallel implementation a daunting task. Moreover, with the proliferation of parallel architectures and programming paradigms, the typical scientist is faced with a plethora of questions that must be answered in order to obtain an acceptable parallel implementation of the solution algorithm. In this paper, we consider three representative irregular applications: unstructured remeshing, sparse matrix computations, and N-body problems, and parallelize them using various popular programming paradigms on a wide spectrum of computer platforms ranging from state-of-the-art supercomputers to PC clusters. We present the underlying problems, the solution algorithms, and the parallel implementation strategies. Smart load-balancing, partitioning, and ordering techniques are used to enhance parallel performance. Overall results demonstrate the complexity of efficiently parallelizing irregular algorithms.
Non-Cartesian parallel imaging reconstruction.
Wright, Katherine L; Hamilton, Jesse I; Griswold, Mark A; Gulani, Vikas; Seiberlich, Nicole
2014-11-01
Non-Cartesian parallel imaging has played an important role in reducing data acquisition time in MRI. The use of non-Cartesian trajectories can enable more efficient coverage of k-space, which can be leveraged to reduce scan times. These trajectories can be undersampled to achieve even faster scan times, but the resulting images may contain aliasing artifacts. Just as Cartesian parallel imaging can be used to reconstruct images from undersampled Cartesian data, non-Cartesian parallel imaging methods can mitigate aliasing artifacts by using additional spatial encoding information in the form of the nonhomogeneous sensitivities of multi-coil phased arrays. This review will begin with an overview of non-Cartesian k-space trajectories and their sampling properties, followed by an in-depth discussion of several selected non-Cartesian parallel imaging algorithms. Three representative non-Cartesian parallel imaging methods will be described, including Conjugate Gradient SENSE (CG SENSE), non-Cartesian generalized autocalibrating partially parallel acquisition (GRAPPA), and Iterative Self-Consistent Parallel Imaging Reconstruction (SPIRiT). After a discussion of these three techniques, several potential promising clinical applications of non-Cartesian parallel imaging will be covered. © 2014 Wiley Periodicals, Inc.
Directory of Open Access Journals (Sweden)
Kraemer Robert
2011-11-01
Full Text Available Abstract Background Therapeutic strategies aiming to reduce ischemia/reperfusion injury by conditioning tissue tolerance against ischemia appear attractive not only from a scientific perspective, but also in clinics. Although previous studies indicate that remote ischemic intermittent preconditioning (RIPC is a systemic phenomenon, only a few studies have focused on the elucidation of its mechanisms of action especially in the clinical setting. Therefore, the aim of this study is to evaluate the acute microcirculatory effects of remote ischemic preconditioning on a distinct cutaneous location at the lower extremity which is typically used as a harvesting site for free flap reconstructive surgery in a human in-vivo setting. Methods Microcirculatory data of 27 healthy subjects (25 males, age 24 ± 4 years, BMI 23.3 were evaluated continuously at the anterolateral aspect of the left thigh during RIPC using combined Laser-Doppler and photospectrometry (Oxygen-to-see, Lea Medizintechnik, Germany. After baseline microcirculatory measurement, remote ischemia was induced using a tourniquet on the contralateral upper arm for three cycles of 5 min. Results After RIPC, tissue oxygen saturation and capillary blood flow increased up to 29% and 35% during the third reperfusion phase versus baseline measurement, respectively (both p = 0.001. Postcapillary venous filling pressure decreased statistically significant by 16% during second reperfusion phase (p = 0.028. Conclusion Remote intermittent ischemic preconditioning affects cutaneous tissue oxygen saturation, arterial capillary blood flow and postcapillary venous filling pressure at a remote cutaneous location of the lower extremity. To what extent remote preconditioning might ameliorate reperfusion injury in soft tissue trauma or free flap transplantation further clinical trials have to evaluate. Trial registration ClinicalTrials.gov: NCT01235286
Directory of Open Access Journals (Sweden)
Xiaoliang Gan
2013-01-01
Full Text Available The study aimed to investigate whether sevoflurane preconditioning can protect against small intestinal ischemia reperfusion (IIR injury and to explore whether mast cell (MC is involved in the protections provided by sevoflurane preconditioning. Sprague-Dawley rats exposed to sevoflurane or treated with MC stabilizer cromolyn sodium (CS were subjected to 75-minute superior mesenteric artery occlusion followed by 2-hour reperfusion in the presence or absence of MC degranulator compound 48/80 (CP. Small intestinal ischemia reperfusion resulted in severe intestinal injury as demonstrated by significant elevations in intestinal injury scores and p47phox and gp91phox, ICAM-1 protein expressions and malondialdehyde and IL-6 contents, and MPO activities as well as significant reductions in SOD activities, accompanied with concomitant increases in mast cell degranulation evidenced by significant increases in MC counts, tryptase expression, and β-hexosaminidase concentrations, and those alterations were further upregulated in the presence of CP. Sevoflurane preconditioning dramatically attenuated the previous IIR-induced alterations except MC counts, tryptase, and β-hexosaminidase which were significantly reduced by CS treatment. Furthermore, CP exacerbated IIR injury was abrogated by CS but not by sevoflurane preconditioning. The data collectively indicate that sevoflurane preconditioning confers protections against IIR injury, and MC is not involved in the protective process.
International Nuclear Information System (INIS)
Cookson, Daniel T.; Zaman, Zubayr; Gordon-Smith, James; Ireland, Hamish M.; Hayes, Peter C.
2011-01-01
Purpose: To investigate the reproducibility and technical and clinical success of the parallel technique of transjugular intrahepatic portosystemic shunt (TIPS) reduction in the management of refractory hepatic encephalopathy (HE). Materials and Methods: A 10-mm-diameter self-expanding stent graft and a 5–6-mm-diameter balloon-expandable stent were placed in parallel inside the existing TIPS in 8 patients via a dual unilateral transjugular approach. Changes in portosystemic pressure gradient and HE grade were used as primary end points. Results: TIPS reduction was technically successful in all patients. Mean ± standard deviation portosystemic pressure gradient before and after shunt reduction was 4.9 ± 3.6 mmHg (range, 0–12 mmHg) and 10.5 ± 3.9 mmHg (range, 6–18 mmHg). Duration of follow-up was 137 ± 117.8 days (range, 18–326 days). Clinical improvement of HE occurred in 5 patients (62.5%) with resolution of HE in 4 patients (50%). Single episodes of recurrent gastrointestinal hemorrhage occurred in 3 patients (37.5%). These were self-limiting in 2 cases and successfully managed in 1 case by correction of coagulopathy and blood transfusion. Two of these patients (25%) died, one each of renal failure and hepatorenal failure. Conclusion: The parallel technique of TIPS reduction is reproducible and has a high technical success rate. A dual unilateral transjugular approach is advantageous when performing this procedure. The parallel technique allows repeat bidirectional TIPS adjustment and may be of significant clinical benefit in the management of refractory HE.
Directory of Open Access Journals (Sweden)
Jianfei Zhang
2013-01-01
Full Text Available Graphics processing unit (GPU has obtained great success in scientific computations for its tremendous computational horsepower and very high memory bandwidth. This paper discusses the efficient way to implement polynomial preconditioned conjugate gradient solver for the finite element computation of elasticity on NVIDIA GPUs using compute unified device architecture (CUDA. Sliced block ELLPACK (SBELL format is introduced to store sparse matrix arising from finite element discretization of elasticity with fewer padding zeros than traditional ELLPACK-based formats. Polynomial preconditioning methods have been investigated both in convergence and running time. From the overall performance, the least-squares (L-S polynomial method is chosen as a preconditioner in PCG solver to finite element equations derived from elasticity for its best results on different example meshes. In the PCG solver, mixed precision algorithm is used not only to reduce the overall computational, storage requirements and bandwidth but to make full use of the capacity of the GPU devices. With SBELL format and mixed precision algorithm, the GPU-based L-S preconditioned CG can get a speedup of about 7–9 to CPU-implementation.
Accurate reanalysis of structures by a preconditioned conjugate gradient method
Czech Academy of Sciences Publication Activity Database
Kirsch, U.; Kočvara, Michal; Zowe, J.
2002-01-01
Roč. 55, č. 2 (2002), s. 233-251 ISSN 0029-5981 R&D Projects: GA AV ČR IAA1075005 Grant - others:BMBF(DE) 03ZOM3ER Institutional research plan: CEZ:AV0Z1075907 Keywords : preconditioned conjugate gradient s * structural reanalysis Subject RIV: BA - General Mathematics Impact factor: 1.468, year: 2002
Saklani, Reetu; Jaggi, Amteshwar; Singh, Nirmal
2010-07-01
We tested the neuroprotective effect of milrinone, a phosphodiesterase III inhibitor, in pharmacological preconditioning. Bilateral carotid artery occlusion for 12 min followed by reperfusion for 24 h produced ischemia-reperfusion (I/R) cerebral injury in male Swiss albino mice. Cerebral infarct size was measured using triphenyltetrazolium chloride staining. Memory was assessed using the Morris water maze test, and motor coordination was evaluated using the inclined beam walking test, rota-rod test, and lateral push test. Milrinone (50 microg/kg & 100 microg/kg i.v.) was administered 24 h before surgery in a separate group of animals to induce pharmacological preconditioning. I/R increased cerebral infarct size and impaired memory and motor coordination. Milrinone treatment significantly decreased cerebral infarct size and reversed I/R-induced impairments in memory and motor coordination. This neuroprotective effect was blocked by ruthenium red (3 mg/kg, s.c.), an intracellular ryanodine receptor blocker. These findings indicate that milrinone preconditioning exerts a marked neuroprotective effect on the ischemic brain, putatively due to increased intracellular calcium levels activating calcium-sensitive signal transduction cascades.
Effects of Ordering Strategies and Programming Paradigms on Sparse Matrix Computations
Oliker, Leonid; Li, Xiaoye; Husbands, Parry; Biswas, Rupak; Biegel, Bryan (Technical Monitor)
2002-01-01
The Conjugate Gradient (CG) algorithm is perhaps the best-known iterative technique to solve sparse linear systems that are symmetric and positive definite. For systems that are ill-conditioned, it is often necessary to use a preconditioning technique. In this paper, we investigate the effects of various ordering and partitioning strategies on the performance of parallel CG and ILU(O) preconditioned CG (PCG) using different programming paradigms and architectures. Results show that for this class of applications: ordering significantly improves overall performance on both distributed and distributed shared-memory systems, that cache reuse may be more important than reducing communication, that it is possible to achieve message-passing performance using shared-memory constructs through careful data ordering and distribution, and that a hybrid MPI+OpenMP paradigm increases programming complexity with little performance gains. A implementation of CG on the Cray MTA does not require special ordering or partitioning to obtain high efficiency and scalability, giving it a distinct advantage for adaptive applications; however, it shows limited scalability for PCG due to a lack of thread level parallelism.
An inherently parallel method for solving discretized diffusion equations
International Nuclear Information System (INIS)
Eccleston, B.R.; Palmer, T.S.
1999-01-01
A Monte Carlo approach to solving linear systems of equations is being investigated in the context of the solution of discretized diffusion equations. While the technique was originally devised decades ago, changes in computer architectures (namely, massively parallel machines) have driven the authors to revisit this technique. There are a number of potential advantages to this approach: (1) Analog Monte Carlo techniques are inherently parallel; this is not necessarily true to today's more advanced linear equation solvers (multigrid, conjugate gradient, etc.); (2) Some forms of this technique are adaptive in that they allow the user to specify locations in the problem where resolution is of particular importance and to concentrate the work at those locations; and (3) These techniques permit the solution of very large systems of equations in that matrix elements need not be stored. The user could trade calculational speed for storage if elements of the matrix are calculated on the fly. The goal of this study is to compare the parallel performance of Monte Carlo linear solvers to that of a more traditional parallelized linear solver. The authors observe the linear speedup that they expect from the Monte Carlo algorithm, given that there is no domain decomposition to cause significant communication overhead. Overall, PETSc outperforms the Monte Carlo solver for the test problem. The PETSc parallel performance improves with larger numbers of unknowns for a given number of processors. Parallel performance of the Monte Carlo technique is independent of the size of the matrix and the number of processes. They are investigating modifications to the scheme to accommodate matrix problems with positive off-diagonal elements. They are also currently coding an on-the-fly version of the algorithm to investigate the solution of very large linear systems
Mengxuan, Zhong
2017-06-01
The gradient preconditioning algorithms based on Hessian matrices in time-domain full waveform inversion (FWI) are widely used now, but consume a lot of memory and do not fit the FWI of large models or actual seismic data well. To avoid the huge storage consumption, the gradient preconditioning approach based on seismic wave energy has been proposed it simulates the “approximated wave field” with the acoustic wave equation and uses the energy of the simulated wavefield to precondition the gradient. The method does not require computing and storing the Hessian matrix or its inverse and can effectively eliminate the effect caused by geometric diffusion and uneven illumination on gradient. The result of experiments in this article with field data from South China Sea confirms that the time-domain FWI using the gradient preconditioning based on seismic wave energy (GPWE) can achieve higher inversion accuracy for the deep high-velocity model and its underlying strata.
Functional recovery in rat spinal cord injury induced by hyperbaric oxygen preconditioning.
Lu, Pei-Gang; Hu, Sheng-Li; Hu, Rong; Wu, Nan; Chen, Zhi; Meng, Hui; Lin, Jiang-Kai; Feng, Hua
2012-12-01
It is a common belief that neurosurgical interventions can cause inevitable damage resulting from the procedure itself in surgery especially for intramedullary spinal cord tumors. The present study was designed to examine if hyperbaric oxygen preconditioning (HBO-PC) was neuroprotective against surgical injuries using a rat model of spinal cord injury (SCI). Sprague-Dawley rats were randomly divided into three groups: HBO-PC group, hypobaric hypoxic preconditioning (HH-PC) control group, and normobaric control group. All groups were subjected to SCI by weight drop device. Rats from each group were examined for neurological behavior and electrophysiological function. Tissue sections were analyzed by using immunohistochemistry, TdT-mediated dUTP-biotin nick end labeling, and axonal tract tracing. Significant neurological deficits were observed after SCI and HBO-PC and HH-PC improved neurological deficits 1 week post-injury. The latencies of motor-evoked potential and somatosensory-evoked potential were significantly delayed after SCI, which was attenuated by HBO-PC and HH-PC. Compared with normobaric control group, pretreatment with HBO and hypobaric hypoxia significantly reduced the number of TdT-mediated dUTP-biotin nick end labeling-positive cells, and increased nestin-positive cells. HBO-PC and HH-PC enhanced axonal growth after SCI. In conclusion, preconditioning with HBO and hypobaric hypoxia can facilitate functional recovery and suppress cell apoptosis after SCI and may prove to be a useful preventive strategy to neurosurgical SCI.
Experimental investigation on preconditioned rate induced tipping in a thermoacoustic system.
Tony, J; Subarna, S; Syamkumar, K S; Sudha, G; Akshay, S; Gopalakrishnan, E A; Surovyatkina, E; Sujith, R I
2017-07-14
Many systems found in nature are susceptible to tipping, where they can shift from one stable dynamical state to another. This shift in dynamics can be unfavorable in systems found in various fields ranging from ecology to finance. Hence, it is important to identify the factors that can lead to tipping in a physical system. Tipping can mainly be brought about by a change in parameter or due to the influence of external fluctuations. Further, the rate at which the parameter is varied also determines the final state that the system attains. Here, we show preconditioned rate induced tipping in experiments and in a theoretical model of a thermoacoustic system. We provide a specific initial condition (preconditioning) and vary the parameter at a rate higher than a critical rate to observe tipping. We find that the critical rate is a function of the initial condition. Our study is highly relevant because the parameters that dictate the asymptotic behavior of many physical systems are temporally dynamic.
Anesthetic Preconditioning as Endogenous Neuroprotection in Glaucoma
Directory of Open Access Journals (Sweden)
Tsung-Han Chou
2018-01-01
Full Text Available Blindness in glaucoma is the result of death of Retinal Ganglion Cells (RGCs and their axons. RGC death is generally preceded by a stage of reversible dysfunction and structural remodeling. Current treatments aimed at reducing intraocular pressure (IOP are ineffective or incompletely effective in management of the disease. IOP-independent neuroprotection or neuroprotection as adjuvant to IOP lowering in glaucoma remains a challenge as effective agents without side effects have not been identified yet. We show in DBA/2J mice with spontaneous IOP elevation and glaucoma that the lifespan of functional RGCs can be extended by preconditioning RGCs with retrobulbar lidocaine in one eye at four months of age that temporary blocks RGC axonal transport. The contralateral, PBS-injected eye served as control. Lidocaine-induced impairment of axonal transport to superior colliculi was assessed by intravitreal injection of cholera toxin B. Long-term (nine months effect of lidocaine were assessed on RGC electrical responsiveness (PERG, IOP, expression of relevant protein (BDNF, TrkB, PSD95, GFAP, Synaptophysin, and GAPDH and RGC density. While lidocaine treatment did not alter the age-related increase of IOP, TrkB expression was elevated, GFAP expression was decreased, RGC survival was improved by 35%, and PERG function was preserved. Results suggest that the lifespan of functional RGCs in mouse glaucoma can be extended by preconditioning RGCs in early stages of the disease using a minimally invasive treatment with retrobulbar lidocaine, a common ophthalmologic procedure. Lidocaine is inexpensive, safe and is approved by Food and Drug Administration (FDA to be administered intravenously.
Xue, Yuquan; Xu, Zhibin; Chen, Haiwen; Gan, Weimin; Chong, Tie
2017-07-01
To evaluate whether low energy shock wave preconditioning could reduce renal ischemic reperfusion injury caused by renal artery occlusion. The right kidneys of 64 male Sprague Dawley rats were removed to establish an isolated kidney model. The rats were then divided into four treatment groups: Group 1 was the sham treatment group; Group 2, received only low-energy (12 kv, 1 Hz, 200 times) shock wave preconditioning; Group 3 received the same low-energy shock wave preconditioning as Group 2, and then the left renal artery was occluded for 45 minutes; and Group 4 had the left renal artery occluded for 45 minutes. At 24 hours and one-week time points after reperfusion, serum inducible nitric oxide synthase (iNOS), neutrophil gelatinase-associated lipocalin (NGAL), kidney injury molecule-1 (KIM-1), creatinine (Cr), and cystatin C (Cys C) levels were measured, malondialdehyde (MDA) in kidney tissue was detected, and changes in nephric morphology were evaluated by light and electron microscopy. Twenty-four hours after reperfusion, serum iNOS, NGAL, Cr, Cys C, and MDA levels in Group 3 were significantly lower than those in Group 4; light and electron microscopy showed that the renal tissue injury in Group 3 was significantly lighter than that in Group 4. One week after reperfusion, serum NGAL, KIM-1, and Cys C levels in Group 3 were significantly lower than those in Group 4. Low-energy shock wave preconditioning can reduce renal ischemic reperfusion injury caused by renal artery occlusion in an isolated kidney rat model.
Parallelization of TMVA Machine Learning Algorithms
Hajili, Mammad
2017-01-01
This report reflects my work on Parallelization of TMVA Machine Learning Algorithms integrated to ROOT Data Analysis Framework during summer internship at CERN. The report consists of 4 impor- tant part - data set used in training and validation, algorithms that multiprocessing applied on them, parallelization techniques and re- sults of execution time changes due to number of workers.
[Three-dimensional parallel collagen scaffold promotes tendon extracellular matrix formation].
Zheng, Zefeng; Shen, Weiliang; Le, Huihui; Dai, Xuesong; Ouyang, Hongwei; Chen, Weishan
2016-03-01
To investigate the effects of three-dimensional parallel collagen scaffold on the cell shape, arrangement and extracellular matrix formation of tendon stem cells. Parallel collagen scaffold was fabricated by unidirectional freezing technique, while random collagen scaffold was fabricated by freeze-drying technique. The effects of two scaffolds on cell shape and extracellular matrix formation were investigated in vitro by seeding tendon stem/progenitor cells and in vivo by ectopic implantation. Parallel and random collagen scaffolds were produced successfully. Parallel collagen scaffold was more akin to tendon than random collagen scaffold. Tendon stem/progenitor cells were spindle-shaped and unified orientated in parallel collagen scaffold, while cells on random collagen scaffold had disorder orientation. Two weeks after ectopic implantation, cells had nearly the same orientation with the collagen substance. In parallel collagen scaffold, cells had parallel arrangement, and more spindly cells were observed. By contrast, cells in random collagen scaffold were disorder. Parallel collagen scaffold can induce cells to be in spindly and parallel arrangement, and promote parallel extracellular matrix formation; while random collagen scaffold can induce cells in random arrangement. The results indicate that parallel collagen scaffold is an ideal structure to promote tendon repairing.
Energy Technology Data Exchange (ETDEWEB)
Azmy, Yousry
2014-06-10
We employ the Integral Transport Matrix Method (ITMM) as the kernel of new parallel solution methods for the discrete ordinates approximation of the within-group neutron transport equation. The ITMM abandons the repetitive mesh sweeps of the traditional source iterations (SI) scheme in favor of constructing stored operators that account for the direct coupling factors among all the cells' fluxes and between the cells' and boundary surfaces' fluxes. The main goals of this work are to develop the algorithms that construct these operators and employ them in the solution process, determine the most suitable way to parallelize the entire procedure, and evaluate the behavior and parallel performance of the developed methods with increasing number of processes, P. The fastest observed parallel solution method, Parallel Gauss-Seidel (PGS), was used in a weak scaling comparison with the PARTISN transport code, which uses the source iteration (SI) scheme parallelized with the Koch-baker-Alcouffe (KBA) method. Compared to the state-of-the-art SI-KBA with diffusion synthetic acceleration (DSA), this new method- even without acceleration/preconditioning-is completitive for optically thick problems as P is increased to the tens of thousands range. For the most optically thick cells tested, PGS reduced execution time by an approximate factor of three for problems with more than 130 million computational cells on P = 32,768. Moreover, the SI-DSA execution times's trend rises generally more steeply with increasing P than the PGS trend. Furthermore, the PGS method outperforms SI for the periodic heterogeneous layers (PHL) configuration problems. The PGS method outperforms SI and SI-DSA on as few as P = 16 for PHL problems and reduces execution time by a factor of ten or more for all problems considered with more than 2 million computational cells on P = 4.096.
Energy Technology Data Exchange (ETDEWEB)
Hong, Kyung-Soo [Department of Biochemistry, Pusan National University School of Medicine, Yangsan (Korea, Republic of); Research Center for Ischemic Tissue regeneration, Pusan National University School of Medicine, Yangsan (Korea, Republic of); Park, Jun-Ik [Department of Biochemistry, Pusan National University School of Medicine, Yangsan (Korea, Republic of); Kim, Mi-Ju; Kim, Hak-Bong; Lee, Jae-Won [Department of Biochemistry, Pusan National University School of Medicine, Yangsan (Korea, Republic of); Research Center for Ischemic Tissue regeneration, Pusan National University School of Medicine, Yangsan (Korea, Republic of); Dao, Trong Tuan; Oh, Won Keun [BK21 Project Team, College of Pharmacy, Chosun University, Gwangju (Korea, Republic of); Kang, Chi-Dug, E-mail: kcdshbw@pusan.ac.kr [Department of Biochemistry, Pusan National University School of Medicine, Yangsan (Korea, Republic of); Kim, Sun-Hee, E-mail: ksh7738@pusan.ac.kr [Department of Biochemistry, Pusan National University School of Medicine, Yangsan (Korea, Republic of); Research Center for Ischemic Tissue regeneration, Pusan National University School of Medicine, Yangsan (Korea, Republic of)
2012-03-01
SIRT1 has been found to function as a Class III deacetylase that affects the acetylation status of histones and other important cellular nonhistone proteins involved in various cellular pathways including stress responses and apoptosis. In this study, we investigated the role of SIRT1 signaling in the hypoxic down-regulations of c-Myc and β-catenin and hypoxic preconditioning effect of the red wine polyphenols such as piceatannol, myricetin, quercetin and resveratrol. We found that the expression of SIRT1 was significantly increased in hypoxia-exposed or hypoxic preconditioned HepG2 cells, which was closely associated with the up-regulation of HIF-1α and down-regulation of c-Myc and β-catenin expression via deacetylation of these proteins. In addition, blockade of SIRT1 activation using siRNA or amurensin G, a new potent SIRT1 inhibitor, abolished hypoxia-induced HIF-1α expression but increased c-Myc and β-catenin expression. SIRT1 was also found to stabilize HIF-1α protein and destabilize c-Myc, β-catenin and PHD2 under hypoxia. We also found that myricetin, quercetin, piceatannol and resveratrol up-regulated HIF-1α and down-regulated c-Myc, PHD2 and β-catenin expressions via SIRT1 activation, in a manner that mimics hypoxic preconditioning. This study provides new insights of the molecular mechanisms of hypoxic preconditioning and suggests that polyphenolic SIRT1 activators could be used to mimic hypoxic/ischemic preconditioning. -- Graphical abstract: Polyphenols mimicked hypoxic preconditioning by up-regulating HIF-1α and SIRT1 and down-regulating c-Myc, PHD2, and β-catenin. HepG2 cells were pretreated with the indicated doses of myricetin (MYR; A), quercetin (QUR; B), or piceatannol (PIC; C) for 4 h and then exposed to hypoxia for 4 h. Levels of HIF-1α, SIRT1, c-Myc, β-catenin, and PHD2 were determined by western blot analysis. The data are representative of three individual experiments. Highlights: ► SIRT1 expression is increased in hypoxia
International Nuclear Information System (INIS)
Hong, Kyung-Soo; Park, Jun-Ik; Kim, Mi-Ju; Kim, Hak-Bong; Lee, Jae-Won; Dao, Trong Tuan; Oh, Won Keun; Kang, Chi-Dug; Kim, Sun-Hee
2012-01-01
SIRT1 has been found to function as a Class III deacetylase that affects the acetylation status of histones and other important cellular nonhistone proteins involved in various cellular pathways including stress responses and apoptosis. In this study, we investigated the role of SIRT1 signaling in the hypoxic down-regulations of c-Myc and β-catenin and hypoxic preconditioning effect of the red wine polyphenols such as piceatannol, myricetin, quercetin and resveratrol. We found that the expression of SIRT1 was significantly increased in hypoxia-exposed or hypoxic preconditioned HepG2 cells, which was closely associated with the up-regulation of HIF-1α and down-regulation of c-Myc and β-catenin expression via deacetylation of these proteins. In addition, blockade of SIRT1 activation using siRNA or amurensin G, a new potent SIRT1 inhibitor, abolished hypoxia-induced HIF-1α expression but increased c-Myc and β-catenin expression. SIRT1 was also found to stabilize HIF-1α protein and destabilize c-Myc, β-catenin and PHD2 under hypoxia. We also found that myricetin, quercetin, piceatannol and resveratrol up-regulated HIF-1α and down-regulated c-Myc, PHD2 and β-catenin expressions via SIRT1 activation, in a manner that mimics hypoxic preconditioning. This study provides new insights of the molecular mechanisms of hypoxic preconditioning and suggests that polyphenolic SIRT1 activators could be used to mimic hypoxic/ischemic preconditioning. -- Graphical abstract: Polyphenols mimicked hypoxic preconditioning by up-regulating HIF-1α and SIRT1 and down-regulating c-Myc, PHD2, and β-catenin. HepG2 cells were pretreated with the indicated doses of myricetin (MYR; A), quercetin (QUR; B), or piceatannol (PIC; C) for 4 h and then exposed to hypoxia for 4 h. Levels of HIF-1α, SIRT1, c-Myc, β-catenin, and PHD2 were determined by western blot analysis. The data are representative of three individual experiments. Highlights: ► SIRT1 expression is increased in hypoxia
Impact of ischemic preconditioning on functional sympatholysis during handgrip exercise in humans.
Horiuchi, M.; Endo, J.; Thijssen, D.H.J.
2015-01-01
Repeated bouts of ischemia followed by reperfusion, known as ischemic preconditioning (IPC), is found to improve exercise performance. As redistribution of blood from the inactive areas to active skeletal muscles during exercise (i.e., functional sympatholysis) is important for exercise performance,
Aspects of computation on asynchronous parallel processors
International Nuclear Information System (INIS)
Wright, M.
1989-01-01
The increasing availability of asynchronous parallel processors has provided opportunities for original and useful work in scientific computing. However, the field of parallel computing is still in a highly volatile state, and researchers display a wide range of opinion about many fundamental questions such as models of parallelism, approaches for detecting and analyzing parallelism of algorithms, and tools that allow software developers and users to make effective use of diverse forms of complex hardware. This volume collects the work of researchers specializing in different aspects of parallel computing, who met to discuss the framework and the mechanics of numerical computing. The far-reaching impact of high-performance asynchronous systems is reflected in the wide variety of topics, which include scientific applications (e.g. linear algebra, lattice gauge simulation, ordinary and partial differential equations), models of parallelism, parallel language features, task scheduling, automatic parallelization techniques, tools for algorithm development in parallel environments, and system design issues
Parallel programming with Python
Palach, Jan
2014-01-01
A fast, easy-to-follow and clear tutorial to help you develop Parallel computing systems using Python. Along with explaining the fundamentals, the book will also introduce you to slightly advanced concepts and will help you in implementing these techniques in the real world. If you are an experienced Python programmer and are willing to utilize the available computing resources by parallelizing applications in a simple way, then this book is for you. You are required to have a basic knowledge of Python development to get the most of this book.
Numerical solution of large nonlinear boundary value problems by quadratic minimization techniques
International Nuclear Information System (INIS)
Glowinski, R.; Le Tallec, P.
1984-01-01
The objective of this paper is to describe the numerical treatment of large highly nonlinear two or three dimensional boundary value problems by quadratic minimization techniques. In all the different situations where these techniques were applied, the methodology remains the same and is organized as follows: 1) derive a variational formulation of the original boundary value problem, and approximate it by Galerkin methods; 2) transform this variational formulation into a quadratic minimization problem (least squares methods) or into a sequence of quadratic minimization problems (augmented lagrangian decomposition); 3) solve each quadratic minimization problem by a conjugate gradient method with preconditioning, the preconditioning matrix being sparse, positive definite, and fixed once for all in the iterative process. This paper will illustrate the methodology above on two different examples: the description of least squares solution methods and their application to the solution of the unsteady Navier-Stokes equations for incompressible viscous fluids; the description of augmented lagrangian decomposition techniques and their application to the solution of equilibrium problems in finite elasticity
Krylov Subspace Methods for Saddle Point Problems with Indefinite Preconditioning
Czech Academy of Sciences Publication Activity Database
Rozložník, Miroslav; Simoncini, V.
2002-01-01
Roč. 24, č. 2 (2002), s. 368-391 ISSN 0895-4798 R&D Projects: GA ČR GA101/00/1035; GA ČR GA201/00/0080 Institutional research plan: AV0Z1030915 Keywords : saddle point problems * preconditioning * indefinite linear systems * finite precision arithmetic * conjugate gradients Subject RIV: BA - General Mathematics Impact factor: 0.753, year: 2002
International Nuclear Information System (INIS)
Yan Yongbin; Luo Xuechun; Zhang Riqing; Wang Xiaoyin; Zuo Lin; Liu Wei
2000-01-01
ischemic preconditioning (IPC) will protect the heart from the damage caused by a subsequent long ischemia period. 31 P spectra of isolated perfused rat heart measured by the nuclear magnetic resonance (NMR) surface coil technique can be used to continually, dynamically and noninvasively obtain metabolism information. This paper explores the IPC mechanisms by NMR. This study shows that IPC has no effect on enhancing the ATP and PCr levels during reperfusion but makes significantly slows and smooths the changes of intracellular pH and ATP during ischemia periods. The ATP and PCr recovery rate of the IPC group after ischemia is significantly higher than that of the control group. In conclusion, the above results support that IPC can protect the rat heart by reducing damage during the ischemia period
Hybrid parallel execution model for logic-based specification languages
Tsai, Jeffrey J P
2001-01-01
Parallel processing is a very important technique for improving the performance of various software development and maintenance activities. The purpose of this book is to introduce important techniques for parallel executation of high-level specifications of software systems. These techniques are very useful for the construction, analysis, and transformation of reliable large-scale and complex software systems. Contents: Current Approaches; Overview of the New Approach; FRORL Requirements Specification Language and Its Decomposition; Rewriting and Data Dependency, Control Flow Analysis of a Lo
Parallel 3-D method of characteristics in MPACT
International Nuclear Information System (INIS)
Kochunas, B.; Dovvnar, T. J.; Liu, Z.
2013-01-01
A new parallel 3-D MOC kernel has been developed and implemented in MPACT which makes use of the modular ray tracing technique to reduce computational requirements and to facilitate parallel decomposition. The parallel model makes use of both distributed and shared memory parallelism which are implemented with the MPI and OpenMP standards, respectively. The kernel is capable of parallel decomposition of problems in space, angle, and by characteristic rays up to 0(104) processors. Initial verification of the parallel 3-D MOC kernel was performed using the Takeda 3-D transport benchmark problems. The eigenvalues computed by MPACT are within the statistical uncertainty of the benchmark reference and agree well with the averages of other participants. The MPACT k eff differs from the benchmark results for rodded and un-rodded cases by 11 and -40 pcm, respectively. The calculations were performed for various numbers of processors and parallel decompositions up to 15625 processors; all producing the same result at convergence. The parallel efficiency of the worst case was 60%, while very good efficiency (>95%) was observed for cases using 500 processors. The overall run time for the 500 processor case was 231 seconds and 19 seconds for the case with 15625 processors. Ongoing work is focused on developing theoretical performance models and the implementation of acceleration techniques to minimize the number of iterations to converge. (authors)
Combining Compile-Time and Run-Time Parallelization
Directory of Open Access Journals (Sweden)
Sungdo Moon
1999-01-01
Full Text Available This paper demonstrates that significant improvements to automatic parallelization technology require that existing systems be extended in two ways: (1 they must combine high‐quality compile‐time analysis with low‐cost run‐time testing; and (2 they must take control flow into account during analysis. We support this claim with the results of an experiment that measures the safety of parallelization at run time for loops left unparallelized by the Stanford SUIF compiler’s automatic parallelization system. We present results of measurements on programs from two benchmark suites – SPECFP95 and NAS sample benchmarks – which identify inherently parallel loops in these programs that are missed by the compiler. We characterize remaining parallelization opportunities, and find that most of the loops require run‐time testing, analysis of control flow, or some combination of the two. We present a new compile‐time analysis technique that can be used to parallelize most of these remaining loops. This technique is designed to not only improve the results of compile‐time parallelization, but also to produce low‐cost, directed run‐time tests that allow the system to defer binding of parallelization until run‐time when safety cannot be proven statically. We call this approach predicated array data‐flow analysis. We augment array data‐flow analysis, which the compiler uses to identify independent and privatizable arrays, by associating predicates with array data‐flow values. Predicated array data‐flow analysis allows the compiler to derive “optimistic” data‐flow values guarded by predicates; these predicates can be used to derive a run‐time test guaranteeing the safety of parallelization.
Late preconditioning is blocked by racemic ketamine, but not by S(+)-ketamine
Müllenheim, J.; Rulands, R.; Wietschorke, T.; Frässdorf, J.; Preckel, B.; Schlack, W.
2001-01-01
Racemic ketamine blocks K(ATP) channels in isolated cells and abolishes short-term cardioprotection against prolonged ischemia. We investigated the effects of racemic ketamine and S(+)-ketamine on ischemic late preconditioning (LPC) in the rabbit heart in vivo. A coronary occluder was chronically
Lee, Jun Hee; Yoon, Yeo Min; Lee, Sang Hun
2017-06-21
Mesenchymal stem cells (MSC) are ideal materials for stem cell-based therapy. As MSCs reside in hypoxic microenvironments (low oxygen tension of 1% to 7%), several studies have focused on the beneficial effects of hypoxic preconditioning on MSC survival; however, the mechanisms underlying such effects remain unclear. This study aimed to uncover the potential mechanism involving 78-kDa glucose-regulated protein (GRP78) to explain the enhanced MSC bioactivity and survival in hindlimb ischemia. Under hypoxia (2% O₂), the expression of GRP78 was significantly increased via hypoxia-inducible factor (HIF)-1α. Hypoxia-induced GRP78 promoted the proliferation and migration potential of MSCs through the HIF-1α-GRP78-Akt signal axis. In a murine hind-limb ischemia model, hypoxic preconditioning enhanced the survival and proliferation of transplanted MSCs through suppression of the cell death signal pathway and augmentation of angiogenic cytokine secretion. These effects were regulated by GRP78. Our findings indicate that hypoxic preconditioning promotes survival, proliferation, and angiogenic cytokine secretion of MSCs via the HIF-1α-GRP78-Akt signal pathway, suggesting that hypoxia-preconditioned MSCs might provide a therapeutic strategy for MSC-based therapies and that GRP78 represents a potential target for the development of functional MSCs.
Convergence Analysis of the Preconditioned Group Splitting Methods in Boundary Value Problems
Directory of Open Access Journals (Sweden)
Norhashidah Hj. Mohd Ali
2012-01-01
Full Text Available The construction of a specific splitting-type preconditioner in block formulation applied to a class of group relaxation iterative methods derived from the centred and rotated (skewed finite difference approximations has been shown to improve the convergence rates of these methods. In this paper, we present some theoretical convergence analysis on this preconditioner specifically applied to the linear systems resulted from these group iterative schemes in solving an elliptic boundary value problem. We will theoretically show the relationship between the spectral radiuses of the iteration matrices of the preconditioned methods which affects the rate of convergence of these methods. We will also show that the spectral radius of the preconditioned matrices is smaller than that of their unpreconditioned counterparts if the relaxation parameter is in a certain optimum range. Numerical experiments will also be presented to confirm the agreement between the theoretical and the experimental results.
Compiler Technology for Parallel Scientific Computation
Directory of Open Access Journals (Sweden)
Can Özturan
1994-01-01
Full Text Available There is a need for compiler technology that, given the source program, will generate efficient parallel codes for different architectures with minimal user involvement. Parallel computation is becoming indispensable in solving large-scale problems in science and engineering. Yet, the use of parallel computation is limited by the high costs of developing the needed software. To overcome this difficulty we advocate a comprehensive approach to the development of scalable architecture-independent software for scientific computation based on our experience with equational programming language (EPL. Our approach is based on a program decomposition, parallel code synthesis, and run-time support for parallel scientific computation. The program decomposition is guided by the source program annotations provided by the user. The synthesis of parallel code is based on configurations that describe the overall computation as a set of interacting components. Run-time support is provided by the compiler-generated code that redistributes computation and data during object program execution. The generated parallel code is optimized using techniques of data alignment, operator placement, wavefront determination, and memory optimization. In this article we discuss annotations, configurations, parallel code generation, and run-time support suitable for parallel programs written in the functional parallel programming language EPL and in Fortran.
Parallelization of the Physical-Space Statistical Analysis System (PSAS)
Larson, J. W.; Guo, J.; Lyster, P. M.
1999-01-01
Atmospheric data assimilation is a method of combining observations with model forecasts to produce a more accurate description of the atmosphere than the observations or forecast alone can provide. Data assimilation plays an increasingly important role in the study of climate and atmospheric chemistry. The NASA Data Assimilation Office (DAO) has developed the Goddard Earth Observing System Data Assimilation System (GEOS DAS) to create assimilated datasets. The core computational components of the GEOS DAS include the GEOS General Circulation Model (GCM) and the Physical-space Statistical Analysis System (PSAS). The need for timely validation of scientific enhancements to the data assimilation system poses computational demands that are best met by distributed parallel software. PSAS is implemented in Fortran 90 using object-based design principles. The analysis portions of the code solve two equations. The first of these is the "innovation" equation, which is solved on the unstructured observation grid using a preconditioned conjugate gradient (CG) method. The "analysis" equation is a transformation from the observation grid back to a structured grid, and is solved by a direct matrix-vector multiplication. Use of a factored-operator formulation reduces the computational complexity of both the CG solver and the matrix-vector multiplication, rendering the matrix-vector multiplications as a successive product of operators on a vector. Sparsity is introduced to these operators by partitioning the observations using an icosahedral decomposition scheme. PSAS builds a large (approx. 128MB) run-time database of parameters used in the calculation of these operators. Implementing a message passing parallel computing paradigm into an existing yet developing computational system as complex as PSAS is nontrivial. One of the technical challenges is balancing the requirements for computational reproducibility with the need for high performance. The problem of computational
Programming massively parallel processors a hands-on approach
Kirk, David B
2010-01-01
Programming Massively Parallel Processors discusses basic concepts about parallel programming and GPU architecture. ""Massively parallel"" refers to the use of a large number of processors to perform a set of computations in a coordinated parallel way. The book details various techniques for constructing parallel programs. It also discusses the development process, performance level, floating-point format, parallel patterns, and dynamic parallelism. The book serves as a teaching guide where parallel programming is the main topic of the course. It builds on the basics of C programming for CUDA, a parallel programming environment that is supported on NVI- DIA GPUs. Composed of 12 chapters, the book begins with basic information about the GPU as a parallel computer source. It also explains the main concepts of CUDA, data parallelism, and the importance of memory access efficiency using CUDA. The target audience of the book is graduate and undergraduate students from all science and engineering disciplines who ...
Incomplete block factorization preconditioning for indefinite elliptic problems
Energy Technology Data Exchange (ETDEWEB)
Guo, Chun-Hua [Univ. of Calgary, Alberta (Canada)
1996-12-31
The application of the finite difference method to approximate the solution of an indefinite elliptic problem produces a linear system whose coefficient matrix is block tridiagonal and symmetric indefinite. Such a linear system can be solved efficiently by a conjugate residual method, particularly when combined with a good preconditioner. We show that specific incomplete block factorization exists for the indefinite matrix if the mesh size is reasonably small. And this factorization can serve as an efficient preconditioner. Some efforts are made to estimate the eigenvalues of the preconditioned matrix. Numerical results are also given.
Mena, Hebe Agustina; Zubiry, Paula Romina; Dizier, Blandine; Schattner, Mirta; Boisson-Vidal, Catherine; Negrotto, Soledad
2018-05-02
We have previously demonstrated that acidic preconditioning of human endothelial colony-forming cells (ECFC) increased proliferation, migration, and tubulogenesis in vitro, and increased their regenerative potential in a murine model of hind limb ischemia without baseline disease. We now analyze whether this strategy is also effective under adverse conditions for vasculogenesis, such as the presence of ischemia-related toxic molecules or diabetes, one of the main target diseases for cell therapy due to their well-known healing impairments. Cord blood-derived CD34 + cells were seeded in endothelial growth culture medium (EGM2) and ECFC colonies were obtained after 14-21 days. ECFC were exposed at pH 6.6 (preconditioned) or pH 7.4 (nonpreconditioned) for 6 h, and then pH was restored at 7.4. A model of type 2 diabetes induced by a high-fat and high-sucrose diet was developed in nude mice and hind limb ischemia was induced in these animals by femoral artery ligation. A P value < 0.05 was considered statistically significant (by one-way analysis of variance). We found that acidic preconditioning increased ECFC adhesion and the release of pro-angiogenic molecules, and protected ECFC from the cytotoxic effects of monosodium urate crystals, histones, and tumor necrosis factor (TNF)α, which induced necrosis, pyroptosis, and apoptosis, respectively. Noncytotoxic concentrations of high glucose, TNFα, or their combination reduced ECFC proliferation, stromal cell-derived factor (SDF)1-driven migration, and tubule formation on a basement membrane matrix, whereas almost no inhibition was observed in preconditioned ECFC. In type 2 diabetic mice, intravenous administration of preconditioned ECFC significantly induced blood flow recovery at the ischemic limb as measured by Doppler, compared with the phosphate-buffered saline (PBS) and nonpreconditioned ECFC groups. Moreover, the histologic analysis of gastrocnemius muscles showed an increased vascular density and reduced
International Nuclear Information System (INIS)
Mao, Xiaoan; Jaworski, Artur J
2010-01-01
This paper describes the development of the experimental setup and measurement methodologies to study the physics of oscillatory flows in the vicinity of parallel-plate stacks by using the particle image velocimetry (PIV) techniques. Parallel-plate configurations often appear as internal structures in thermoacoustic devices and are responsible for the hydrodynamic energy transfer processes. The flow around selected stack configurations is induced by a standing acoustic wave, whose amplitude can be varied. Depending on the direction of the flow within the acoustic cycle, relative to the stack, it can be treated as an entrance flow or a wake flow. The insight into the flow behaviour, its kinematics, dynamics and scales of turbulence, is obtained using the classical Reynolds decomposition to separate the instantaneous velocity fields into ensemble-averaged mean velocity fields and fluctuations in a set of predetermined phases within an oscillation cycle. The mean velocity field and the fluctuation intensity distributions are investigated over the acoustic oscillation cycle. The velocity fluctuation is further divided into large- and small-scale fluctuations by using fast Fourier transform (FFT) spatial filtering techniques
User-friendly parallelization of GAUDI applications with Python
International Nuclear Information System (INIS)
Mato, Pere; Smith, Eoin
2010-01-01
GAUDI is a software framework in C++ used to build event data processing applications using a set of standard components with well-defined interfaces. Simulation, high-level trigger, reconstruction, and analysis programs used by several experiments are developed using GAUDI. These applications can be configured and driven by simple Python scripts. Given the fact that a considerable amount of existing software has been developed using serial methodology, and has existed in some cases for many years, implementation of parallelisation techniques at the framework level may offer a way of exploiting current multi-core technologies to maximize performance and reduce latencies without re-writing thousands/millions of lines of code. In the solution we have developed, the parallelization techniques are introduced to the high level Python scripts which configure and drive the applications, such that the core C++ application code requires no modification, and that end users need make only minimal changes to their scripts. The developed solution leverages from existing generic Python modules that support parallel processing. Naturally, the parallel version of a given program should produce results consistent with its serial execution. The evaluation of several prototypes incorporating various parallelization techniques are presented and discussed.
User-friendly parallelization of GAUDI applications with Python
Energy Technology Data Exchange (ETDEWEB)
Mato, Pere; Smith, Eoin, E-mail: pere.mato@cern.c [PH Department, CERN, 1211 Geneva 23 (Switzerland)
2010-04-01
GAUDI is a software framework in C++ used to build event data processing applications using a set of standard components with well-defined interfaces. Simulation, high-level trigger, reconstruction, and analysis programs used by several experiments are developed using GAUDI. These applications can be configured and driven by simple Python scripts. Given the fact that a considerable amount of existing software has been developed using serial methodology, and has existed in some cases for many years, implementation of parallelisation techniques at the framework level may offer a way of exploiting current multi-core technologies to maximize performance and reduce latencies without re-writing thousands/millions of lines of code. In the solution we have developed, the parallelization techniques are introduced to the high level Python scripts which configure and drive the applications, such that the core C++ application code requires no modification, and that end users need make only minimal changes to their scripts. The developed solution leverages from existing generic Python modules that support parallel processing. Naturally, the parallel version of a given program should produce results consistent with its serial execution. The evaluation of several prototypes incorporating various parallelization techniques are presented and discussed.
Rajaeian, Babak; Allard, Sébastien; Joll, Cynthia; Heitz, Anna
2018-07-01
Silver impregnated activated carbon (SIAC) has been found to be effective in mitigating the formation of brominated-disinfection by products during drinking water treatment. However, there are still uncertainties regarding its silver leaching properties, and strategies for the prevention of silver leaching have remained elusive. This study focused on the evaluation of one type of commercially available SIAC for its ability to remove bromide while minimising silver leaching from the material. Both synthetic and real water matrices were tested. Depending on solution pH, it was found that changing the surface charge properties of SIAC, as measured by the point of zero charge pH, can result in additional bromide removal while minimising the extent of silver leaching. To better understand the mechanism of silver leaching from the SIAC, eight preconditioning environments, i.e. variable pH and ionic strength were tested for a fixed amount of SIAC and two preconditioning environments were selected for a more detailed investigation. Experiments carried out in synthetic water showed that preconditioning at pH 10.4 did not deteriorate the capacity of SIAC to remove bromide, but significantly decreased the release of silver in the form of ionic silver (Ag + ), silver bromide (AgBr) and silver chloride (AgCl) from 40% for the pristine to 3% for the treated SIAC. This was confirmed using a groundwater sample. These results suggest that preconditioned SIAC has the potential to be an effective method for bromide removal with minimised silver leaching in a long-term field application for drinking water production. Copyright © 2018 Elsevier Ltd. All rights reserved.
Energy Technology Data Exchange (ETDEWEB)
Philip, Bobby, E-mail: philipb@ornl.gov [Oak Ridge National Laboratory, One Bethel Valley Road, Oak Ridge, TN 37831 (United States); Berrill, Mark A.; Allu, Srikanth; Hamilton, Steven P.; Sampath, Rahul S.; Clarno, Kevin T. [Oak Ridge National Laboratory, One Bethel Valley Road, Oak Ridge, TN 37831 (United States); Dilts, Gary A. [Los Alamos National Laboratory, PO Box 1663, Los Alamos, NM 87545 (United States)
2015-04-01
This paper describes an efficient and nonlinearly consistent parallel solution methodology for solving coupled nonlinear thermal transport problems that occur in nuclear reactor applications over hundreds of individual 3D physical subdomains. Efficiency is obtained by leveraging knowledge of the physical domains, the physics on individual domains, and the couplings between them for preconditioning within a Jacobian Free Newton Krylov method. Details of the computational infrastructure that enabled this work, namely the open source Advanced Multi-Physics (AMP) package developed by the authors is described. Details of verification and validation experiments, and parallel performance analysis in weak and strong scaling studies demonstrating the achieved efficiency of the algorithm are presented. Furthermore, numerical experiments demonstrate that the preconditioner developed is independent of the number of fuel subdomains in a fuel rod, which is particularly important when simulating different types of fuel rods. Finally, we demonstrate the power of the coupling methodology by considering problems with couplings between surface and volume physics and coupling of nonlinear thermal transport in fuel rods to an external radiation transport code.
The Performance of an Object-Oriented, Parallel Operating System
Directory of Open Access Journals (Sweden)
David R. Kohr, Jr.
1994-01-01
Full Text Available The nascent and rapidly evolving state of parallel systems often leaves parallel application developers at the mercy of inefficient, inflexible operating system software. Given the relatively primitive state of parallel systems software, maximizing the performance of parallel applications not only requires judicious tuning of the application software, but occasionally, the replacement of specific system software modules with others that can more readily respond to the imposed pattern of resource demands. To assess the feasibility of application and performance tuning via malleable system software and to understand the performance penalties for detailed operating system performance data capture, we describe a set of performance instrumentation techniques for parallel, object-oriented operating systems and a set of performance experiments with Choices, an experimental, object-oriented operating system designed for use with parallel sys- tems. These performance experiments show that (a the performance overhead for operating system data capture is modest, (b the penalty for malleable, object-oriented operating systems is negligible, but (c techniques are needed to strictly enforce adherence of implementation to design if operating system modules are to be replaced.
Hoffmann, Gerd-Albert; Wolfer, Tim; Zeitler, Jochen; Franke, Jörg; Suttmann, Oliver; Overmeyer, Ludger
2017-02-01
Optical data communication is increasingly interesting for many applications in industrial processes. Therefore mass production is required to meet the requested price and lot sizes. Polymer optical waveguides show great promises to comply with price requirements while providing sufficient optical quality for short range data transmission. A high efficient fabrication technology using polymer materials could be able to create the essential backbone for 3D-optical data transmission in the future. The approach for high efficient fabrication technology of micro optics described in this paper is based on a self-assembly effect of fluids on preconditioned 3D-thermoformed polymer foils. Adjusting the surface energy on certain areas on the flexible substrate by flexographic printing mechanism is presented in this paper. With this technique conditioning lines made of silicone containing UV-varnish are printed on top of the foils and create gaps with the exposed substrate material in between. Subsequent fabrication processes are selected whether the preconditioned foil is coated with acrylate containing waveguide material prior or after the thermoforming process. Due to the different surface energy this material tends to dewet from the conditioning lines. It acts like regional barriers and sets the width of the arising waveguides. With this fabrication technology it is possible to produce multiple waveguides with a single coating process. The relevant printing process parameters that affect the quality of the generated waveguides are discussed and results of the produced waveguides with width ranging from 10 to 300 μm are shown.
Ohmichi, Yuya
2017-07-01
In this letter, we propose a simple and efficient framework of dynamic mode decomposition (DMD) and mode selection for large datasets. The proposed framework explicitly introduces a preconditioning step using an incremental proper orthogonal decomposition (POD) to DMD and mode selection algorithms. By performing the preconditioning step, the DMD and mode selection can be performed with low memory consumption and therefore can be applied to large datasets. Additionally, we propose a simple mode selection algorithm based on a greedy method. The proposed framework is applied to the analysis of three-dimensional flow around a circular cylinder.
Implementations of BLAST for parallel computers.
Jülich, A
1995-02-01
The BLAST sequence comparison programs have been ported to a variety of parallel computers-the shared memory machine Cray Y-MP 8/864 and the distributed memory architectures Intel iPSC/860 and nCUBE. Additionally, the programs were ported to run on workstation clusters. We explain the parallelization techniques and consider the pros and cons of these methods. The BLAST programs are very well suited for parallelization for a moderate number of processors. We illustrate our results using the program blastp as an example. As input data for blastp, a 799 residue protein query sequence and the protein database PIR were used.
Parallel hierarchical radiosity rendering
Energy Technology Data Exchange (ETDEWEB)
Carter, Michael [Iowa State Univ., Ames, IA (United States)
1993-07-01
In this dissertation, the step-by-step development of a scalable parallel hierarchical radiosity renderer is documented. First, a new look is taken at the traditional radiosity equation, and a new form is presented in which the matrix of linear system coefficients is transformed into a symmetric matrix, thereby simplifying the problem and enabling a new solution technique to be applied. Next, the state-of-the-art hierarchical radiosity methods are examined for their suitability to parallel implementation, and scalability. Significant enhancements are also discovered which both improve their theoretical foundations and improve the images they generate. The resultant hierarchical radiosity algorithm is then examined for sources of parallelism, and for an architectural mapping. Several architectural mappings are discussed. A few key algorithmic changes are suggested during the process of making the algorithm parallel. Next, the performance, efficiency, and scalability of the algorithm are analyzed. The dissertation closes with a discussion of several ideas which have the potential to further enhance the hierarchical radiosity method, or provide an entirely new forum for the application of hierarchical methods.
On the Eigenvalues and Eigenvectors of Block Triangular Preconditioned Block Matrices
Pestana, Jennifer
2014-01-01
Block lower triangular matrices and block upper triangular matrices are popular preconditioners for 2×2 block matrices. In this note we show that a block lower triangular preconditioner gives the same spectrum as a block upper triangular preconditioner and that the eigenvectors of the two preconditioned matrices are related. © 2014 Society for Industrial and Applied Mathematics.
Stress preconditioning of spreading depression in the locust CNS.
Directory of Open Access Journals (Sweden)
Corinne I Rodgers
Full Text Available Cortical spreading depression (CSD is closely associated with important pathologies including stroke, seizures and migraine. The mechanisms underlying SD in its various forms are still incompletely understood. Here we describe SD-like events in an invertebrate model, the ventilatory central pattern generator (CPG of locusts. Using K(+ -sensitive microelectrodes, we measured extracellular K(+ concentration ([K(+](o in the metathoracic neuropile of the CPG while monitoring CPG output electromyographically from muscle 161 in the second abdominal segment to investigate the role K(+ in failure of neural circuit operation induced by various stressors. Failure of ventilation in response to different stressors (hyperthermia, anoxia, ATP depletion, Na(+/K(+ ATPase impairment, K(+ injection was associated with a disturbance of CNS ion homeostasis that shares the characteristics of CSD and SD-like events in vertebrates. Hyperthermic failure was preconditioned by prior heat shock (3 h, 45 degrees C and induced-thermotolerance was associated with an increase in the rate of clearance of extracellular K(+ that was not linked to changes in ATP levels or total Na(+/K(+ ATPase activity. Our findings suggest that SD-like events in locusts are adaptive to terminate neural network operation and conserve energy during stress and that they can be preconditioned by experience. We propose that they share mechanisms with CSD in mammals suggesting a common evolutionary origin.
Nehra, Sarita; Bhardwaj, Varun; Bansal, Anju; Saraswat, Deepika
2017-09-26
Chronic hypobaric hypoxia (cHH) mediated cardiac insufficiencies are associated with pathological damage. Sustained redox stress and work load are major causative agents of cardiac insufficiencies under cHH. Despite the advancements made in pharmacological (anti-oxidants, vasodilators) and non-pharmacological therapeutics (acclimatization strategies and schedules), only partial success has been achieved in improving cardiac acclimatization to cHH. This necessitates the need for potent combinatorial therapies to improve cardiac acclimatization at high altitudes. We hypothesize that a combinatorial therapy comprising preconditioning to mild aerobic treadmill exercise and supplementation with nanocurcumin formulation (NCF) consisting of nanocurcumin (NC) and pyrroloquinoline quinone (PQQ) might improve cardiac adaptation at high altitudes. Adult Sprague-Dawley rats pre-conditioned to treadmill exercise and supplemented with NCF were exposed to cHH (7620 m altitude corresponding to pO2~8% at 28±2°C, relative humidity 55%±1%) for 3 weeks. The rat hearts were analyzed for changes in markers of oxidative stress (free radical leakage, lipid peroxidation, manganese-superoxide dismutase [MnSOD] activity), cardiac injury (circulating cardiac troponin I [TnI] and T [cTnT], myocardial creatine kinase [CK-MB]), metabolic damage (lactate dehydrogenase [LDH] and acetyl-coenzyme A levels, lactate and pyruvate levels) and bio-energetic insufficiency (ATP, p-AMPKα). Significant modulations (p≤0.05) in cardiac redox status, metabolic damage, cardiac injury and bio-energetics were observed in rats receiving both NCF supplementation and treadmill exercise-preconditioning compared with rats receiving only one of the treatments. The combinatorial therapeutic strategy showed a tremendous improvement in cardiac acclimatization to cHH compared to either exercise-preconditioning or NCF supplementation alone which was evident from the effective modulation in redox, metabolic, contractile
Portable, parallel, reusable Krylov space codes
Energy Technology Data Exchange (ETDEWEB)
Smith, B.; Gropp, W. [Argonne National Lab., IL (United States)
1994-12-31
Krylov space accelerators are an important component of many algorithms for the iterative solution of linear systems. Each Krylov space method has it`s own particular advantages and disadvantages, therefore it is desirable to have a variety of them available all with an identical, easy to use, interface. A common complaint application programmers have with available software libraries for the iterative solution of linear systems is that they require the programmer to use the data structures provided by the library. The library is not able to work with the data structures of the application code. Hence, application programmers find themselves constantly recoding the Krlov space algorithms. The Krylov space package (KSP) is a data-structure-neutral implementation of a variety of Krylov space methods including preconditioned conjugate gradient, GMRES, BiCG-Stab, transpose free QMR and CGS. Unlike all other software libraries for linear systems that the authors are aware of, KSP will work with any application codes data structures, in Fortran or C. Due to it`s data-structure-neutral design KSP runs unchanged on both sequential and parallel machines. KSP has been tested on workstations, the Intel i860 and Paragon, Thinking Machines CM-5 and the IBM SP1.
Amelioration of rCBF and PbtO2 following TBI at high altitude by hyperbaric oxygen pre-conditioning.
Hu, Shengli; Li, Fei; Luo, Haishui; Xia, Yongzhi; Zhang, Jiuquan; Hu, Rong; Cui, Gaoyu; Meng, Hui; Feng, Hua
2010-03-01
Hypobaric hypoxia at high altitude can lead to brain damage and pre-conditioning with hyperbaric oxygen (HBO) can reduce ischemic/hypoxic brain injury. This study investigates the effects of high altitude on traumatic brain injury (TBI) and examines the neuroprotection provided by HBO preconditioning against TBI. Rats were randomly divided into four groups: HBO pre-conditioning group (HBOP, n=10), high altitude group (HA, n=10), plain control group (PC, n=10) and plain sham operation group (sham, n=10). All groups were subjected to head trauma by weight drop device except for the sham group. Rats from each group were examined for neurological function, regional cerebral blood flow (rCBF) and brain tissue oxygen pressure (PbtO(2)) and were killed for analysis by transmission electron microscope. The score of neurological deficits in the HA group was highest, followed by the HBOP group and the PC group, respectively. Both rCBF and PbtO(2) were the lowest in the HA group. Brain morphology and structure seen via the transmission electron microscope was diminished in the HA group, while fewer pathological injuries occurred in the HBOP and PC groups. High altitude aggravates TBI significantly and HBO pre-conditioning can attenuate TBI in rats at high altitude by improvement of rCBF and PbtO(2). Pre-treatment with HBO might be beneficial for people traveling to high altitude locations.
Tahamtan, Mahshid; Allahtavakoli, Mohammad; Abbasnejad, Mehdi; Roohbakhsh, Ali; Taghipour, Zahra; Taghavi, Mohsen; Khodadadi, Hassan; Shamsizadeh, Ali
2013-12-01
There is evidence that exercise decreases ischemia/reperfusion injury in rats. Since behavioral deficits are the main outcome in patients after stroke, our study was designed to investigate whether exercise preconditioning improves the acute behavioral functions and also brain inflammatory injury following cerebral ischemia. Male rats weighing 250-300 g were randomly allocated into five experimental groups. Exercise was performed on a treadmill 30min/day for 3 weeks. Ischemia was induced by 4-vessel occlusion method. Recognition memory was assessed by novel object recognition task (NORT) and step-through passive avoidance task. Sensorimotor function and motor movements were evaluated by adhesive removal test and ledged beam-walking test, respectively. Brain inflammatory injury was evaluated by histological assessment. In NORT, the discrimination ratio was decreased after ischemia (P test, a significant reduction in response latency was observed in the ischemic group. Exercise preconditioning significantly decreased the response latency in the ischemic rats (P test, latency to touch and remove the sticky labels from forepaw was increased following induction of ischemia (all P beam-walking test, the slip ratio was increased following ischemia (P < 0.05). In the ischemia group, marked neuronal injury in hippocampus was observed. These neuropathological changes were attenuated by exercise preconditioning (P < 0.001). Our results showed that exercise preconditioning improves behavioral functions and maintains more viable cells in the dorsal hippocampus of the ischemic brain.
International Nuclear Information System (INIS)
Takeuchi, Toshiharu; Kikuchi, Kenjiro; Hasebe, Naoyuki; Ishii, Yoshinao
2011-01-01
Several animal experiments on acute myocardial infarction (AMI) have shown that the cardioprotective effects of ischemic preconditioning are more significant in hypertensive subjects. However, because there are no clinical data on the impact of hypertension on ischemic preconditioning in patients with AMI, whether clinical ischemic preconditioning of prodromal angina was beneficial in AMI patients with hypertension was investigated in the present study. 125 patients with a first anterior AMI who had undergone successful reperfusion therapy were divided into 2 groups, with or without hypertension, and into 2 further subgroups based on the presence or absence of prodromal angina. Dual-isotope (thallium-201(TL)/Tc-99m pyrophosphate) single-photon emission computed tomography (SPECT) was performed within 1 week of reperfusion therapy. Left ventricular (LV) function and LV mass index (LVMI) were measured by left ventriculography and echocardiography, respectively. In patients without hypertension, prodromal angina resulted in significantly less myocardial damage on TL-SPECT, better LV ejection fraction and a greater myocardial blush grade compared to patients without prodromal angina. However, these cardioprotective effects of prodromal angina were significantly diminished in hypertensive patients. Importantly, the myocardial salvage effects of prodromal angina showed a significant negative correlation with LVMI, which was significantly greater in hypertensive patients. The cardioprotective effects of prodromal angina were attenuated in patients with hypertension. Hypertensive LV hypertrophy may crucially limit the effects of ischemic preconditioning in AMI. (author)
International Nuclear Information System (INIS)
Ito, Satoshi; Kawawa, Yasuhiro; Yamada, Yoshifumi
2010-01-01
The signal obtained in the phase-scrambling Fourier transform (PSFT) imaging technique can be transformed to the signal described by the Fresnel transform of the objects, in which the amplitude of the PSFT presents some kind of blurred image of the objects. Therefore, the signal can be considered to exist in the object domain as well as the Fourier domain of the object. This notable feature makes it possible to assign weights to the reconstructed images by applying a weighting function to the PSFT signal after data acquisition, and as a result, pseudo-parallel image reconstruction using these aliased image data with different weights on the images is feasible. In this study, the improvements in image quality with such pseudo-parallel imaging were examined and demonstrated. The weighting function of the PSFT signal that provides a given weight on the image is estimated using the obtained image data and is iteratively updated after sensitivity encoding (SENSE)-based image reconstruction. Simulation studies showed that reconstruction errors were dramatically reduced and that the spatial resolution was also improved in almost all image spaces. The proposed method was applied to signals synthesized from MR image data with phase variations to verify its effectiveness. It was found that the image quality was improved and that images almost entirely free of aliasing artifacts could be obtained. (author)
International Nuclear Information System (INIS)
Chen, G.S.
1997-01-01
We apply and compare the preconditioned generalized conjugate gradient methods to solve the linear system equation that arises in the two-dimensional neutron and photon transport equation in this paper. Several subroutines are developed on the basis of preconditioned generalized conjugate gradient methods for time-independent, two-dimensional neutron and photon transport equation in the transport theory. These generalized conjugate gradient methods are used. TFQMR (transpose free quasi-minimal residual algorithm), CGS (conjuage gradient square algorithm), Bi-CGSTAB (bi-conjugate gradient stabilized algorithm) and QMRCGSTAB (quasi-minimal residual variant of bi-conjugate gradient stabilized algorithm). These sub-routines are connected to computer program DORT. Several problems are tested on a personal computer with Intel Pentium CPU. (author)
Convergence Analysis for the Multiplicative Schwarz Preconditioned Inexact Newton Algorithm
Liu, Lulu
2016-10-26
The multiplicative Schwarz preconditioned inexact Newton (MSPIN) algorithm, based on decomposition by field type rather than by subdomain, was recently introduced to improve the convergence of systems with unbalanced nonlinearities. This paper provides a convergence analysis of the MSPIN algorithm. Under reasonable assumptions, it is shown that MSPIN is locally convergent, and desired superlinear or even quadratic convergence can be obtained when the forcing terms are picked suitably.
Convergence Analysis for the Multiplicative Schwarz Preconditioned Inexact Newton Algorithm
Liu, Lulu; Keyes, David E.
2016-01-01
The multiplicative Schwarz preconditioned inexact Newton (MSPIN) algorithm, based on decomposition by field type rather than by subdomain, was recently introduced to improve the convergence of systems with unbalanced nonlinearities. This paper provides a convergence analysis of the MSPIN algorithm. Under reasonable assumptions, it is shown that MSPIN is locally convergent, and desired superlinear or even quadratic convergence can be obtained when the forcing terms are picked suitably.
Electroacupuncture preconditioning reduces cerebral ischemic injury via BDNF and SDF-1α in mice
Directory of Open Access Journals (Sweden)
Kim Ji Hyun
2013-01-01
Full Text Available Abstract Background This study was designed to determine if electroacupuncture (EA preconditioning improves tissue outcome and functional outcome following experimentally induced cerebral ischemia in mice. In addition, we investigated whether the expression of brain-derived neurotrophic factor (BDNF and stromal cell derived factor-1α (SDF-1α and infarct volume were related with improvement in neurological and motor function by interventions in this study. Methods After treatment with EA at the acupoints ‘Baihui (GV20’ and ‘Dazhui (GV14’ for 20 min, BDNF was assessed in the cortical tissues based on Western blot and the SDF-1α and vascular endothelial growth factor (VEGF levels in the plasma determined by ELISA. To assess the protective effects of EA against ischemic injury, the mice received once a day 20 min EA preconditioning for three days prior to the ischemic event. Focal cerebral ischemia was then induced by photothrombotic cortical ischemia. Infarct volumes, neurobehavioral deficit and motor deficit were evaluated 24 h after focal cerebral ischemia. Results The expression of BDNF protein increased significantly from 6 h, reaching a plateau at 12 h after the end of EA treatment in the cerebral cortex. Furthermore, SDF-1α, not VEGF, increased singnificantly from 12 h to 48 h after EA stimulation in the plasma. Moreover, EA preconditioning reduced the infarct volume by 43.5% when compared to control mice at 24 h after photothrombotic cortical ischemia. Consistent with a smaller infarct size, EA preconditioning showed prominent improvement of neurological function and motor function such as vestibule-motor function, sensori-motor function and asymmetric forelimb use. The expression of BDNF colocalized within neurons and SDF-1α colocalized within the cerebral vascular endothelium was observed throughout the ischemic cortex by EA. Conclusions Pretreatment with EA increased the production of BDNF and SDF-1α, which elicited
A systematic approach to robust preconditioning for gradient-based inverse scattering algorithms
International Nuclear Information System (INIS)
Nordebo, Sven; Fhager, Andreas; Persson, Mikael; Gustafsson, Mats
2008-01-01
This paper presents a systematic approach to robust preconditioning for gradient-based nonlinear inverse scattering algorithms. In particular, one- and two-dimensional inverse problems are considered where the permittivity and conductivity profiles are unknown and the input data consist of the scattered field over a certain bandwidth. A time-domain least-squares formulation is employed and the inversion algorithm is based on a conjugate gradient or quasi-Newton algorithm together with an FDTD-electromagnetic solver. A Fisher information analysis is used to estimate the Hessian of the error functional. A robust preconditioner is then obtained by incorporating a parameter scaling such that the scaled Fisher information has a unit diagonal. By improving the conditioning of the Hessian, the convergence rate of the conjugate gradient or quasi-Newton methods are improved. The preconditioner is robust in the sense that the scaling, i.e. the diagonal Fisher information, is virtually invariant to the numerical resolution and the discretization model that is employed. Numerical examples of image reconstruction are included to illustrate the efficiency of the proposed technique
International Nuclear Information System (INIS)
Petridis, C.; Ries, T.; Cramer, M.C.; Graessner, J.; Petersen, K.U.; Reitmeier, F.; Jaehne, M.; Weiss, F.; Adam, G.; Habermann, C.R.
2007-01-01
Purpose: To evaluate an ultra-fast sequence for MR sialography requiring no post-processing and to compare the acquisition technique regarding the effect of oral stimulation with a parallel acquisition technique in patients with salivary gland diseases. Materials and Methods: 128 patients with salivary gland disease were prospectively examined using a 1.5-T superconducting system with a 30 mT/m maximum gradient capability and a maximum slew rate of 125 mT/m/sec. A single-shot turbo-spin-echo sequence (ss-TSE) with an acquisition time of 2.8 sec was used in transverse and oblique sagittal orientation. All images were obtained with and without a parallel imaging technique. The evaluation of the ductal system of the parotid and submandibular gland was performed using a visual scale of 1-5 for each side. The images were assessed by two independent experienced radiologists. An ANOVA with posthoc comparisons and an overall two tailed significance level of p=0.05 was used for the statistical evaluation. An intraclass correlation was computed to evaluate interobserver variability and a correlation of >0.8 was determined, thereby indicating a high correlation. Results: Depending on the diagnosed diseases and the absence of abruption of the ducts, all parts of excretory ducts were able to be visualized in all patients using the developed technique with an overall rating for all ducts of 2.70 (SD±0.89). A high correlation was achieved between the two observers with an intraclass correlation of 0.73. Oral application of a sialogogum improved the visibility of excretory ducts significantly (p<0.001). In contrast, the use of a parallel imaging technique led to a significant decrease in image quality (p=0,011). (orig.)
Hosseini, S.M.; Wilson, W.; Ito, K.; Donkelaar, van C.C.
2014-01-01
It is known that initial loading curves of soft biological tissues are substantially different from subsequent loadings. The later loading curves are generally used for assessing the mechanical properties of a tissue, and the first loading cycles, referred to as preconditioning, are omitted.
Valdés, Felipe
2011-06-01
A new regularized single source equation for analyzing scattering from homogeneous penetrable objects is presented. The proposed equation is a linear combination of a Calderón-preconditioned single source electric field integral equation and a single source magnetic field integral equation. The equation is immune to low-frequency and dense-mesh breakdown, and free from spurious resonances. Unlike dual source formulations, this equation involves operator products that cannot be discretized using standard procedures for discretizing standalone electric, magnetic, and combined field operators. Instead, the single source equation proposed here is discretized using a recently developed technique that achieves a well-conditioned mapping from div- to curl-conforming function spaces, thereby fully respecting the space mapping properties of the operators involved, and guaranteeing accuracy and stability. Numerical results show that the proposed equation and discretization technique give rise to rapidly convergent solutions. They also validate the equation\\'s resonant free character. © 2006 IEEE.
Preconditioning 2D Integer Data for Fast Convex Hull Computations.
Cadenas, José Oswaldo; Megson, Graham M; Luengo Hendriks, Cris L
2016-01-01
In order to accelerate computing the convex hull on a set of n points, a heuristic procedure is often applied to reduce the number of points to a set of s points, s ≤ n, which also contains the same hull. We present an algorithm to precondition 2D data with integer coordinates bounded by a box of size p × q before building a 2D convex hull, with three distinct advantages. First, we prove that under the condition min(p, q) ≤ n the algorithm executes in time within O(n); second, no explicit sorting of data is required; and third, the reduced set of s points forms a simple polygonal chain and thus can be directly pipelined into an O(n) time convex hull algorithm. This paper empirically evaluates and quantifies the speed up gained by preconditioning a set of points by a method based on the proposed algorithm before using common convex hull algorithms to build the final hull. A speedup factor of at least four is consistently found from experiments on various datasets when the condition min(p, q) ≤ n holds; the smaller the ratio min(p, q)/n is in the dataset, the greater the speedup factor achieved.
Moving force identification based on modified preconditioned conjugate gradient method
Chen, Zhen; Chan, Tommy H. T.; Nguyen, Andy
2018-06-01
This paper develops a modified preconditioned conjugate gradient (M-PCG) method for moving force identification (MFI) by improving the conjugate gradient (CG) and preconditioned conjugate gradient (PCG) methods with a modified Gram-Schmidt algorithm. The method aims to obtain more accurate and more efficient identification results from the responses of bridge deck caused by vehicles passing by, which are known to be sensitive to ill-posed problems that exist in the inverse problem. A simply supported beam model with biaxial time-varying forces is used to generate numerical simulations with various analysis scenarios to assess the effectiveness of the method. Evaluation results show that regularization matrix L and number of iterations j are very important influence factors to identification accuracy and noise immunity of M-PCG. Compared with the conventional counterpart SVD embedded in the time domain method (TDM) and the standard form of CG, the M-PCG with proper regularization matrix has many advantages such as better adaptability and more robust to ill-posed problems. More importantly, it is shown that the average optimal numbers of iterations of M-PCG can be reduced by more than 70% compared with PCG and this apparently makes M-PCG a preferred choice for field MFI applications.
Using Motivational Interviewing Techniques to Address Parallel Process in Supervision
Giordano, Amanda; Clarke, Philip; Borders, L. DiAnne
2013-01-01
Supervision offers a distinct opportunity to experience the interconnection of counselor-client and counselor-supervisor interactions. One product of this network of interactions is parallel process, a phenomenon by which counselors unconsciously identify with their clients and subsequently present to their supervisors in a similar fashion…
An environment for parallel structuring of Fortran programs
International Nuclear Information System (INIS)
Sridharan, K.; McShea, M.; Denton, C.; Eventoff, B.; Browne, J.C.; Newton, P.; Ellis, M.; Grossbard, D.; Wise, T.; Clemmer, D.
1990-01-01
The paper describes and illustrates an environment for interactive support of the detection and implementation of macro-level parallelism in Fortran programs. The approach couples algorithms for dependence analysis with both innovative techniques for complexity management and capabilities for the measurement and analysis of the parallel computation structures generated through use of the environment. The resulting environment is complementary to the more common approach of seeking local parallelism by loop unrolling, either by an automatic compiler or manually. (orig.)
On a model of three-dimensional bursting and its parallel implementation
Tabik, S.; Romero, L. F.; Garzón, E. M.; Ramos, J. I.
2008-04-01
A mathematical model for the simulation of three-dimensional bursting phenomena and its parallel implementation are presented. The model consists of four nonlinearly coupled partial differential equations that include fast and slow variables, and exhibits bursting in the absence of diffusion. The differential equations have been discretized by means of a second-order accurate in both space and time, linearly-implicit finite difference method in equally-spaced grids. The resulting system of linear algebraic equations at each time level has been solved by means of the Preconditioned Conjugate Gradient (PCG) method. Three different parallel implementations of the proposed mathematical model have been developed; two of these implementations, i.e., the MPI and the PETSc codes, are based on a message passing paradigm, while the third one, i.e., the OpenMP code, is based on a shared space address paradigm. These three implementations are evaluated on two current high performance parallel architectures, i.e., a dual-processor cluster and a Shared Distributed Memory (SDM) system. A novel representation of the results that emphasizes the most relevant factors that affect the performance of the paralled implementations, is proposed. The comparative analysis of the computational results shows that the MPI and the OpenMP implementations are about twice more efficient than the PETSc code on the SDM system. It is also shown that, for the conditions reported here, the nonlinear dynamics of the three-dimensional bursting phenomena exhibits three stages characterized by asynchronous, synchronous and then asynchronous oscillations, before a quiescent state is reached. It is also shown that the fast system reaches steady state in much less time than the slow variables.
Comparison results on preconditioned SOR-type iterative method for Z-matrices linear systems
Wang, Xue-Zhong; Huang, Ting-Zhu; Fu, Ying-Ding
2007-09-01
In this paper, we present some comparison theorems on preconditioned iterative method for solving Z-matrices linear systems, Comparison results show that the rate of convergence of the Gauss-Seidel-type method is faster than the rate of convergence of the SOR-type iterative method.
Calibrationless Parallel Magnetic Resonance Imaging: A Joint Sparsity Model
Directory of Open Access Journals (Sweden)
Angshul Majumdar
2013-12-01
Full Text Available State-of-the-art parallel MRI techniques either explicitly or implicitly require certain parameters to be estimated, e.g., the sensitivity map for SENSE, SMASH and interpolation weights for GRAPPA, SPIRiT. Thus all these techniques are sensitive to the calibration (parameter estimation stage. In this work, we have proposed a parallel MRI technique that does not require any calibration but yields reconstruction results that are at par with (or even better than state-of-the-art methods in parallel MRI. Our proposed method required solving non-convex analysis and synthesis prior joint-sparsity problems. This work also derives the algorithms for solving them. Experimental validation was carried out on two datasets—eight channel brain and eight channel Shepp-Logan phantom. Two sampling methods were used—Variable Density Random sampling and non-Cartesian Radial sampling. For the brain data, acceleration factor of 4 was used and for the other an acceleration factor of 6 was used. The reconstruction results were quantitatively evaluated based on the Normalised Mean Squared Error between the reconstructed image and the originals. The qualitative evaluation was based on the actual reconstructed images. We compared our work with four state-of-the-art parallel imaging techniques; two calibrated methods—CS SENSE and l1SPIRiT and two calibration free techniques—Distributed CS and SAKE. Our method yields better reconstruction results than all of them.
Parallel fuzzy connected image segmentation on GPU
Zhuge, Ying; Cao, Yong; Udupa, Jayaram K.; Miller, Robert W.
2011-01-01
Purpose: Image segmentation techniques using fuzzy connectedness (FC) principles have shown their effectiveness in segmenting a variety of objects in several large applications. However, one challenge in these algorithms has been their excessive computational requirements when processing large image datasets. Nowadays, commodity graphics hardware provides a highly parallel computing environment. In this paper, the authors present a parallel fuzzy connected image segmentation algorithm impleme...
Directory of Open Access Journals (Sweden)
Meisam Shahhoseini
2017-01-01
Full Text Available Objective(s:Every year, a large number of people lose their lives due to stroke. Stroke is the second leading cause of death worldwide. Surprisingly, recent studies have shown that preconditioning with hyperoxia (HO increases tissue tolerance to ischemia, ultimately reducing damages caused by stroke. Addressed in this study are beneficial contributions from HO preconditioning into reduced harm to be incurred by the attack, as well as its effect on the expression levels of vascular endothelial growth factor (VEGF and endostatin. Materials and Methods: A set of experiments was conducted where a number of rats were divided into three groups. The animals in the first group received 90% oxygen for 4 hr a day, for 6 days. The second group was housed in room air and the third group was a sham (surgical stress. After 60 min of ischemia, 24 hr blood flow, neurological deficit score (NDS and infarct volume (IV in the group MCAO (Middle Cerebral Artery Occlusion were investigated. Immediately following a 48 hr HO pre-treatment, sampling was performed to measure the expression levels of VEGF and endostatin. Results: Preconditioning with alternating HO led to reduced infarct volume and NDS. Moreover, pre-treatment with HO resulted in increased VEGF expression while decreasing endostatin. Conclusion: Although further studies are deemed necessary to clarify the mechanisms of ischemic tolerance, apparently, somewhat intermittent hyperoxia can be associated with positive impacts by increasing VEGF and decreasing expression of endostatin.
Czech Academy of Sciences Publication Activity Database
Axelsson, Owe; Farouq, S.; Neytcheva, M.
2017-01-01
Roč. 74, č. 1 (2017), s. 19-37 ISSN 1017-1398 Institutional support: RVO:68145535 Keywords : PDE-constrained optimization problems * finite elements * iterative solution methods * preconditioning Subject RIV: BA - General Mathematics OBOR OECD: Applied mathematics Impact factor: 1.241, year: 2016 https://link.springer.com/article/10.1007%2Fs11075-016-0136-5
Integrative Dynamic Reconfiguration in a Parallel Stream Processing Engine
DEFF Research Database (Denmark)
Madsen, Kasper Grud Skat; Zhou, Yongluan; Cao, Jianneng
2017-01-01
Load balancing, operator instance collocations and horizontal scaling are critical issues in Parallel Stream Processing Engines to achieve low data processing latency, optimized cluster utilization and minimized communication cost respectively. In previous work, these issues are typically tackled...... solution called ALBIC, which support general jobs. We implement the proposed techniques on top of Apache Storm, an open-source Parallel Stream Processing Engine. The extensive experimental results over both synthetic and real datasets show that our techniques clearly outperform existing approaches....
Massively parallel multicanonical simulations
Gross, Jonathan; Zierenberg, Johannes; Weigel, Martin; Janke, Wolfhard
2018-03-01
Generalized-ensemble Monte Carlo simulations such as the multicanonical method and similar techniques are among the most efficient approaches for simulations of systems undergoing discontinuous phase transitions or with rugged free-energy landscapes. As Markov chain methods, they are inherently serial computationally. It was demonstrated recently, however, that a combination of independent simulations that communicate weight updates at variable intervals allows for the efficient utilization of parallel computational resources for multicanonical simulations. Implementing this approach for the many-thread architecture provided by current generations of graphics processing units (GPUs), we show how it can be efficiently employed with of the order of 104 parallel walkers and beyond, thus constituting a versatile tool for Monte Carlo simulations in the era of massively parallel computing. We provide the fully documented source code for the approach applied to the paradigmatic example of the two-dimensional Ising model as starting point and reference for practitioners in the field.
Effects Of Ischemic Preconditioning On The Renal Ischemia- Reperfusion Injury
Directory of Open Access Journals (Sweden)
Anyamanesh S
2003-07-01
Full Text Available During kidney and other organ transplantation, the organ to be transplanted, must inevitably remain out of the body with little or no blood perfusion at all for a long period of time (ischemia. These events have been suggested to cause the formation of oxygen- derived free radicals (OFR. Reperfusion (reintroduction of blood flow will further exacerbate the initial damage caused by the ischemic insult and may result in the production of free radicals. The aim of this study was to investigate whether induction of brief periods of renal artery occlusion (ischemic pre¬conditioning, IPC can provide protection from the effects of a subsequent period of ischemia and reperfusion (IR in the rat kidney."nMaterials and Methods: In this regard, 28 white, male rats were randomly and equally divided into four groups: Control (sham- operated, IPC alone, IR alone (30 min ischemia followed by 10 min reperfusion, and IPC- IR. Preconditioning involved the sequential clamping of the right renal artery for 5 min and declamping for 5 min for a total of 3 cycles. To demonstrate the effectiveness of IPC regimen, vitamin E as an endogenous antioxidant and an index of lipid peroxidation was measured by HPLC after its extraction from right renal venous plasma and right renal tissue."nResults: Results of this study showed that the amount of vitamin E of renal tissue and venous plasma in the IR group had a significant decrease when compared to the control group (P< 0.0001. Whereas the amount of this vitamin in both renal tissue and venous plasma of the IPC- IR group was significantly higher than that in the IR group (P< 0.0001, but did not show any significant difference with the control group."nConclusion: In this study, preconditioning method prevented the reduction of the endogenous antioxidant (Vit. E in encountering the following sustained ischemic insult. Therefore, we suggest that ischemic preconditioning can be used to protect the Vit. E level of kidney from its
Parallel visualization on leadership computing resources
Energy Technology Data Exchange (ETDEWEB)
Peterka, T; Ross, R B [Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439 (United States); Shen, H-W [Department of Computer Science and Engineering, Ohio State University, Columbus, OH 43210 (United States); Ma, K-L [Department of Computer Science, University of California at Davis, Davis, CA 95616 (United States); Kendall, W [Department of Electrical Engineering and Computer Science, University of Tennessee at Knoxville, Knoxville, TN 37996 (United States); Yu, H, E-mail: tpeterka@mcs.anl.go [Sandia National Laboratories, California, Livermore, CA 94551 (United States)
2009-07-01
Changes are needed in the way that visualization is performed, if we expect the analysis of scientific data to be effective at the petascale and beyond. By using similar techniques as those used to parallelize simulations, such as parallel I/O, load balancing, and effective use of interprocess communication, the supercomputers that compute these datasets can also serve as analysis and visualization engines for them. Our team is assessing the feasibility of performing parallel scientific visualization on some of the most powerful computational resources of the U.S. Department of Energy's National Laboratories in order to pave the way for analyzing the next generation of computational results. This paper highlights some of the conclusions of that research.
Parallel optoelectronic trinary signed-digit division
Alam, Mohammad S.
1999-03-01
The trinary signed-digit (TSD) number system has been found to be very useful for parallel addition and subtraction of any arbitrary length operands in constant time. Using the TSD addition and multiplication modules as the basic building blocks, we develop an efficient algorithm for performing parallel TSD division in constant time. The proposed division technique uses one TSD subtraction and two TSD multiplication steps. An optoelectronic correlator based architecture is suggested for implementation of the proposed TSD division algorithm, which fully exploits the parallelism and high processing speed of optics. An efficient spatial encoding scheme is used to ensure better utilization of space bandwidth product of the spatial light modulators used in the optoelectronic implementation.
Parallel visualization on leadership computing resources
International Nuclear Information System (INIS)
Peterka, T; Ross, R B; Shen, H-W; Ma, K-L; Kendall, W; Yu, H
2009-01-01
Changes are needed in the way that visualization is performed, if we expect the analysis of scientific data to be effective at the petascale and beyond. By using similar techniques as those used to parallelize simulations, such as parallel I/O, load balancing, and effective use of interprocess communication, the supercomputers that compute these datasets can also serve as analysis and visualization engines for them. Our team is assessing the feasibility of performing parallel scientific visualization on some of the most powerful computational resources of the U.S. Department of Energy's National Laboratories in order to pave the way for analyzing the next generation of computational results. This paper highlights some of the conclusions of that research.
Language constructs for modular parallel programs
Energy Technology Data Exchange (ETDEWEB)
Foster, I.
1996-03-01
We describe programming language constructs that facilitate the application of modular design techniques in parallel programming. These constructs allow us to isolate resource management and processor scheduling decisions from the specification of individual modules, which can themselves encapsulate design decisions concerned with concurrence, communication, process mapping, and data distribution. This approach permits development of libraries of reusable parallel program components and the reuse of these components in different contexts. In particular, alternative mapping strategies can be explored without modifying other aspects of program logic. We describe how these constructs are incorporated in two practical parallel programming languages, PCN and Fortran M. Compilers have been developed for both languages, allowing experimentation in substantial applications.
Czech Academy of Sciences Publication Activity Database
Axelsson, Owe; Farouq, S.; Neytcheva, M.
2017-01-01
Roč. 74, č. 1 (2017), s. 19-37 ISSN 1017-1398 Institutional support: RVO:68145535 Keywords : PDE-constrained optimization problems * finite elements * iterative solution method s * preconditioning Subject RIV: BA - General Mathematics OBOR OECD: Applied mathematics Impact factor: 1.241, year: 2016 https://link.springer.com/article/10.1007%2Fs11075-016-0136-5
Shao, Guo; Zhou, Wei-Hua; Gao, Cui-Ying; Zhang, Ran; Lu, Guo-Wei
2007-02-01
To observe change of binding activity of HIF-1 with erythropoietin (EPO) hypoxia response element (HRE) in the hippocampus of mice preconditioned to hypoxia and explore relationship between the changes and the preconditioning. The hippocampus was removed from mice exposed to hypoxia for 0 run (control group), 1 run (H1 group) and 4 runs(H4 group). Electrophoretic mobility shift assays (EMSA), chromatin immunoprecipitation (ChIP)and real time PCR were used to detect the change of activity of HIF-1 on HRE of EPO. Both in vitro and in vivo binding tests showed that the HIF-1 DNA-binding activities were increased in group H1 and markedly increased in group H4. The increase of HIF-1 and HRE of EPO binding activities is thought be involved in hypoxic preconditioning.
On the use of rigid body modes in the deflated preconditioned conjugate gradient method
Jönsthövel, T.B.; Van Gijzen, M.B.; Vuik, C.; Scarpas, A.
2011-01-01
Large discontinuities in material properties, such as encountered in composite materials, lead to ill-conditioned systems of linear equations. These discontinuities give rise to small eigenvalues that may negatively affect the convergence of iterative solution methods such as the Preconditioned
Fräßdorf, Jan; Huhn, Ragnar; Weber, Nina C.; Ebel, Dirk; Wingert, Nadja; Preckel, Benedikt; Toma, Octavian; Schlack, Wolfgang; Hollmann, Markus W.
2010-01-01
Background Sevoflurane induces preconditioning (SevoPC) 1 he effect of aprotinin and the involvement of endothelial nitric-oxide synthase (NOS) on SevoPC are unknown We investigated (1) whether SevoPC is strengthened by multiple preconditioning cycles (2) whether SevoPC is blocked by aprotinin, and
International Nuclear Information System (INIS)
Bylaska, Eric J.; Weare, Jonathan Q.; Weare, John H.
2013-01-01
Parallel in time simulation algorithms are presented and applied to conventional molecular dynamics (MD) and ab initio molecular dynamics (AIMD) models of realistic complexity. Assuming that a forward time integrator, f (e.g., Verlet algorithm), is available to propagate the system from time t i (trajectory positions and velocities x i = (r i , v i )) to time t i+1 (x i+1 ) by x i+1 = f i (x i ), the dynamics problem spanning an interval from t 0 …t M can be transformed into a root finding problem, F(X) = [x i − f(x (i−1 )] i =1,M = 0, for the trajectory variables. The root finding problem is solved using a variety of root finding techniques, including quasi-Newton and preconditioned quasi-Newton schemes that are all unconditionally convergent. The algorithms are parallelized by assigning a processor to each time-step entry in the columns of F(X). The relation of this approach to other recently proposed parallel in time methods is discussed, and the effectiveness of various approaches to solving the root finding problem is tested. We demonstrate that more efficient dynamical models based on simplified interactions or coarsening time-steps provide preconditioners for the root finding problem. However, for MD and AIMD simulations, such preconditioners are not required to obtain reasonable convergence and their cost must be considered in the performance of the algorithm. The parallel in time algorithms developed are tested by applying them to MD and AIMD simulations of size and complexity similar to those encountered in present day applications. These include a 1000 Si atom MD simulation using Stillinger-Weber potentials, and a HCl + 4H 2 O AIMD simulation at the MP2 level. The maximum speedup ((serial execution time)/(parallel execution time) ) obtained by parallelizing the Stillinger-Weber MD simulation was nearly 3.0. For the AIMD MP2 simulations, the algorithms achieved speedups of up to 14.3. The parallel in time algorithms can be implemented in a
Compiling Scientific Programs for Scalable Parallel Systems
National Research Council Canada - National Science Library
Kennedy, Ken
2001-01-01
...). The research performed in this project included new techniques for recognizing implicit parallelism in sequential programs, a powerful and precise set-based framework for analysis and transformation...
Z-buffer image assembly processing in high parallel visualization processing
International Nuclear Information System (INIS)
Kaneko, Isamu; Muramatsu, Kazuhiro
2000-03-01
On the platform of the parallel computer with many processors, the domain decomposition method is used as a popular means of parallel processing. In these days when the simulation scale becomes much larger and takes a lot of time, the simultaneous visualization processing with the actual computation is much more needed, and especially in case of a real-time visualization, the domain decomposition technique is indispensable. In case of parallel rendering processing, the rendered results must be gathered to one processor to compose the integrated picture in the last stage. This integration is usually conducted by the method using Z-buffer values. This process, however, induces the crucial problems of much lower speed processing and local memory shortage in case of parallel processing exceeding more than several tens of processors. In this report, the two new solutions are proposed. The one is the adoption of a special operator (Reduce operator) in the parallelization process, and the other is a buffer compression by deleting the background informations. This report includes the performance results of these new techniques to investigate their effect with use of the parallel computer Paragon. (author)
Czech Academy of Sciences Publication Activity Database
Kouhia, R.; Tůma, Miroslav; Mäkinen, J.; Fedoroff, A.; Marjamäki, H.
108-109, October (2012), s. 110-117 ISSN 0045-7949 R&D Projects: GA ČR(CZ) GAP108/11/0853 Institutional research plan: CEZ:AV0Z10300504 Keywords : non-linear eigenvalue problem * equilibrium equations * critical points * preconditioned iterations Subject RIV: BA - General Mathematics Impact factor: 1.509, year: 2012
Mitochondrial cyclophilin-D as a critical mediator of ischaemic preconditioning
Hausenloy, Derek J.; Lim, Shiang Y.; Ong, Sang-Ging; Davidson, Sean M.; Yellon, Derek M.
2010-01-01
Aims It has been suggested that mitochondrial reactive oxygen species (ROS), Akt and Erk1/2 and more recently the mitochondrial permeability transition pore (mPTP) may act as mediators of ischaemic preconditioning (IPC), although the actual interplay between these mediators is unclear. The aim of the present study is to determine whether the cyclophilin-D (CYPD) component of the mPTP is required by IPC to generate mitochondrial ROS and subsequently activate Akt and Erk1/2. Methods and results...
Portable parallel programming in a Fortran environment
International Nuclear Information System (INIS)
May, E.N.
1989-01-01
Experience using the Argonne-developed PARMACs macro package to implement a portable parallel programming environment is described. Fortran programs with intrinsic parallelism of coarse and medium granularity are easily converted to parallel programs which are portable among a number of commercially available parallel processors in the class of shared-memory bus-based and local-memory network based MIMD processors. The parallelism is implemented using standard UNIX (tm) tools and a small number of easily understood synchronization concepts (monitors and message-passing techniques) to construct and coordinate multiple cooperating processes on one or many processors. Benchmark results are presented for parallel computers such as the Alliant FX/8, the Encore MultiMax, the Sequent Balance, the Intel iPSC/2 Hypercube and a network of Sun 3 workstations. These parallel machines are typical MIMD types with from 8 to 30 processors, each rated at from 1 to 10 MIPS processing power. The demonstration code used for this work is a Monte Carlo simulation of the response to photons of a ''nearly realistic'' lead, iron and plastic electromagnetic and hadronic calorimeter, using the EGS4 code system. 6 refs., 2 figs., 2 tabs
de la Barca, Juan Manuel Chao; Huang, Nuan-Ting; Jiao, Haihan; Tessier, Lydie; Gadras, Cédric; Simard, Gilles; Natoli, Riccardo; Tcherkez, Guillaume; Reynier, Pascal; Valter, Krisztina
2017-01-01
Light is the primary stimulus for vision, but may also cause damage to the retina. Pre-exposing the retina to sub-lethal amount of light (or preconditioning) improves chances for retinal cells to survive acute damaging light stress. This study aims at exploring the changes in retinal metabolome after mild light stress and identifying mechanisms that may be involved in preconditioning. Retinas from 12 rats exposed to mild light stress (1000 lux × for 12 h) and 12 controls were collected one and seven days after light stress (LS). One retina was used for targeted metabolomics analysis using the Biocrates p180 kit while the fellow retina was used for histological and immunohistochemistry analysis. Immunohistochemistry confirmed that in this experiment, a mild LS with retinal immune response and minimal photoreceptor loss occurred. Compared to controls, LS induced an increased concentration in phosphatidylcholines. The concentration in some amino acids and biogenic amines, particularly those related to the nitric oxide pathway (like asymmetric dimethylarginine (ADMA), arginine and citrulline) also increased 1 day after LS. 7 days after LS, the concentration in two sphingomyelins and phenylethylamine was found to be higher. We further found that in controls, retina metabolome was different between males and females: male retinas had an increased concentration in tyrosine, acetyl-ornithine, phosphatidylcholines and (acyl)-carnitines. Besides retinal sexual metabolic dimorphism, this study shows that preconditioning is mostly associated with re-organisation of lipid metabolism and changes in amino acid composition, likely reflecting the involvement of arginine-dependent NO signalling.
International Nuclear Information System (INIS)
Rosa, M.; Warsa, J. S.; Chang, J. H.
2006-01-01
A Fourier analysis is conducted for the discrete-ordinates (SN) approximation of the neutron transport problem solved with Richardson iteration (Source Iteration) and Richardson iteration preconditioned with Transport Synthetic Acceleration (TSA), using the Parallel Block-Jacobi (PBJ) algorithm. Both 'traditional' TSA (TTSA) and a 'modified' TSA (MTSA), in which only the scattering in the low order equations is reduced by some non-negative factor β and < 1, are considered. The results for the un-accelerated algorithm show that convergence of the PBJ algorithm can degrade. The PBJ algorithm with TTSA can be effective provided the β parameter is properly tuned for a given scattering ratio c, but is potentially unstable. Compared to TTSA, MTSA is less sensitive to the choice of β, more effective for the same computational effort (c'), and it is unconditionally stable. (authors)
On the Automatic Parallelization of Sparse and Irregular Fortran Programs
Directory of Open Access Journals (Sweden)
Yuan Lin
1999-01-01
Full Text Available Automatic parallelization is usually believed to be less effective at exploiting implicit parallelism in sparse/irregular programs than in their dense/regular counterparts. However, not much is really known because there have been few research reports on this topic. In this work, we have studied the possibility of using an automatic parallelizing compiler to detect the parallelism in sparse/irregular programs. The study with a collection of sparse/irregular programs led us to some common loop patterns. Based on these patterns new techniques were derived that produced good speedups when manually applied to our benchmark codes. More importantly, these parallelization methods can be implemented in a parallelizing compiler and can be applied automatically.
Ara, Jahan; De Montpellier, Sybille
2013-09-01
Perinatal hypoxia-ischemia (HI) results in brain injury, whereas mild hypoxic episodes result in preconditioning, which can significantly reduce the vulnerability of the brain to subsequent severe hypoxia-ischemia. Hypoxic-preconditioning (PC) has been shown to enhance cell survival and differentiation of progenitor cells in the central nervous system (CNS). The purpose of this study was to determine whether pretreatment with PC prior to HI stimulates subventricular zone (SVZ) proliferation and neurogenesis in newborn piglets. One-day-old piglets were subjected to PC (8% O2/92% N2) for 3h and 24h later were exposed to HI produced by combination of hypoxia (5% FiO2) for a pre-defined period of 30min and ischemia induced by a period of 10min of hypotension. Here we demonstrate that SVZ derived neural stem/progenitor cells (NSPs) from PC, HI and PC+HI piglets proliferated as neurospheres, expressed neural progenitor and neurodevelopmental markers, and that greater proportion of the spheres generated are multipotential. Neurosphere assay revealed that preconditioning pretreatment increased the number of NSP-derived neurospheres in SVZ following HI compared to normoxic and HI controls. NSPs from preconditioned SVZ generated twice as many neurons and astrocytes in vitro. Injections with 5-Bromo-2-deoxyuridine (BrdU) after PC revealed a robust proliferative response within the SVZ that continued for one week. PC also increased neurogenesis in vivo, doublecortin positive cells with migratory profiles were observed streaming from the SVZ to striatum and neocortex. These findings show that the induction of proliferation and neurogenesis by PC might be a positive adaptation for an efficient repair and plasticity in the event of a hypoxic-ischemic insult. Copyright © 2013 Elsevier B.V. All rights reserved.
Butt, Hira; Mehmood, Azra; Ali, Muhammad; Tasneem, Saba; Anjum, Muhammad Sohail; Tarar, Moazzam N; Khan, Shaheen N; Riazuddin, Sheikh
2017-09-01
Oxidative microenvironment of burnt skin restricts the outcome of cell based therapies of thermal skin injuries. The aim of this study was to precondition human dermal fibroblasts with an antioxidant such as vitamin E to improve their survival and therapeutic abilities in heat induced oxidative in vitro environment. Fibroblasts were treated with 100μM vitamin E for 24h at 37°C followed by heat shock for 10min at 51°C in fresh serum free medium. Preconditioning with vitamin E reduced cell injury as demonstrated by decreased expression of annexin-V, cytochrome p450 (CYP450) mediated oxidative reactions, senescence and release of lactate dehydrogenase (LDH) accomplished by down-regulated expression of pro-apoptotic BAX gene. Vitamin E preconditioned cells exhibited remarkable improvement in cell viability, release of paracrine factors such as epidermal growth factor (EGF), basic fibroblast growth factor (bFGF), vascular endothelial growth factor (VEGF), stromal derived factor-1alpha (SDF-1α) and also showed significantly up-regulated levels of PCNA, VEGF, BCL-XL, FGF7, FGF23, FLNβ and Col7α genes presumably through activation of phosphatidylinositol 3-kinase (PI3-K)/Akt pathway. The results suggest that pretreatment of fibroblasts with vitamin E prior to transplantation in burnt skin speeds up the wound healing process by improving the antioxidant scavenging responses in oxidative environment of transplanted burn wounds. Copyright © 2017 Elsevier Inc. All rights reserved.
Automatic parallelization of while-Loops using speculative execution
International Nuclear Information System (INIS)
Collard, J.F.
1995-01-01
Automatic parallelization of imperative sequential programs has focused on nests of for-loops. The most recent of them consist in finding an affine mapping with respect to the loop indices to simultaneously capture the temporal and spatial properties of the parallelized program. Such a mapping is usually called a open-quotes space-time transformation.close quotes This work describes an extension of these techniques to while-loops using speculative execution. We show that space-time transformations are a good framework for summing up previous restructuration techniques of while-loop, such as pipelining. Moreover, we show that these transformations can be derived and applied automatically
Physics Structure Analysis of Parallel Waves Concept of Physics Teacher Candidate
International Nuclear Information System (INIS)
Sarwi, S; Linuwih, S; Supardi, K I
2017-01-01
The aim of this research was to find a parallel structure concept of wave physics and the factors that influence on the formation of parallel conceptions of physics teacher candidates. The method used qualitative research which types of cross-sectional design. These subjects were five of the third semester of basic physics and six of the fifth semester of wave course students. Data collection techniques used think aloud and written tests. Quantitative data were analysed with descriptive technique-percentage. The data analysis technique for belief and be aware of answers uses an explanatory analysis. Results of the research include: 1) the structure of the concept can be displayed through the illustration of a map containing the theoretical core, supplements the theory and phenomena that occur daily; 2) the trend of parallel conception of wave physics have been identified on the stationary waves, resonance of the sound and the propagation of transverse electromagnetic waves; 3) the influence on the parallel conception that reading textbooks less comprehensive and knowledge is partial understanding as forming the structure of the theory. (paper)
Keldysh formalism for multiple parallel worlds
International Nuclear Information System (INIS)
Ansari, M.; Nazarov, Y. V.
2016-01-01
We present a compact and self-contained review of the recently developed Keldysh formalism for multiple parallel worlds. The formalism has been applied to consistent quantum evaluation of the flows of informational quantities, in particular, to the evaluation of Renyi and Shannon entropy flows. We start with the formulation of the standard and extended Keldysh techniques in a single world in a form convenient for our presentation. We explain the use of Keldysh contours encompassing multiple parallel worlds. In the end, we briefly summarize the concrete results obtained with the method.
Keldysh formalism for multiple parallel worlds
Ansari, M.; Nazarov, Y. V.
2016-03-01
We present a compact and self-contained review of the recently developed Keldysh formalism for multiple parallel worlds. The formalism has been applied to consistent quantum evaluation of the flows of informational quantities, in particular, to the evaluation of Renyi and Shannon entropy flows. We start with the formulation of the standard and extended Keldysh techniques in a single world in a form convenient for our presentation. We explain the use of Keldysh contours encompassing multiple parallel worlds. In the end, we briefly summarize the concrete results obtained with the method.
Keldysh formalism for multiple parallel worlds
Energy Technology Data Exchange (ETDEWEB)
Ansari, M.; Nazarov, Y. V., E-mail: y.v.nazarov@tudelft.nl [Delft University of Technology, Kavli Institute of Nanoscience (Netherlands)
2016-03-15
We present a compact and self-contained review of the recently developed Keldysh formalism for multiple parallel worlds. The formalism has been applied to consistent quantum evaluation of the flows of informational quantities, in particular, to the evaluation of Renyi and Shannon entropy flows. We start with the formulation of the standard and extended Keldysh techniques in a single world in a form convenient for our presentation. We explain the use of Keldysh contours encompassing multiple parallel worlds. In the end, we briefly summarize the concrete results obtained with the method.
Luo, Yukun; Fang, Jun; Fan, Lin; Lin, Chaogui; Chen, Zhaoyang; Chen, Lianglong
2012-10-01
To investigate the role of connexin 43-formed hemichannels in cell volume regulation induced by simulated ischemia/reperfusion (SI/R). Mouse cardiomyocytes isolated on a Langendorff apparatus with enzyme solution were aliquoted into control, SI/R and SI/R +octanol groups. Calcein-AM was used to stain the cells and the cell volume was measured with confocal microscope by stack scanning. Trypan blue was used to measure the cell viability after the treatments. Calcein-AM staining and cofocal microscopy yielded stable and reproducible results for cell volume measurement. Mouse cardiomyocytes subjected to simulated SI/R showed obvious cell swelling as compared with the control cells [(126∓6)% vs 100%, Poctanol preconditioning significantly attenuated the cell swelling [(113∓6)%, Poctanol preconditioning obviously reduced the viability of the cells with SI/R challenge [(31∓2)%, Poctanol can alleviate the cell swelling to enhance the viability of the cardiomyocytes following SI/R.
Formentini, Laura; Pereira, Marta P; Sánchez-Cenizo, Laura; Santacatterina, Fulvio; Lucas, José J; Navarro, Carmen; Martínez-Serrano, Alberto; Cuezva, José M
2014-04-01
A key transducer in energy conservation and signaling cell death is the mitochondrial H(+)-ATP synthase. The expression of the ATPase inhibitory factor 1 (IF1) is a strategy used by cancer cells to inhibit the activity of the H(+)-ATP synthase to generate a ROS signal that switches on cellular programs of survival. We have generated a mouse model expressing a mutant of human IF1 in brain neurons to assess the role of the H(+)-ATP synthase in cell death in vivo. The expression of hIF1 inhibits the activity of oxidative phosphorylation and mediates the shift of neurons to an enhanced aerobic glycolysis. Metabolic reprogramming induces brain preconditioning affording protection against quinolinic acid-induced excitotoxicity. Mechanistically, preconditioning involves the activation of the Akt/p70S6K and PARP repair pathways and Bcl-xL protection from cell death. Overall, our findings provide the first in vivo evidence highlighting the H(+)-ATP synthase as a target to prevent neuronal cell death.
Parallel computation of nondeterministic algorithms in VLSI
Energy Technology Data Exchange (ETDEWEB)
Hortensius, P D
1987-01-01
This work examines parallel VLSI implementations of nondeterministic algorithms. It is demonstrated that conventional pseudorandom number generators are unsuitable for highly parallel applications. Efficient parallel pseudorandom sequence generation can be accomplished using certain classes of elementary one-dimensional cellular automata. The pseudorandom numbers appear in parallel on each clock cycle. Extensive study of the properties of these new pseudorandom number generators is made using standard empirical random number tests, cycle length tests, and implementation considerations. Furthermore, it is shown these particular cellular automata can form the basis of efficient VLSI architectures for computations involved in the Monte Carlo simulation of both the percolation and Ising models from statistical mechanics. Finally, a variation on a Built-In Self-Test technique based upon cellular automata is presented. These Cellular Automata-Logic-Block-Observation (CALBO) circuits improve upon conventional design for testability circuitry.
Vasilescu, C; Olteanu, M; Flondor, P
2012-01-01
In a recent paper the authors hypothesized that the so called fractal-like enzyme kinetics of intracellular reactions may explain the preconditioning effect in biology (Vasilescu C, Olteanu M, Flondor P, Revue Roumaine de Chimie. 2011; 56(7): 751-7). Inside cells the reaction kinetics is very well described by fractal-like kinetics. In the present work some clinical implications of this model are analyzed. Endotoxin tolerance is a particular case of preconditioning and shows similarities with the immunodepression seen in some sepsis patients. This idea offers a theoretical support for modulation of the enzymatic activity of the cell by changing the fractal dimension of the cytoskeleton.
International Nuclear Information System (INIS)
Belliard, M.; Grandotto, M.
2003-01-01
In the framework of the two-phase fluid simulations of the steam generators of pressurized water nuclear reactors, we present in this paper a geometric version of a pseudo-Full MultiGrid (pseudo- FMG) Full Approximation Storage (FAS) preconditioning of balance equations in the GENEPI code. In our application, the 3D steady state flow is reached by a transient computation using a semi-implicit fractional step algorithm for the averaged two-phase mixture balance equations (mass, momentum and energy for the secondary flow). Our application, running on workstation clusters, is based on a CEA code-linker and the PVM package. The difficulties to apply the geometric FAS multigrid method to the momentum and mass balance equations are addressed. The use of a sequential pseudo-FMG FAS twogrid method for both energy and mass/momentum balance equations, using dynamic multigrid cycles, leads to perceptibly improvements in the computation convergences. An original parallel red-black pseudo-FMG FAS three-grid algorithm is presented too. The numerical tests (steam generator mockup simulations) underline the sizable increase in speed of convergence of the computations, essentially for the ones involving a large number of freedom degrees (about 100 thousand cells). The two-phase mixture balance equation residuals are quickly reduced: the reached speed-up stands between 2 and 3 following the number of grids. The effects on the convergence behavior of the numerical parameters are investigated
Least-squares reverse time migration with local Radon-based preconditioning
Dutta, Gaurav
2017-03-08
Least-squares migration (LSM) can produce images with better balanced amplitudes and fewer artifacts than standard migration. The conventional objective function used for LSM minimizes the L2-norm of the data residual between the predicted and the observed data. However, for field-data applications in which the recorded data are noisy and undersampled, the conventional formulation of LSM fails to provide the desired uplift in the quality of the inverted image. We have developed a leastsquares reverse time migration (LSRTM) method using local Radon-based preconditioning to overcome the low signal-tonoise ratio (S/N) problem of noisy or severely undersampled data. A high-resolution local Radon transform of the reflectivity is used, and sparseness constraints are imposed on the inverted reflectivity in the local Radon domain. The sparseness constraint is that the inverted reflectivity is sparse in the Radon domain and each location of the subsurface is represented by a limited number of geologic dips. The forward and the inverse mapping of the reflectivity to the local Radon domain and vice versa is done through 3D Fourier-based discrete Radon transform operators. The weights for the preconditioning are chosen to be varying locally based on the relative amplitudes of the local dips or assigned using quantile measures. Numerical tests on synthetic and field data validate the effectiveness of our approach in producing images with good S/N and fewer aliasing artifacts when compared with standard RTM or standard LSRTM.
Bylaska, Eric J; Weare, Jonathan Q; Weare, John H
2013-08-21
Parallel in time simulation algorithms are presented and applied to conventional molecular dynamics (MD) and ab initio molecular dynamics (AIMD) models of realistic complexity. Assuming that a forward time integrator, f (e.g., Verlet algorithm), is available to propagate the system from time ti (trajectory positions and velocities xi = (ri, vi)) to time ti + 1 (xi + 1) by xi + 1 = fi(xi), the dynamics problem spanning an interval from t0[ellipsis (horizontal)]tM can be transformed into a root finding problem, F(X) = [xi - f(x(i - 1)]i = 1, M = 0, for the trajectory variables. The root finding problem is solved using a variety of root finding techniques, including quasi-Newton and preconditioned quasi-Newton schemes that are all unconditionally convergent. The algorithms are parallelized by assigning a processor to each time-step entry in the columns of F(X). The relation of this approach to other recently proposed parallel in time methods is discussed, and the effectiveness of various approaches to solving the root finding problem is tested. We demonstrate that more efficient dynamical models based on simplified interactions or coarsening time-steps provide preconditioners for the root finding problem. However, for MD and AIMD simulations, such preconditioners are not required to obtain reasonable convergence and their cost must be considered in the performance of the algorithm. The parallel in time algorithms developed are tested by applying them to MD and AIMD simulations of size and complexity similar to those encountered in present day applications. These include a 1000 Si atom MD simulation using Stillinger-Weber potentials, and a HCl + 4H2O AIMD simulation at the MP2 level. The maximum speedup (serial execution/timeparallel execution time) obtained by parallelizing the Stillinger-Weber MD simulation was nearly 3.0. For the AIMD MP2 simulations, the algorithms achieved speedups of up to 14.3. The parallel in time algorithms can be implemented in a
Research in Parallel Algorithms and Software for Computational Aerosciences
Domel, Neal D.
1996-01-01
Phase 1 is complete for the development of a computational fluid dynamics CFD) parallel code with automatic grid generation and adaptation for the Euler analysis of flow over complex geometries. SPLITFLOW, an unstructured Cartesian grid code developed at Lockheed Martin Tactical Aircraft Systems, has been modified for a distributed memory/massively parallel computing environment. The parallel code is operational on an SGI network, Cray J90 and C90 vector machines, SGI Power Challenge, and Cray T3D and IBM SP2 massively parallel machines. Parallel Virtual Machine (PVM) is the message passing protocol for portability to various architectures. A domain decomposition technique was developed which enforces dynamic load balancing to improve solution speed and memory requirements. A host/node algorithm distributes the tasks. The solver parallelizes very well, and scales with the number of processors. Partially parallelized and non-parallelized tasks consume most of the wall clock time in a very fine grain environment. Timing comparisons on a Cray C90 demonstrate that Parallel SPLITFLOW runs 2.4 times faster on 8 processors than its non-parallel counterpart autotasked over 8 processors.
RESVERATROL PRECONDITIONING INDUCES A NOVEL EXTENDED WINDOW OF ISCHEMIC TOLERANCE IN THE MOUSE BRAIN
Koronowski, Kevin B.; Dave, Kunjan R.; Saul, Isabel; Camarena, Vladimir; Thompson, John W.; Neumann, Jake T.; Young, Juan I.; Perez-Pinzon, Miguel A.
2015-01-01
Background and Purpose Prophylactic treatments that afford neuroprotection against stroke may emerge from the field of preconditioning. Resveratrol mimics ischemic preconditioning, reducing ischemic brain injury when administered two days prior to global ischemia in rats. This protection is linked to Sirt1 and enhanced mitochondrial function possibly through its repression of UCP2. BDNF is another neuroprotective protein associated with Sirt1. In this study we sought to identify the conditions of resveratrol preconditioning (RPC) that most robustly induce neuroprotection against focal ischemia in mice. Methods We tested four different RPC paradigms against a middle cerebral artery occlusion (MCAo) model of stroke. Infarct volume and neurological score were calculated 24 hours following MCAo. Sirt1-chromatin binding was evaluated by ChIP-qPCR. Percoll gradients were used to isolate synaptic fractions and changes in protein expression were determined via Western blot analysis. BDNF concentration was measured using a BDNF-specific ELISA assay. Results While repetitive RPC induced neuroprotection from MCAo, strikingly one application of RPC 14 days prior to MCAo showed the most robust protection, reducing infarct volume by 33% and improving neurological score by 28%. Fourteen days following RPC, Sirt1 protein was increased 1.5 fold and differentially bound to the UCP2 and BDNF promoter regions. Accordingly, synaptic UCP2 protein decreased by 23% and cortical BDNF concentration increased 26%. Conclusions RPC induces a novel extended window of ischemic tolerance in the brain that lasts for at least 14 days. Our data suggest that this tolerance may be mediated by Sirt1, through upregulation of BDNF and downregulation of UCP2. PMID:26159789
MINARET: Towards a time-dependent neutron transport parallel solver
International Nuclear Information System (INIS)
Baudron, A.M.; Lautard, J.J.; Maday, Y.; Mula, O.
2013-01-01
We present the newly developed time-dependent 3D multigroup discrete ordinates neutron transport solver that has recently been implemented in the MINARET code. The solver is the support for a study about computing acceleration techniques that involve parallel architectures. In this work, we will focus on the parallelization of two of the variables involved in our equation: the angular directions and the time. This last variable has been parallelized by a (time) domain decomposition method called the para-real in time algorithm. (authors)
Preconditions of commercial use in tourism of individual´s death
TŮMOVÁ, Blanka
2008-01-01
This bachelor thesis deals with the processing the theme Dark Tourism introducing an unusual and so far not very well-known type of tourism in the Czech Republic. The concept Dark Tourism (also known as Thanatourism) refers to visiting sites which offer a presentation of death or suffering and it is identified with visitations to places where tragedies or historically noteworthy death has occurred and that continue to impact our lives. This thesis researches preconditions of commercial use in...
The precondition of social mobility in Ignalina NPP and its area
International Nuclear Information System (INIS)
Mikshys, A.
1998-01-01
In the paper some preconditions of social mobility in the northern Lithuania (Ignalina nuclear power plant) and in its area are analyzed. The results of the sociological research reveal the desire of some part of the inhabitants of the nuclear power plant area to change their social status and the place of residence. The difficult social and demographically situation in this region as significant is noted. The author proposes some mean for the normalization of this situation. (author)
T2CG1, a package of preconditioned conjugate gradient solvers for TOUGH2
International Nuclear Information System (INIS)
Moridis, G.; Pruess, K.; Antunez, E.
1994-03-01
Most of the computational work in the numerical simulation of fluid and heat flows in permeable media arises in the solution of large systems of linear equations. The simplest technique for solving such equations is by direct methods. However, because of large storage requirements and accumulation of roundoff errors, the application of direct solution techniques is limited, depending on matrix bandwidth, to systems of a few hundred to at most a few thousand simultaneous equations. T2CG1, a package of preconditioned conjugate gradient solvers, has been added to TOUGH2 to complement its direct solver and significantly increase the size of problems tractable on PCs. T2CG1 includes three different solvers: a Bi-Conjugate Gradient (BCG) solver, a Bi-Conjugate Gradient Squared (BCGS) solver, and a Generalized Minimum Residual (GMRES) solver. Results from six test problems with up to 30,000 equations show that T2CG1 (1) is significantly (and invariably) faster and requires far less memory than the MA28 direct solver, (2) it makes possible the solution of very large three-dimensional problems on PCs, and (3) that the BCGS solver is the fastest of the three in the tested problems. Sample problems are presented related to heat and fluid flow at Yucca Mountain and WIPP, environmental remediation by the Thermal Enhanced Vapor Extraction System, and geothermal resources
Liu, Lulu
2013-01-01
The fully implicit approach is attractive in reservoir simulation for reasons of numerical stability and the avoidance of splitting errors when solving multiphase flow problems, but a large nonlinear system must be solved at each time step, so efficient and robust numerical methods are required to treat the nonlinearity. The Additive Schwarz Preconditioned Inexact Newton (ASPIN) framework, as an option for the outermost solver, successfully handles strong nonlinearities in computational fluid dynamics, but is barely explored for the highly nonlinear models of complex multiphase flow with capillarity, heterogeneity, and complex geometry. In this paper, the fully implicit ASPIN method is demonstrated for a finite volume discretization based on incompressible two-phase reservoir simulators in the presence of capillary forces and gravity. Numerical experiments show that the number of global nonlinear iterations is not only scalable with respect to the number of processors, but also significantly reduced compared with the standard inexact Newton method with a backtracking technique. Moreover, the ASPIN method, in contrast with the IMPES method, saves overall execution time because of the savings in timestep size.
Preßler, Anna-Lena; Könen, Tanja; Hasselhorn, Marcus; Krajewski, Kristin
2014-01-01
The aim of the present study was to empirically disentangle the interdependencies of the impact of nonverbal intelligence, working memory capacities, and phonological processing skills on early reading decoding and spelling within a latent variable approach. In a sample of 127 children, these cognitive preconditions were assessed before the onset…
Out-of-order parallel discrete event simulation for electronic system-level design
Chen, Weiwei
2014-01-01
This book offers readers a set of new approaches and tools a set of tools and techniques for facing challenges in parallelization with design of embedded systems.? It provides an advanced parallel simulation infrastructure for efficient and effective system-level model validation and development so as to build better products in less time.? Since parallel discrete event simulation (PDES) has the potential to exploit the underlying parallel computational capability in today's multi-core simulation hosts, the author begins by reviewing the parallelization of discrete event simulation, identifyin
Parallel Monte Carlo simulation of aerosol dynamics
Zhou, K.; He, Z.; Xiao, M.; Zhang, Z.
2014-01-01
is simulated with a stochastic method (Marcus-Lushnikov stochastic process). Operator splitting techniques are used to synthesize the deterministic and stochastic parts in the algorithm. The algorithm is parallelized using the Message Passing Interface (MPI
Step by step parallel programming method for molecular dynamics code
International Nuclear Information System (INIS)
Orii, Shigeo; Ohta, Toshio
1996-07-01
Parallel programming for a numerical simulation program of molecular dynamics is carried out with a step-by-step programming technique using the two phase method. As a result, within the range of a certain computing parameters, it is found to obtain parallel performance by using the level of parallel programming which decomposes the calculation according to indices of do-loops into each processor on the vector parallel computer VPP500 and the scalar parallel computer Paragon. It is also found that VPP500 shows parallel performance in wider range computing parameters. The reason is that the time cost of the program parts, which can not be reduced by the do-loop level of the parallel programming, can be reduced to the negligible level by the vectorization. After that, the time consuming parts of the program are concentrated on less parts that can be accelerated by the do-loop level of the parallel programming. This report shows the step-by-step parallel programming method and the parallel performance of the molecular dynamics code on VPP500 and Paragon. (author)
Can endurance exercise preconditioning prevention disuse muscle atrophy?
Directory of Open Access Journals (Sweden)
Michael P Wiggs
2015-03-01
Full Text Available Emerging evidence suggests that exercise training can provide a level of protection against disuse muscle atrophy. Endurance exercise training imposes oxidative, metabolic, and heat stress on skeletal muscle which activates a variety of cellular signaling pathways that ultimately leads to the increased expression of proteins that have been demonstrated to protect muscle from inactivity –induced atrophy. This review will highlight the effect of exercise-induced oxidative stress on endogenous enzymatic antioxidant capacity (i.e., superoxide dismutase, glutathione peroxidase, and catalase, the role of oxidative and metabolic stress on PGC1-α, and finally highlight the effect heat stress and HSP70 induction. Finally, this review will discuss the supporting scientific evidence that these proteins can attenuate muscle atrophy through exercise preconditioning.
Energy Technology Data Exchange (ETDEWEB)
Bylaska, Eric J., E-mail: Eric.Bylaska@pnnl.gov [Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352 (United States); Weare, Jonathan Q., E-mail: weare@uchicago.edu [Department of Mathematics, University of Chicago, Chicago, Illinois 60637 (United States); Weare, John H., E-mail: jweare@ucsd.edu [Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093 (United States)
2013-08-21
Parallel in time simulation algorithms are presented and applied to conventional molecular dynamics (MD) and ab initio molecular dynamics (AIMD) models of realistic complexity. Assuming that a forward time integrator, f (e.g., Verlet algorithm), is available to propagate the system from time t{sub i} (trajectory positions and velocities x{sub i} = (r{sub i}, v{sub i})) to time t{sub i+1} (x{sub i+1}) by x{sub i+1} = f{sub i}(x{sub i}), the dynamics problem spanning an interval from t{sub 0}…t{sub M} can be transformed into a root finding problem, F(X) = [x{sub i} − f(x{sub (i−1})]{sub i} {sub =1,M} = 0, for the trajectory variables. The root finding problem is solved using a variety of root finding techniques, including quasi-Newton and preconditioned quasi-Newton schemes that are all unconditionally convergent. The algorithms are parallelized by assigning a processor to each time-step entry in the columns of F(X). The relation of this approach to other recently proposed parallel in time methods is discussed, and the effectiveness of various approaches to solving the root finding problem is tested. We demonstrate that more efficient dynamical models based on simplified interactions or coarsening time-steps provide preconditioners for the root finding problem. However, for MD and AIMD simulations, such preconditioners are not required to obtain reasonable convergence and their cost must be considered in the performance of the algorithm. The parallel in time algorithms developed are tested by applying them to MD and AIMD simulations of size and complexity similar to those encountered in present day applications. These include a 1000 Si atom MD simulation using Stillinger-Weber potentials, and a HCl + 4H{sub 2}O AIMD simulation at the MP2 level. The maximum speedup ((serial execution time)/(parallel execution time) ) obtained by parallelizing the Stillinger-Weber MD simulation was nearly 3.0. For the AIMD MP2 simulations, the algorithms achieved speedups of up
Directory of Open Access Journals (Sweden)
Qingqing Zhang
Full Text Available Hydrogen sulfide (H2S is the third most common endogenously produced gaseous signaling molecule, but its impact on hepatic ischemia/reperfusion (I/R injury, especially on mitochondrial function, remains unclear. In this study, rats were randomized into Sham, I/R, ischemia preconditioning (IPC or sodium hydrosulfide (NaHS, an H2S donor preconditioning groups. To establish a model of segmental (70% warm hepatic ischemia, the hepatic artery, left portal vein and median liver lobes were occluded for 60 min and then unclamped to allow reperfusion. Preconditioning with 12.5, 25 or 50 μmol/kg NaHS prior to the I/R insult significantly increased serum H2S levels, and, similar to IPC, NaHS preconditioning decreased alanine aminotransferase (ALT and aspartate aminotransferase (AST levels in the plasma and prevented hepatocytes from undergoing I/R-induced necrosis. Moreover, a sub-toxic dose of NaHS (25 μmol/kg did not disrupt the systemic hemodynamics but dramatically inhibited mitochondrial permeability transition pore (MPTP opening and thus prevented mitochondrial-related cell death and apoptosis. Mechanistic studies revealed that NaHS preconditioning markedly increased the expression of phosphorylated protein kinase B (p-Akt, phosphorylated glycogen synthase kinase-3 beta (p-GSK-3β and B-cell lymphoma-2 (Bcl-2 and decreased the release of mitochondrial cytochrome c and cleaved caspase-3/9 levels. Therefore, NaHS administration prior to hepatic I/R ameliorates mitochondrial and hepatocellular damage through the inhibition of MPTP opening and the activation of Akt-GSK-3β signaling. Furthermore, this study provides experimental evidence for the clinical use of H2S to reduce liver damage after perioperative I/R injury.
International Nuclear Information System (INIS)
He, Shu-Fang; Jin, Shi-Yun; Wu, Hao; Wang, Bin; Wu, Yun-Xiang; Zhang, Shu-Jie; Irwin, Michael G.; Wong, Tak-Ming; Zhang, Ye
2015-01-01
Preconditioning against myocardial ischemia–reperfusion (I/R) injury can be suppressed in some pathological conditions. This study was designed to investigate whether morphine preconditioning (MPC) exerts cardioprotection in doxorubicin (DOX)-induced heart failure in rats and the mechanisms involved. Phosphatidylinositol-3 kinase/protein kinase B (PI3K/Akt), extracellular signal-regulated kinase (ERK) and glycogen synthase kinase (GSK)-3β pathways were examined. Normal and DOX-induced failing rat hearts were subjected to I/R injury using a Langendorff perfusion system with or without MPC or ischemic preconditioning (IPC). The PI3K inhibitor (wortmannin) or ERK inhibitor (PD98059) was infused before MPC. In normal hearts, both MPC and IPC significantly reduced infarct size and the rise in lactate dehydrogenase (LDH) level caused by I/R injury. Pretreatment with wortmannin or PD98059 abrogated the protective effects of MPC and suppressed the phosphorylation of Akt, ERK and GSK-3β. In failing rat hearts, however, MPC retained its cardioprotection while IPC did not. This protective effect was abolished by PD98059 but not wortmannin. MPC increased the level of p-ERK rather than p-Akt. The phosphorylation of GSK-3β induced by MPC was reversed by PD98059 only. IPC did not elevate the expression of p-ERK, p-Akt and p-GSK-3β in failing rat hearts. We conclude that MPC is cardioprotective in rats with DOX-induced heart failure while IPC is not. The effect of MPC appears to be mediated via the ERK/GSK-3β pathway independent of PI3K/Akt. - Highlights: • Morphine and ischemic preconditioning are cardioprotective in normal rat hearts. • Ischemic preconditioning fails to confer cardioprotection in rats with heart failure. • Morphine retains cardioprotection in doxorubicin-induced heart failure. • Morphine exerts cardioprotection via the ERK/GSK-β pathway independent of PI3K/Akt.
Energy Technology Data Exchange (ETDEWEB)
He, Shu-Fang; Jin, Shi-Yun; Wu, Hao; Wang, Bin; Wu, Yun-Xiang [Department of Anesthesiology, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601 (China); Zhang, Shu-Jie [Department of Ultrasound, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601 (China); Irwin, Michael G.; Wong, Tak-Ming [Department of Anesthesiology, University of Hong Kong (Hong Kong); Zhang, Ye, E-mail: zhangye_hassan@aliyun.com [Department of Anesthesiology, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601 (China)
2015-11-01
Preconditioning against myocardial ischemia–reperfusion (I/R) injury can be suppressed in some pathological conditions. This study was designed to investigate whether morphine preconditioning (MPC) exerts cardioprotection in doxorubicin (DOX)-induced heart failure in rats and the mechanisms involved. Phosphatidylinositol-3 kinase/protein kinase B (PI3K/Akt), extracellular signal-regulated kinase (ERK) and glycogen synthase kinase (GSK)-3β pathways were examined. Normal and DOX-induced failing rat hearts were subjected to I/R injury using a Langendorff perfusion system with or without MPC or ischemic preconditioning (IPC). The PI3K inhibitor (wortmannin) or ERK inhibitor (PD98059) was infused before MPC. In normal hearts, both MPC and IPC significantly reduced infarct size and the rise in lactate dehydrogenase (LDH) level caused by I/R injury. Pretreatment with wortmannin or PD98059 abrogated the protective effects of MPC and suppressed the phosphorylation of Akt, ERK and GSK-3β. In failing rat hearts, however, MPC retained its cardioprotection while IPC did not. This protective effect was abolished by PD98059 but not wortmannin. MPC increased the level of p-ERK rather than p-Akt. The phosphorylation of GSK-3β induced by MPC was reversed by PD98059 only. IPC did not elevate the expression of p-ERK, p-Akt and p-GSK-3β in failing rat hearts. We conclude that MPC is cardioprotective in rats with DOX-induced heart failure while IPC is not. The effect of MPC appears to be mediated via the ERK/GSK-3β pathway independent of PI3K/Akt. - Highlights: • Morphine and ischemic preconditioning are cardioprotective in normal rat hearts. • Ischemic preconditioning fails to confer cardioprotection in rats with heart failure. • Morphine retains cardioprotection in doxorubicin-induced heart failure. • Morphine exerts cardioprotection via the ERK/GSK-β pathway independent of PI3K/Akt.
Institute of Scientific and Technical Information of China (English)
Fang Su; An-Chen Guo; Wei-Wei Li; Yi-Long Zhao; Zheng-Yi Qu; Yong-Jun Wang; Qun Wang; Yu-Lan Zhu
2017-01-01
Increasing evidence suggests that low to moderate ethanol ingestion protects against the deleterious effects of subsequent ischemia/reperfusion;however,the underlying mechanism has not been elucidated.In the present study,we showed that expression of the neuronal large-conductance,Ca2+-activated K+ channel (BKCa) α-subunit was upregulated in cultured neurons exposed to oxygen-glucose deprivatior/reoxygenation (OGD/R) compared with controls.Preconditioning with low-dose ethanol (10 mmol/L) increased cell survival rate in neurons subjected to OGD/R,attenuated the OGD/R-induced elevation of cytosolic Ca2+ levels,and reduced the number of apoptotic neurons.Western blots revealed that ethanol preconditioning upregulated expression of the anti-apoptotic protein Bcl-2 and downregulated the pro-apoptotic protein Bax.The protective effect of ethanol preconditioning was antagonized by a BKCa channel inhibitor,paxilline.Inside-out patches in primary neurons also demonstrated the direct activation of the BKCa channel by 10 mmol/L ethanol.The above results indicated that low-dose ethanol preconditioning exerts its neuroprotective effects by attenuating the elevation of cytosolic Ca2+ and preventing neuronal apoptosis,and this is mediated by BKCa channel activation.
Su, Fang; Guo, An-Chen; Li, Wei-Wei; Zhao, Yi-Long; Qu, Zheng-Yi; Wang, Yong-Jun; Wang, Qun; Zhu, Yu-Lan
2017-02-01
Increasing evidence suggests that low to moderate ethanol ingestion protects against the deleterious effects of subsequent ischemia/reperfusion; however, the underlying mechanism has not been elucidated. In the present study, we showed that expression of the neuronal large-conductance, Ca 2+ -activated K + channel (BK Ca ) α-subunit was upregulated in cultured neurons exposed to oxygen-glucose deprivation/reoxygenation (OGD/R) compared with controls. Preconditioning with low-dose ethanol (10 mmol/L) increased cell survival rate in neurons subjected to OGD/R, attenuated the OGD/R-induced elevation of cytosolic Ca 2+ levels, and reduced the number of apoptotic neurons. Western blots revealed that ethanol preconditioning upregulated expression of the anti-apoptotic protein Bcl-2 and downregulated the pro-apoptotic protein Bax. The protective effect of ethanol preconditioning was antagonized by a BK Ca channel inhibitor, paxilline. Inside-out patches in primary neurons also demonstrated the direct activation of the BK Ca channel by 10 mmol/L ethanol. The above results indicated that low-dose ethanol preconditioning exerts its neuroprotective effects by attenuating the elevation of cytosolic Ca 2+ and preventing neuronal apoptosis, and this is mediated by BK Ca channel activation.
Parallelization of a spherical Sn transport theory algorithm
International Nuclear Information System (INIS)
Haghighat, A.
1989-01-01
The work described in this paper derives a parallel algorithm for an R-dependent spherical S N transport theory algorithm and studies its performance by testing different sample problems. The S N transport method is one of the most accurate techniques used to solve the linear Boltzmann equation. Several studies have been done on the vectorization of the S N algorithms; however, very few studies have been performed on the parallelization of this algorithm. Weinke and Hommoto have looked at the parallel processing of the different energy groups, and Azmy recently studied the parallel processing of the inner iterations of an X-Y S N nodal transport theory method. Both studies have reported very encouraging results, which have prompted us to look at the parallel processing of an R-dependent S N spherical geometry algorithm. This geometry was chosen because, in spite of its simplicity, it contains the complications of the curvilinear geometries (i.e., redistribution of neutrons over the discretized angular bins)
Baranova, K A; Rybnikova, E A; Mironova, V I; Samoilov, M O
2010-07-01
We report here our immunocytochemical studies establishing that the development of a depression-like state in rats following unavoidable stress in a "learned helplessness" model is accompanied by stable activation of the expression of transcription factor NGFI-A in the dorsal hippocampus (field CA1) and the magnocellular paraventricular nucleus of the hypothalamus, along with an early wave of post-stress expression, which died down rapidly, in the ventral hippocampus (the dentate gyrus) and a long period of up to five days of high-level expression in the neocortex. In rats subjected to three sessions of preconditioning consisting of moderate hypobaric hypoxia (360 mmHg, 2 h, with intervals of 24 h), which did not form depression in these circumstances, there were significant changes in the dynamics of immunoreactive protein content in the hippocampus, with a stable increase in expression in the ventral hippocampus and only transient and delayed (by five days) expression in field CA1. In the neocortex (layer II), preconditioning eliminated the effects of stress, preventing prolongation of the first wave of NGFI-A expression to five days, while in the magnocellular hypothalamus, conversely, preconditioning stimulated a second (delayed) wave of the expression of this transcription factor. The pattern of NGFI-A expression in the hippocampus, neocortex, and hypothalamus seen in non-preconditioned rats appears to reflect the pathological reaction to aversive stress, which, rather than adaptation, produced depressive disorders. Post-stress modification of the expression of the product of the early gene NGFI-A in the brain induced by hypoxic preconditioning probably plays an important role in increased tolerance to severe psychoemotional stresses and is an important component of antidepressant mechanisms.
Cao, Jian; Chen, Jing-Bo; Dai, Meng-Xue
2018-01-01
An efficient finite-difference frequency-domain modeling of seismic wave propagation relies on the discrete schemes and appropriate solving methods. The average-derivative optimal scheme for the scalar wave modeling is advantageous in terms of the storage saving for the system of linear equations and the flexibility for arbitrary directional sampling intervals. However, using a LU-decomposition-based direct solver to solve its resulting system of linear equations is very costly for both memory and computational requirements. To address this issue, we consider establishing a multigrid-preconditioned BI-CGSTAB iterative solver fit for the average-derivative optimal scheme. The choice of preconditioning matrix and its corresponding multigrid components is made with the help of Fourier spectral analysis and local mode analysis, respectively, which is important for the convergence. Furthermore, we find that for the computation with unequal directional sampling interval, the anisotropic smoothing in the multigrid precondition may affect the convergence rate of this iterative solver. Successful numerical applications of this iterative solver for the homogenous and heterogeneous models in 2D and 3D are presented where the significant reduction of computer memory and the improvement of computational efficiency are demonstrated by comparison with the direct solver. In the numerical experiments, we also show that the unequal directional sampling interval will weaken the advantage of this multigrid-preconditioned iterative solver in the computing speed or, even worse, could reduce its accuracy in some cases, which implies the need for a reasonable control of directional sampling interval in the discretization.
Energy Technology Data Exchange (ETDEWEB)
Cai, X C; Marcinkowski, L; Vassilevski, P S
2005-02-10
This paper extends previous results on nonlinear Schwarz preconditioning ([4]) to unstructured finite element elliptic problems exploiting now nonlocal (but small) subspaces. The non-local finite element subspaces are associated with subdomains obtained from a non-overlapping element partitioning of the original set of elements and are coarse outside the prescribed element subdomain. The coarsening is based on a modification of the agglomeration based AMGe method proposed in [8]. Then, the algebraic construction from [9] of the corresponding non-linear finite element subproblems is applied to generate the subspace based nonlinear preconditioner. The overall nonlinearly preconditioned problem is solved by an inexact Newton method. Numerical illustration is also provided.
Verkade, P.J.; Meijel, B. van; Brink, C.; Os-Medendorp, H. van; Koekkoek, B.; Francke, A.L.
2010-01-01
Background: Case management programmes for home-dwelling people with dementia and their informal carers exist in multiple forms and shapes. The aim of this research was to identify the essential components of case management for people with dementia as well as the preconditions for an effective
Parallel fabrication of macroporous scaffolds.
Dobos, Andrew; Grandhi, Taraka Sai Pavan; Godeshala, Sudhakar; Meldrum, Deirdre R; Rege, Kaushal
2018-07-01
Scaffolds generated from naturally occurring and synthetic polymers have been investigated in several applications because of their biocompatibility and tunable chemo-mechanical properties. Existing methods for generation of 3D polymeric scaffolds typically cannot be parallelized, suffer from low throughputs, and do not allow for quick and easy removal of the fragile structures that are formed. Current molds used in hydrogel and scaffold fabrication using solvent casting and porogen leaching are often single-use and do not facilitate 3D scaffold formation in parallel. Here, we describe a simple device and related approaches for the parallel fabrication of macroporous scaffolds. This approach was employed for the generation of macroporous and non-macroporous materials in parallel, in higher throughput and allowed for easy retrieval of these 3D scaffolds once formed. In addition, macroporous scaffolds with interconnected as well as non-interconnected pores were generated, and the versatility of this approach was employed for the generation of 3D scaffolds from diverse materials including an aminoglycoside-derived cationic hydrogel ("Amikagel"), poly(lactic-co-glycolic acid) or PLGA, and collagen. Macroporous scaffolds generated using the device were investigated for plasmid DNA binding and cell loading, indicating the use of this approach for developing materials for different applications in biotechnology. Our results demonstrate that the device-based approach is a simple technology for generating scaffolds in parallel, which can enhance the toolbox of current fabrication techniques. © 2018 Wiley Periodicals, Inc.
The peptide NDP-MSH induces phenotype changes in the heart that resemble ischemic preconditioning.
Catania, Anna; Lonati, Caterina; Sordi, Andrea; Leonardi, Patrizia; Carlin, Andrea; Gatti, Stefano
2010-01-01
alpha-Melanocyte-stimulating hormone (alpha-MSH) is a pro-opiomelanocortin (POMC)-derived peptide that exerts multiple protective effects on host cells. Previous investigations showed that treatment with alpha-MSH or synthetic melanocortin agonists reduces heart damage in reperfusion injury and transplantation. The aim of this preclinical research was to determine whether melanocortin treatment induces preconditioning-like cardioprotection. In particular, the plan was to assess whether melanocortin administration causes phenotype changes similar to those induced by repetitive ischemic events. The idea was conceived because both ischemic preconditioning and melanocortin signaling largely depend on cAMP response element binding protein (CREB) phosphorylation. Rats received single i.v. injections of 750microg/kg of the alpha-MSH analogue Nle(4),DPhe(7)-alpha-MSH (NDP-MSH) or saline and were sacrificed at 0.5, 1, 3, or 5h. Western blot analysis showed that rat hearts expressed melanocortin 1 receptor (MC1R) protein. Treatment with NDP-MSH was associated with early and marked increase in interleukin 6 (IL-6) mRNA. This was followed by signal transducer and activator of transcription 3 (STAT3) phosphorylation and induction of suppressor of cytokine signaling 3 (SOCS3). There were no changes in expression of other cytokines of the IL-6 family. Expression of IL-10, IL-1beta, and TNF-alpha was likewise unaltered. In hearts of rats treated with NDP-MSH there was increased expression of the orphan nuclear receptor Nur77. The data indicate that NDP-MSH induces phenotype changes that closely resemble ischemic preconditioning and likely contribute to its established protection against reperfusion injury. In addition, the increased expression of Nur77 and SOCS3 could be part of a broader anti-inflammatory effect.
Role of Endogenous Opioid System in Ischemic-Induced Late Preconditioning.
Directory of Open Access Journals (Sweden)
Jan Fraessdorf
Full Text Available Opioid receptors (OR are involved in myocardial late preconditioning (LPC induced by morphine and δ1-opioid receptor (δ1-OR agonists. The role of OR in ischemic-induced LPC is unknown. We investigated whether 1 OR are involved in the trigger and/or mediation phase of LPC and 2 a time course effect on the expression of different opioid receptors and their endogenous ligands exists.Male Wistar rats were randomly allocated to four groups (each group n = 8. Awake animals were ischemic preconditioned by a 5 minutes coronary occlusion. 24 hours later, anesthetized animals underwent 25 minutes coronary occlusion followed by 2 hours of reperfusion. The role of OR was investigated by treatment with intraperitoneal naloxone (Nal 10 minutes prior to LPC (Nal-LPC; trigger phase or 10 min prior to sustained ischemia (LPC-Nal; mediation phase.LPC reduced infarct size from 61±10% in controls to 25±9% (P<0.001. Naloxone during trigger or mediation phase completely abolished LPC-induced cardioprotection (59±9% and 62±9%; P<0.001 vs. LPC. 8, 12 and 24 hours after the ischemic stimulus, expression of δ-OR in the heart was increased, whereas μ-opioid receptor (μ-OR and κ-opioid receptor (κ-OR were not. Plasma concentrations of β-endorphin and leu-enkephalin but not dynorphin were increased by LPC.Ischemic LPC is triggererd and mediated by OR. Expression of δ-OR and plasma levels of endogenous opioid peptides are increased after ischemic LPC.
Gurel, Ebru; Ustunova, Savas; Kapucu, Aysegul; Yilmazer, Nadim; Eerbeek, Otto; Nederlof, Rianne; Hollmann, Markus W.; Demirci-Tansel, Cihan; Zuurbier, Coert J.
2013-01-01
Diabetes mellitus (DM) has been reported to alter the cardiac response to ischemia-reperfusion (IR). In addition, cardioprotection induced by ischemic preconditioning (IPC) is often impaired in diabetes. We have previously shown that the subcellular localisation of the glycolytic enzyme hexokinase
MADmap: A Massively Parallel Maximum-Likelihood Cosmic Microwave Background Map-Maker
Energy Technology Data Exchange (ETDEWEB)
Cantalupo, Christopher; Borrill, Julian; Jaffe, Andrew; Kisner, Theodore; Stompor, Radoslaw
2009-06-09
MADmap is a software application used to produce maximum-likelihood images of the sky from time-ordered data which include correlated noise, such as those gathered by Cosmic Microwave Background (CMB) experiments. It works efficiently on platforms ranging from small workstations to the most massively parallel supercomputers. Map-making is a critical step in the analysis of all CMB data sets, and the maximum-likelihood approach is the most accurate and widely applicable algorithm; however, it is a computationally challenging task. This challenge will only increase with the next generation of ground-based, balloon-borne and satellite CMB polarization experiments. The faintness of the B-mode signal that these experiments seek to measure requires them to gather enormous data sets. MADmap is already being run on up to O(1011) time samples, O(108) pixels and O(104) cores, with ongoing work to scale to the next generation of data sets and supercomputers. We describe MADmap's algorithm based around a preconditioned conjugate gradient solver, fast Fourier transforms and sparse matrix operations. We highlight MADmap's ability to address problems typically encountered in the analysis of realistic CMB data sets and describe its application to simulations of the Planck and EBEX experiments. The massively parallel and distributed implementation is detailed and scaling complexities are given for the resources required. MADmap is capable of analysing the largest data sets now being collected on computing resources currently available, and we argue that, given Moore's Law, MADmap will be capable of reducing the most massive projected data sets.
DEFF Research Database (Denmark)
Arshid, S; Tahir, M; Fontes, B
2017-01-01
therapeutic application; however the exact underlying mechanism is not clear. Neutrophils play an important role in the mechanism of injuries caused by ischemia and reperfusion while IPC led to a decrease in neutrophil stimulation and activation. The effect of preconditioning on the neutrophil proteome...... in such conditions, there is no report of a proteomic study providing a broader view of this scenario. Here we describe a group of proteins significantly regulated by ischemia and reperfusion being such regulation prevented by preconditioning. Such finding may provide relevant information for a deeper understanding...
Parallelization and checkpointing of GPU applications through program transformation
Energy Technology Data Exchange (ETDEWEB)
Solano-Quinde, Lizandro Damian [Iowa State Univ., Ames, IA (United States)
2012-01-01
GPUs have emerged as a powerful tool for accelerating general-purpose applications. The availability of programming languages that makes writing general-purpose applications for running on GPUs tractable have consolidated GPUs as an alternative for accelerating general purpose applications. Among the areas that have benefited from GPU acceleration are: signal and image processing, computational fluid dynamics, quantum chemistry, and, in general, the High Performance Computing (HPC) Industry. In order to continue to exploit higher levels of parallelism with GPUs, multi-GPU systems are gaining popularity. In this context, single-GPU applications are parallelized for running in multi-GPU systems. Furthermore, multi-GPU systems help to solve the GPU memory limitation for applications with large application memory footprint. Parallelizing single-GPU applications has been approached by libraries that distribute the workload at runtime, however, they impose execution overhead and are not portable. On the other hand, on traditional CPU systems, parallelization has been approached through application transformation at pre-compile time, which enhances the application to distribute the workload at application level and does not have the issues of library-based approaches. Hence, a parallelization scheme for GPU systems based on application transformation is needed. Like any computing engine of today, reliability is also a concern in GPUs. GPUs are vulnerable to transient and permanent failures. Current checkpoint/restart techniques are not suitable for systems with GPUs. Checkpointing for GPU systems present new and interesting challenges, primarily due to the natural differences imposed by the hardware design, the memory subsystem architecture, the massive number of threads, and the limited amount of synchronization among threads. Therefore, a checkpoint/restart technique suitable for GPU systems is needed. The goal of this work is to exploit higher levels of parallelism and
A parallel graded-mesh FDTD algorithm for human-antenna interaction problems.
Catarinucci, Luca; Tarricone, Luciano
2009-01-01
The finite difference time domain method (FDTD) is frequently used for the numerical solution of a wide variety of electromagnetic (EM) problems and, among them, those concerning human exposure to EM fields. In many practical cases related to the assessment of occupational EM exposure, large simulation domains are modeled and high space resolution adopted, so that strong memory and central processing unit power requirements have to be satisfied. To better afford the computational effort, the use of parallel computing is a winning approach; alternatively, subgridding techniques are often implemented. However, the simultaneous use of subgridding schemes and parallel algorithms is very new. In this paper, an easy-to-implement and highly-efficient parallel graded-mesh (GM) FDTD scheme is proposed and applied to human-antenna interaction problems, demonstrating its appropriateness in dealing with complex occupational tasks and showing its capability to guarantee the advantages of a traditional subgridding technique without affecting the parallel FDTD performance.
Parallel finite elements with domain decomposition and its pre-processing
International Nuclear Information System (INIS)
Yoshida, A.; Yagawa, G.; Hamada, S.
1993-01-01
This paper describes a parallel finite element analysis using a domain decomposition method, and the pre-processing for the parallel calculation. Computer simulations are about to replace experiments in various fields, and the scale of model to be simulated tends to be extremely large. On the other hand, computational environment has drastically changed in these years. Especially, parallel processing on massively parallel computers or computer networks is considered to be promising techniques. In order to achieve high efficiency on such parallel computation environment, large granularity of tasks, a well-balanced workload distribution are key issues. It is also important to reduce the cost of pre-processing in such parallel FEM. From the point of view, the authors developed the domain decomposition FEM with the automatic and dynamic task-allocation mechanism and the automatic mesh generation/domain subdivision system for it. (author)
Parallel algorithms for placement and routing in VLSI design. Ph.D. Thesis
Brouwer, Randall Jay
1991-01-01
The computational requirements for high quality synthesis, analysis, and verification of very large scale integration (VLSI) designs have rapidly increased with the fast growing complexity of these designs. Research in the past has focused on the development of heuristic algorithms, special purpose hardware accelerators, or parallel algorithms for the numerous design tasks to decrease the time required for solution. Two new parallel algorithms are proposed for two VLSI synthesis tasks, standard cell placement and global routing. The first algorithm, a parallel algorithm for global routing, uses hierarchical techniques to decompose the routing problem into independent routing subproblems that are solved in parallel. Results are then presented which compare the routing quality to the results of other published global routers and which evaluate the speedups attained. The second algorithm, a parallel algorithm for cell placement and global routing, hierarchically integrates a quadrisection placement algorithm, a bisection placement algorithm, and the previous global routing algorithm. Unique partitioning techniques are used to decompose the various stages of the algorithm into independent tasks which can be evaluated in parallel. Finally, results are presented which evaluate the various algorithm alternatives and compare the algorithm performance to other placement programs. Measurements are presented on the parallel speedups available.
Directory of Open Access Journals (Sweden)
Xing Cai
2005-01-01
Full Text Available This article addresses the performance of scientific applications that use the Python programming language. First, we investigate several techniques for improving the computational efficiency of serial Python codes. Then, we discuss the basic programming techniques in Python for parallelizing serial scientific applications. It is shown that an efficient implementation of the array-related operations is essential for achieving good parallel performance, as for the serial case. Once the array-related operations are efficiently implemented, probably using a mixed-language implementation, good serial and parallel performance become achievable. This is confirmed by a set of numerical experiments. Python is also shown to be well suited for writing high-level parallel programs.
The role of 17-beta estradiol in ischemic preconditioning protection of the heart.
Babiker, Fawzi A; Hoteit, Lamia J; Joseph, Shaji; Mustafa, Abu Salim; Juggi, Jasbir S
2012-09-01
The protective effects of 17-beta estradiol (E2) on cardiac tissue during ischemia/reperfusion (I/R) injury have not yet been fully elucidated. To assess the protective effects of short- and long-term E2 treatments on cardiac tissue exposed to I/R, and to assess the effects of these treatments in combination with ischemic preconditioning (IPC) on cardiac protection from I/R injury. SPRAGUE DAWLEY RATS WERE ASSIGNED TO THE FOLLOWING TREATMENT PROTOCOLS: control (no preconditioning); IPC (isolated hearts were subjected to two cycles of 5 min global ischemia followed by 10 min of reperfusion); E2 preconditioning (E2PC; isolated hearts were subjected to E2 pharmacological perfusion for 15 min); short-term in vivo E2 pretreatment for 3 h; long-term in vivo E2 pretreatment or withdrawal (ovariectomy followed by a six-week treatment with E2 or a placebo); combined IPC and E2PC; combined IPC and short- or long-term E2 pretreatments or withdrawal. All hearts were isolated and stabilized for at least 30 min before being subjected to 40 min of global ischemia followed by 30 min of reperfusion; left ventricular function and vascular hemodynamics were then assessed. IPC, E2PC and short-term E2 pretreatment led to the recovery of left ventricle function and vascular hemodynamics. Long-term E2 and placebo treatments did not result in any protection compared with untreated controls. The combination of E2PC or short-term E2 treatments with IPC did not block the IPC protection or result in any additional protection to the heart. Long-term E2 treatment blocked IPC protection; however, placebo treatment did not. Short-term treatment with E2 protected the heart against I/R injury through a pathway involving the regulation of tumour necrosis factor-alpha. The combination of short-term E2 treatment with IPC did not provide additional protection to the heart. Short-term E2 treatment may be a suitable alternative for classical estrogen replacement therapy.
Institutionalized Ignorance as a Precondition for Rational Risk Expertise
DEFF Research Database (Denmark)
Merkelsen, Henrik
2011-01-01
the lowest organizational level, where concrete risks occur, to the highest organizational level, where the body of professional risk expertise is situated. The article emphasizes the role of knowledge, responsibility, loyalty, and trust as risk-attenuation factors and concludes by suggesting......The present case study seeks to explain the conditions for experts’ rational risk perception by analyzing the institutional contexts that constitute a field of food safety expertise in Denmark. The study highlights the role of risk reporting and how contextual factors affect risk reporting from...... that the preconditions for the expert's rationality may rather be a lack of risk-specific knowledge due to poor risk reporting than a superior level of risk knowledge....
Explicit solution of Calderon preconditioned time domain integral equations
Ulku, Huseyin Arda
2013-07-01
An explicit marching on-in-time (MOT) scheme for solving Calderon-preconditioned time domain integral equations is proposed. The scheme uses Rao-Wilton-Glisson and Buffa-Christiansen functions to discretize the domain and range of the integral operators and a PE(CE)m type linear multistep to march on in time. Unlike its implicit counterpart, the proposed explicit solver requires the solution of an MOT system with a Gram matrix that is sparse and well-conditioned independent of the time step size. Numerical results demonstrate that the explicit solver maintains its accuracy and stability even when the time step size is chosen as large as that typically used by an implicit solver. © 2013 IEEE.
Parallelized preconditioned model building algorithm for matrix factorization
Kaya, Kamer; Birbil, İlker; Birbil, Ilker; Öztürk, Mehmet Kaan; Ozturk, Mehmet Kaan; Gohari, Amir
2017-01-01
Matrix factorization is a common task underlying several machine learning applications such as recommender systems, topic modeling, or compressed sensing. Given a large and possibly sparse matrix A, we seek two smaller matrices W and H such that their product is as close to A as possible. The objective is minimizing the sum of square errors in the approximation. Typically such problems involve hundreds of thousands of unknowns, so an optimizer must be exceptionally efficient. In this study, a...
Institute of Scientific and Technical Information of China (English)
Yong Zhang; Yanqun Chang; Zhenfang Liu; Qingxi Fu; Xiao Zhang
2006-01-01
BACKGROUND: Neuroglobin (NGB), as newly discovered the third member of the globin family binding oxygen, mainly exists in brain of human beings and vertebrates, and it is closely correlated with the oxygen supply in brain.OBJECTIVE : To observe the changes of the expression of neuroglobin and number of positive cells labeled immunohistochemically following cerebral ischemia in gerbils after hypoxic preconditioning. DESIGN: A complete randomized grouping design and controlled experiment. SETTING: Department of Neurology, Department of Anesthesia, Shandong Provincial Hospital, Shandong University.MATERIALS: Sixty-six adult male Mongolian gerbils of clean degree, about 50-65 g, at an average of 57.5 g were provided by the Experimental Animal Center of Capital Medical University [certificate number of animal quality:SCXK(Beijing)2000-0012]. TRNzil (Tianwei Shidai Company, Beijing), polymerase chain reaction (PCR) primers (synthetized by Invitrogen Company, Shanghai); reverse transcription-PCR (RT-PCR) one-step kit (Toyobo Company); PCR instrument (GeneAmp PCR System 240); mice brain NGB monoclonal antibody (Academy of Military Medical Sciences); DAB (Zhongshan Company, Beijing). METHEDS: The study was completed from December 2004 to June 2005 in Shandong Provincial Hospital. ① The 66 gerbils were randomly divided into sham-operated group (n =6), cerebral ischemia group (n =30) and hypoxic preconditioning group (n =30). The gerbils in the hypoxic preconditioning group were put in the environment which contained O2 (0.08 in volume fraction) and N2 (0.92 in volume fraction) at temperature of 25 ℃ for 2 hours. After 5 hours, the gerbils in the hypoxic preconditioning group and cerebral ischemia group were anesthetized, then bilateral common carotid arteries were ligated. In the sham-operated group, bilateral common carotid arteries were only isolated without ligation and hypoxic preconditioning. ②2 At 1, 5, 10, 30 and 60 minutes after cerebral ischemia, the
Feed-forward volume rendering algorithm for moderately parallel MIMD machines
Yagel, Roni
1993-01-01
Algorithms for direct volume rendering on parallel and vector processors are investigated. Volumes are transformed efficiently on parallel processors by dividing the data into slices and beams of voxels. Equal sized sets of slices along one axis are distributed to processors. Parallelism is achieved at two levels. Because each slice can be transformed independently of others, processors transform their assigned slices with no communication, thus providing maximum possible parallelism at the first level. Within each slice, consecutive beams are incrementally transformed using coherency in the transformation computation. Also, coherency across slices can be exploited to further enhance performance. This coherency yields the second level of parallelism through the use of the vector processing or pipelining. Other ongoing efforts include investigations into image reconstruction techniques, load balancing strategies, and improving performance.
Lotgering, F.K.; Bishai, J.M.; Struijk, P.C.; Blood, A.B.; Hunter, C.J.; Oberg, K.C.; Power, G.G.; Longo, L.D.
2004-01-01
OBJECTIVE: To determine to what extent a series of five 1-minute total umbilical cord occlusions, intended to induce ischemic preconditioning (IP), affects the physiologic responses to a 10-minute total umbilical cord occlusion (damaging insult [DI]) 1 hour later and provides cardio- and
Multigrid preconditioned conjugate-gradient method for large-scale wave-front reconstruction.
Gilles, Luc; Vogel, Curtis R; Ellerbroek, Brent L
2002-09-01
We introduce a multigrid preconditioned conjugate-gradient (MGCG) iterative scheme for computing open-loop wave-front reconstructors for extreme adaptive optics systems. We present numerical simulations for a 17-m class telescope with n = 48756 sensor measurement grid points within the aperture, which indicate that our MGCG method has a rapid convergence rate for a wide range of subaperture average slope measurement signal-to-noise ratios. The total computational cost is of order n log n. Hence our scheme provides for fast wave-front simulation and control in large-scale adaptive optics systems.
Van, Mukaddes; Olguner, Cimen; Koca, Uğur; Sişman, Ali Riza; Muratli, Kivanç; Karci, Ayşe; Mavioğlu, Omür; Kilercik, Hakan
2008-04-01
The harmful effects of ischaemia-reperfusion on skeletal muscle during extremity surgery can be diminished by using medications or ischaemic preconditioning Twenty patients undergoing lower-limb surgery with use of a tourniquet for at least 1 hour were included in the study and randomised into two groups: a control group with only tourniquet application (T group; n=10); and an ischaemic preconditioning plus tourniquet group (IP-T group; n=10). Blood samples were obtained from the femoral vein of the relevant extremity before tourniquet application (baseline), immediately after tourniquet deflation (TD), at 10 minutes after the tourniquet deflation (TD(10min)) in the T group and additionally after ischaemic preconditioning in the IP-T group. Venous blood pH, partial oxygen pressure (P(vO2)), partial carbon dioxide pressure (P(vCO2)), lactate, potassium, sodium and glucose levels were analysed using a blood gas analyser. Plasma thiobarbituric acid reactive substances (TBARS) level, an index of lipid peroxidation and oxidative stress, was measured. Heart rate, noninvasive mean arterial pressure (MAP) and spontaneous breathing rate (SBR) were recorded at baseline, at TD, and TD(1min), TD(5min) and TD(10min). MAP decreased and SBR increased significantly at TD, TD(1min) and TD(5min) compared with baseline, and venous blood TBARS level significantly increased at TD and TD(10min) compared with baseline in the T group (all Plactate levels, which was significant compared with baseline (P<0.05) Ischaemic preconditioning attenuates haemodynamic response and lipid peroxidation during lower-extremity surgery with unilateral tourniquet application.
Czech Academy of Sciences Publication Activity Database
Ravingerová, T.; Farkasová, V.; Griecsová, L.; Čarnická, S.; Murariková, M.; Barlaka, E.; Kolář, František; Barteková, M.; Lonek, L.; Slezák, J.; Lazou, A.
2016-01-01
Roč. 65, Suppl.1 (2016), S55-S64 ISSN 0862-8408 Institutional support: RVO:67985823 Keywords : ischemia/reperfusion * remote preconditioning * innate cardioprotection Subject RIV: FA - Cardiovascular Diseases incl. Cardiotharic Surgery Impact factor: 1.461, year: 2016
Parallel processing approach to transform-based image coding
Normile, James O.; Wright, Dan; Chu, Ken; Yeh, Chia L.
1991-06-01
This paper describes a flexible parallel processing architecture designed for use in real time video processing. The system consists of floating point DSP processors connected to each other via fast serial links, each processor has access to a globally shared memory. A multiple bus architecture in combination with a dual ported memory allows communication with a host control processor. The system has been applied to prototyping of video compression and decompression algorithms. The decomposition of transform based algorithms for decompression into a form suitable for parallel processing is described. A technique for automatic load balancing among the processors is developed and discussed, results ar presented with image statistics and data rates. Finally techniques for accelerating the system throughput are analyzed and results from the application of one such modification described.
International Nuclear Information System (INIS)
Pic, Marc Michel
1995-01-01
Parallel programming covers task-parallelism and data-parallelism. Many problems need both parallelisms. Multi-SIMD computers allow hierarchical approach of these parallelisms. The T++ language, based on C++, is dedicated to exploit Multi-SIMD computers using a programming paradigm which is an extension of array-programming to tasks managing. Our language introduced array of independent tasks to achieve separately (MIMD), on subsets of processors of identical behaviour (SIMD), in order to translate the hierarchical inclusion of data-parallelism in task-parallelism. To manipulate in a symmetrical way tasks and data we propose meta-operations which have the same behaviour on tasks arrays and on data arrays. We explain how to implement this language on our parallel computer SYMPHONIE in order to profit by the locally-shared memory, by the hardware virtualization, and by the multiplicity of communications networks. We analyse simultaneously a typical application of such architecture. Finite elements scheme for Fluid mechanic needs powerful parallel computers and requires large floating points abilities. Lattice gases is an alternative to such simulations. Boolean lattice bases are simple, stable, modular, need to floating point computation, but include numerical noise. Boltzmann lattice gases present large precision of computation, but needs floating points and are only locally stable. We propose a new scheme, called multi-bit, who keeps the advantages of each boolean model to which it is applied, with large numerical precision and reduced noise. Experiments on viscosity, physical behaviour, noise reduction and spurious invariants are shown and implementation techniques for parallel Multi-SIMD computers detailed. (author) [fr
Improving parallel imaging by jointly reconstructing multi-contrast data.
Bilgic, Berkin; Kim, Tae Hyung; Liao, Congyu; Manhard, Mary Kate; Wald, Lawrence L; Haldar, Justin P; Setsompop, Kawin
2018-08-01
To develop parallel imaging techniques that simultaneously exploit coil sensitivity encoding, image phase prior information, similarities across multiple images, and complementary k-space sampling for highly accelerated data acquisition. We introduce joint virtual coil (JVC)-generalized autocalibrating partially parallel acquisitions (GRAPPA) to jointly reconstruct data acquired with different contrast preparations, and show its application in 2D, 3D, and simultaneous multi-slice (SMS) acquisitions. We extend the joint parallel imaging concept to exploit limited support and smooth phase constraints through Joint (J-) LORAKS formulation. J-LORAKS allows joint parallel imaging from limited autocalibration signal region, as well as permitting partial Fourier sampling and calibrationless reconstruction. We demonstrate highly accelerated 2D balanced steady-state free precession with phase cycling, SMS multi-echo spin echo, 3D multi-echo magnetization-prepared rapid gradient echo, and multi-echo gradient recalled echo acquisitions in vivo. Compared to conventional GRAPPA, proposed joint acquisition/reconstruction techniques provide more than 2-fold reduction in reconstruction error. JVC-GRAPPA takes advantage of additional spatial encoding from phase information and image similarity, and employs different sampling patterns across acquisitions. J-LORAKS achieves a more parsimonious low-rank representation of local k-space by considering multiple images as additional coils. Both approaches provide dramatic improvement in artifact and noise mitigation over conventional single-contrast parallel imaging reconstruction. Magn Reson Med 80:619-632, 2018. © 2018 International Society for Magnetic Resonance in Medicine. © 2018 International Society for Magnetic Resonance in Medicine.
Directory of Open Access Journals (Sweden)
P. Itkin
2017-10-01
Full Text Available Ice retreat in the eastern Eurasian Arctic is a consequence of atmospheric and oceanic processes and regional feedback mechanisms acting on the ice cover, both in winter and summer. A correct representation of these processes in numerical models is important, since it will improve predictions of sea ice anomalies along the Northeast Passage and beyond. In this study, we highlight the importance of winter ice dynamics for local summer sea ice anomalies in thickness, volume and extent. By means of airborne sea ice thickness surveys made over pack ice areas in the south-eastern Laptev Sea, we show that years of offshore-directed sea ice transport have a thinning effect on the late-winter sea ice cover. To confirm the preconditioning effect of enhanced offshore advection in late winter on the summer sea ice cover, we perform a sensitivity study using a numerical model. Results verify that the preconditioning effect plays a bigger role for the regional ice extent. Furthermore, they indicate an increase in volume export from the Laptev Sea as a consequence of enhanced offshore advection, which has far-reaching consequences for the entire Arctic sea ice mass balance. Moreover we show that ice dynamics in winter not only preconditions local summer ice extent, but also accelerate fast-ice decay.
2014-01-07
this can have a disastrous effect on convergence rate. Even if steady state is obtained for low Mach number flows (after many iterations ), the results...rally lead do a diagonally dominant left-hand-side matrix, which causes stability problems for implicit Gauss - Seidel schemes. For this reason, matrix... convergence at the stagnation point. The iterations for each airfoil is also reported in Fig. 2. Without preconditioning, dramatic efficiency problems are seen
Kostyuchenko V.; Malinovskaya A.; Mamonova A.
2018-01-01
Introduction. The worldwide expansion of digital technologies and the development of the cyber economy led to emergence of a new digital assets – the cryptographic currency that rapidly growing popularity. The phenomenon of cryptocurrency is relatively new and little investigated. Purpose. The purpose of the article is to substantiate the preconditions for the introduction of accounting and taxation of transactions with cryptic currencies in Ukraine. Results. The article considers the...
Bredeweg, Steef W; Zijlstra, Sjouke; Bessem, Bram; Buist, Ida
2012-09-01
There is no consensus on the aetiology and prevention of running-related injuries in runners. Preconditioning studies among different athlete populations show positive effects on the incidence of sports injuries. A 4-week preconditioning programme in novice runners will reduce the incidence of running-related injuries. Randomised controlled clinical trial; level of evidence, 1. Novice runners (N=432) prepared for a four-mile recreational running event. Participants were allocated to the 4-week preconditioning (PRECON) group (N=211) or the control group (N=221). The PRECON group started a 4-week training programme, prior to the running programme, with walking and hopping exercises. After the 4-week period both groups started a 9-week running programme. In both groups information was registered on running exposure and running-related injuries (RRIs) using an internet-based running log. Primary outcome measure was RRIs per 100 runners. An RRI was defined as any musculoskeletal complaint of the lower extremity or lower back causing restriction of running for at least a week. The incidence of RRIs was 15.2% in the PRECON group and 16.8% in the control group. The difference in RRIs between the groups was not significant (χ(2)=0.161, df=1, p=0.69). This prospective study demonstrated that a 4-week PRECON programme with walking and hopping exercises had no influence on the incidence of RRIs in novice runners.
Zhu, Xiaoling; Yin, Jinbo; Li, Liaoliao; Ma, Lei; Tan, Hongying; Deng, Jiao; Chen, Shaoyang; Zuo, Zhiyi
2013-10-01
Electroacupuncture has been shown to induce a preconditioning effect in the brain. The mechanisms for this protection are not fully elucidated. We hypothesize that this protection is mediated by excitatory amino acid transporters (EAATs) that have been shown to be neuroprotective. To test this hypothesis, two-month old male Sprague-Dawley rats and EAAT type 3 (EAAT3) knockout mice received or did not receive 30-min electroacupuncture once a day for five consecutive days. They were subjected to a 120-min middle cerebral arterial occlusion (MCAO) at 24h after the last electroacupuncture. Neurological outcome was assessed 2days after the MCAO. Brain tissues were harvested at 24h after the last electroacupuncture for Western blotting. Rats subjected to electroacupuncture at the Baihui acupoint had smaller brain infarct volumes and better neurological deficit scores than control rats. Electroacupuncture increased EAAT type 2 (EAAT2) in the cerebral cortex, tended to increase EAAT3 in the hippocampus, and had no effect on EAAT type 1 expression. Dihydrokainate, an EAAT2 inhibitor, worsened the neurological outcome of rats with electroacupuncture pretreatment. Electroacupuncture pretreatment at the Baihui acupoint increased EAAT2 in the cerebral cortex and improved the neurological outcome of EAAT3 knockout mice. Together, our results suggest that EAAT2 may mediate the electroacupuncture preconditioning-induced neuroprotection. Copyright © 2013 Elsevier Ltd. All rights reserved.
Energy Technology Data Exchange (ETDEWEB)
Dobritz, M.; Radkow, T.; Bautz, W.; Fellner, F.A. [Inst. fuer Diagnostische Radiologie, Friedrich-Alexander-Univ. Erlangen-Nuernberg (Germany); Nittka, M. [Siemens Medical Solutions, Erlangen (Germany)
2002-06-01
Purpose: The VIBE (volume interpolated breath-hold examination) sequence in combination with parallel acquisition technique (iPAT: integrated parallel acquisition technique) allows dynamic contrast-enhanced MRI of the liver with high temporal and spatial resolution. The aim of this study was to obtain first clinical experience with this technique for the detection and characterization of focal liver lesions. Materials and Methods: We examined 10 consecutive patients using a 1.5 T MR system (gradient field strength 30 mT/m) with a phased-array coil combination. Following sequences- were acquired: T{sub 2}-w TSE and T{sub 1}-w FLASH, after administration of gadolinium, 6 VIBE sequences with iPAT (TR/TE/matrix/partition thickness/time of acquisition: 6.2 ms/ 3.2 ms/256 x 192/4 mm/13 s), as well as T{sub 1}-weighted FLASH with fat saturation. Two observers evaluated the different sequences concerning the number of lesions and their dignity. Following lesions were found: hepatocellular carcinoma (5 patients), hemangioma (2), metastasis (1), cyst (1), adenoma (1). Results: The VIBE sequences were superior for the detection of lesions with arterial hyperperfusion with a total of 33 focal lesions. 21 lesions were found with T{sub 2}-w TSE and 20 with plain T{sub 1}-weighted FLASH. Diagnostic accuracy increased with the VIBE sequence in comparison to the other sequences. Conclusion: VIBE with iPAT allows MR imaging of the liver with high spatial and temporal resolution providing dynamic contrast-enhanced information about the whole liver. This may lead to improved detection of liver lesions, especially hepatocellular carcinoma. (orig.) [German] Ziel: Die VIBE-Sequenz (Volume Interpolated Breath-hold Examination) in Kombination mit paralleler Bildgebung (iPAT) ermoeglicht eine dynamische kontrastmittel-gestuetzte Untersuchung der Leber in hoher zeitlicher und oertlicher Aufloesung. Ziel war es, erste klinische Erfahrungen mit dieser Technik in der Detektion fokaler
Enhanced nonlinear iterative techniques applied to a nonequilibrium plasma flow
International Nuclear Information System (INIS)
Knoll, D.A.
1998-01-01
The authors study the application of enhanced nonlinear iterative methods to the steady-state solution of a system of two-dimensional convection-diffusion-reaction partial differential equations that describe the partially ionized plasma flow in the boundary layer of a tokamak fusion reactor. This system of equations is characterized by multiple time and spatial scales and contains highly anisotropic transport coefficients due to a strong imposed magnetic field. They use Newton's method to linearize the nonlinear system of equations resulting from an implicit, finite volume discretization of the governing partial differential equations, on a staggered Cartesian mesh. The resulting linear systems are neither symmetric nor positive definite, and are poorly conditioned. Preconditioned Krylov iterative techniques are employed to solve these linear systems. They investigate both a modified and a matrix-free Newton-Krylov implementation, with the goal of reducing CPU cost associated with the numerical formation of the Jacobian. A combination of a damped iteration, mesh sequencing, and a pseudotransient continuation technique is used to enhance global nonlinear convergence and CPU efficiency. GMRES is employed as the Krylov method with incomplete lower-upper (ILU) factorization preconditioning. The goal is to construct a combination of nonlinear and linear iterative techniques for this complex physical problem that optimizes trade-offs between robustness, CPU time, memory requirements, and code complexity. It is shown that a mesh sequencing implementation provides significant CPU savings for fine grid calculations. Performance comparisons of modified Newton-Krylov and matrix-free Newton-Krylov algorithms will be presented
Hsieh, Shang-Hsien
1993-01-01
The principal objective of this research is to develop, test, and implement coarse-grained, parallel-processing strategies for nonlinear dynamic simulations of practical structural problems. There are contributions to four main areas: finite element modeling and analysis of rotational dynamics, numerical algorithms for parallel nonlinear solutions, automatic partitioning techniques to effect load-balancing among processors, and an integrated parallel analysis system.
Using Load Balancing to Scalably Parallelize Sampling-Based Motion Planning Algorithms
Fidel, Adam; Jacobs, Sam Ade; Sharma, Shishir; Amato, Nancy M.; Rauchwerger, Lawrence
2014-01-01
Motion planning, which is the problem of computing feasible paths in an environment for a movable object, has applications in many domains ranging from robotics, to intelligent CAD, to protein folding. The best methods for solving this PSPACE-hard problem are so-called sampling-based planners. Recent work introduced uniform spatial subdivision techniques for parallelizing sampling-based motion planning algorithms that scaled well. However, such methods are prone to load imbalance, as planning time depends on region characteristics and, for most problems, the heterogeneity of the sub problems increases as the number of processors increases. In this work, we introduce two techniques to address load imbalance in the parallelization of sampling-based motion planning algorithms: an adaptive work stealing approach and bulk-synchronous redistribution. We show that applying these techniques to representatives of the two major classes of parallel sampling-based motion planning algorithms, probabilistic roadmaps and rapidly-exploring random trees, results in a more scalable and load-balanced computation on more than 3,000 cores. © 2014 IEEE.
Parallel computing in experimental mechanics and optical measurement: A review (II)
Wang, Tianyi; Kemao, Qian
2018-05-01
With advantages such as non-destructiveness, high sensitivity and high accuracy, optical techniques have successfully integrated into various important physical quantities in experimental mechanics (EM) and optical measurement (OM). However, in pursuit of higher image resolutions for higher accuracy, the computation burden of optical techniques has become much heavier. Therefore, in recent years, heterogeneous platforms composing of hardware such as CPUs and GPUs, have been widely employed to accelerate these techniques due to their cost-effectiveness, short development cycle, easy portability, and high scalability. In this paper, we analyze various works by first illustrating their different architectures, followed by introducing their various parallel patterns for high speed computation. Next, we review the effects of CPU and GPU parallel computing specifically in EM & OM applications in a broad scope, which include digital image/volume correlation, fringe pattern analysis, tomography, hyperspectral imaging, computer-generated holograms, and integral imaging. In our survey, we have found that high parallelism can always be exploited in such applications for the development of high-performance systems.
Using Load Balancing to Scalably Parallelize Sampling-Based Motion Planning Algorithms
Fidel, Adam
2014-05-01
Motion planning, which is the problem of computing feasible paths in an environment for a movable object, has applications in many domains ranging from robotics, to intelligent CAD, to protein folding. The best methods for solving this PSPACE-hard problem are so-called sampling-based planners. Recent work introduced uniform spatial subdivision techniques for parallelizing sampling-based motion planning algorithms that scaled well. However, such methods are prone to load imbalance, as planning time depends on region characteristics and, for most problems, the heterogeneity of the sub problems increases as the number of processors increases. In this work, we introduce two techniques to address load imbalance in the parallelization of sampling-based motion planning algorithms: an adaptive work stealing approach and bulk-synchronous redistribution. We show that applying these techniques to representatives of the two major classes of parallel sampling-based motion planning algorithms, probabilistic roadmaps and rapidly-exploring random trees, results in a more scalable and load-balanced computation on more than 3,000 cores. © 2014 IEEE.
J.A. Cabrera (Jesús); E.A. Ziemba (Elizabeth); L.H. Colbert (Lisa); L.B. Anderson (Lorraine); W.J. Sluiter (Wim); D.J.G.M. Duncker (Dirk); T.A. Butterick (Tammy); J. Sikora (Joseph); H.B. Ward (Herbert B.); R.F. Kelly (Rosemary); E.O. McFalls (Edward)
2012-01-01
textabstractAltered expression of mitochondrial electron transport proteins has been shown in early preconditioned myocardial tissue. We wished to determine whether these alterations persist in the Second Window of Protection (SWOP) and if so, whether a favorable energetic state is facilitated
Zhu, Xiaoling; Yin, Jinbo; Li, Liaoliao; Ma, Lei; Tan, Hongying; Deng, Jiao; Chen, Shaoyang; Zuo, Zhiyi
2013-01-01
Electroacupuncture has been shown to induce a preconditioning effect in the brain. The mechanisms for this protection are not fully elucidated. We hypothesize that this protection is mediated by excitatory amino acid transporters (EAATs) that have been shown to be neuroprotective. To test this hypothesis, two-month old male Sprague-Dawley rats and EAAT type 3 (EAAT3) knockout mice received or did not receive 30-min electroacupuncture once a day for 5 consecutive days. They were subjected to a...
Design strategies for irregularly adapting parallel applications
International Nuclear Information System (INIS)
Oliker, Leonid; Biswas, Rupak; Shan, Hongzhang; Sing, Jaswinder Pal
2000-01-01
Achieving scalable performance for dynamic irregular applications is eminently challenging. Traditional message-passing approaches have been making steady progress towards this goal; however, they suffer from complex implementation requirements. The use of a global address space greatly simplifies the programming task, but can degrade the performance of dynamically adapting computations. In this work, we examine two major classes of adaptive applications, under five competing programming methodologies and four leading parallel architectures. Results indicate that it is possible to achieve message-passing performance using shared-memory programming techniques by carefully following the same high level strategies. Adaptive applications have computational work loads and communication patterns which change unpredictably at runtime, requiring dynamic load balancing to achieve scalable performance on parallel machines. Efficient parallel implementations of such adaptive applications are therefore a challenging task. This work examines the implementation of two typical adaptive applications, Dynamic Remeshing and N-Body, across various programming paradigms and architectural platforms. We compare several critical factors of the parallel code development, including performance, programmability, scalability, algorithmic development, and portability
Parallel computing for event reconstruction in high-energy physics
International Nuclear Information System (INIS)
Wolbers, S.
1993-01-01
Parallel computing has been recognized as a solution to large computing problems. In High Energy Physics offline event reconstruction of detector data is a very large computing problem that has been solved with parallel computing techniques. A review of the parallel programming package CPS (Cooperative Processes Software) developed and used at Fermilab for offline reconstruction of Terabytes of data requiring the delivery of hundreds of Vax-Years per experiment is given. The Fermilab UNIX farms, consisting of 180 Silicon Graphics workstations and 144 IBM RS6000 workstations, are used to provide the computing power for the experiments. Fermilab has had a long history of providing production parallel computing starting with the ACP (Advanced Computer Project) Farms in 1986. The Fermilab UNIX Farms have been in production for over 2 years with 24 hour/day service to experimental user groups. Additional tools for management, control and monitoring these large systems will be described. Possible future directions for parallel computing in High Energy Physics will be given
Parallel analysis tools and new visualization techniques for ultra-large climate data set
Energy Technology Data Exchange (ETDEWEB)
Middleton, Don [National Center for Atmospheric Research, Boulder, CO (United States); Haley, Mary [National Center for Atmospheric Research, Boulder, CO (United States)
2014-12-10
ParVis was a project funded under LAB 10-05: “Earth System Modeling: Advanced Scientific Visualization of Ultra-Large Climate Data Sets”. Argonne was the lead lab with partners at PNNL, SNL, NCAR and UC-Davis. This report covers progress from January 1st, 2013 through Dec 1st, 2014. Two previous reports covered the period from Summer, 2010, through September 2011 and October 2011 through December 2012, respectively. While the project was originally planned to end on April 30, 2013, personnel and priority changes allowed many of the institutions to continue work through FY14 using existing funds. A primary focus of ParVis was introducing parallelism to climate model analysis to greatly reduce the time-to-visualization for ultra-large climate data sets. Work in the first two years was conducted on two tracks with different time horizons: one track to provide immediate help to climate scientists already struggling to apply their analysis to existing large data sets and another focused on building a new data-parallel library and tool for climate analysis and visualization that will give the field a platform for performing analysis and visualization on ultra-large datasets for the foreseeable future. In the final 2 years of the project, we focused mostly on the new data-parallel library and associated tools for climate analysis and visualization.
Chai, Xintao; Wang, Shangxu; Tang, Genyang; Meng, Xiangcui
2017-10-01
The anelastic effects of subsurface media decrease the amplitude and distort the phase of propagating wave. These effects, also referred to as the earth's Q filtering effects, diminish seismic resolution. Ignoring anelastic effects during seismic imaging process generates an image with reduced amplitude and incorrect position of reflectors, especially for highly absorptive media. The numerical instability and the expensive computational cost are major concerns when compensating for anelastic effects during migration. We propose a stable and efficient Q-compensated imaging methodology with compressive sensing, sparsity-promoting, and preconditioning. The stability is achieved by using the Born operator for forward modeling and the adjoint operator for back propagating the residual wavefields. Constructing the attenuation-compensated operators by reversing the sign of attenuation operator is avoided. The method proposed is always stable. To reduce the computational cost that is proportional to the number of wave-equation to be solved (thereby the number of frequencies, source experiments, and iterations), we first subsample over both frequencies and source experiments. We mitigate the artifacts caused by the dimensionality reduction via promoting sparsity of the imaging solutions. We further employ depth- and Q-preconditioning operators to accelerate the convergence rate of iterative migration. We adopt a relatively simple linearized Bregman method to solve the sparsity-promoting imaging problem. Singular value decomposition analysis of the forward operator reveals that attenuation increases the condition number of migration operator, making the imaging problem more ill-conditioned. The visco-acoustic imaging problem converges slower than the acoustic case. The stronger the attenuation, the slower the convergence rate. The preconditioning strategy evidently decreases the condition number of migration operator, which makes the imaging problem less ill-conditioned and
Oses, Carolina; Olivares, Belén; Ezquer, Marcelo; Acosta, Cristian; Bosch, Paul; Donoso, Macarena; Léniz, Patricio; Ezquer, Fernando
2017-01-01
Diabetic neuropathy (DN) is one of the most frequent and troublesome complications of diabetes mellitus. Evidence from diabetic animal models and diabetic patients suggests that reduced availability of neuroprotective and pro-angiogenic factors in the nerves in combination with a chronic pro-inflammatory microenvironment and high level of oxidative stress, contribute to the pathogenesis of DN. Mesenchymal stem cells (MSCs) are of great interest as therapeutic agents for regenerative purposes, since they can secrete a broad range of cytoprotective and anti-inflammatory factors. Therefore, the use of the MSC secretome may represent a promising approach for DN treatment. Recent data indicate that the paracrine potential of MSCs could be boosted by preconditioning these cells with an environmental or pharmacological stimulus, enhancing their therapeutic efficacy. In the present study, we observed that the preconditioning of human adipose tissue-derived MSCs (AD-MSCs) with 150μM or 400μM of the iron chelator deferoxamine (DFX) for 48 hours, increased the abundance of the hypoxia inducible factor 1 alpha (HIF-1α) in a concentration dependent manner, without affecting MSC morphology and survival. Activation of HIF-1α led to the up-regulation of the mRNA levels of pro-angiogenic factors like vascular endothelial growth factor alpha and angiopoietin 1. Furthermore this preconditioning increased the expression of potent neuroprotective factors, including nerve growth factor, glial cell-derived neurotrophic factor and neurotrophin-3, and cytokines with anti-inflammatory activity like IL4 and IL5. Additionally, we observed that these molecules, which could also be used as therapeutics, were also increased in the secretome of MSCs preconditioned with DFX compared to the secretome obtained from non-preconditioned cells. Moreover, DFX preconditioning significantly increased the total antioxidant capacity of the MSC secretome and they showed neuroprotective effects when
Bredeweg, Steef W; Zijlstra, Sjouke; Buist, Ida
2010-09-01
Distance running is a popular recreational exercise. It is a beneficial activity for health and well being. However, running may also cause injuries, especially of the lower extremities. In literature there is no agreement what intrinsic and extrinsic factors cause running related injuries (RRIs). In theory, most RRIs are elicited by training errors, this too much, too soon. In a preconditioning program runners can adapt more gradually to the high mechanical loads of running and will be less susceptible to RRIs. In this study the effectiveness of a 4-week preconditioning program on the incidence of RRIs in novice runners prior to a training program will be studied. The GRONORUN 2 (Groningen Novice Running) study is a two arm randomized controlled trial studying the effect of a 4-week preconditioning (PRECON) program in a group of novice runners. All participants wanted to train for the recreational Groningen 4-Mile running event. The PRECON group started a 4-week preconditioning program with walking and hopping exercises 4 weeks before the start of the training program. The control (CON) and PRECON group started a frequently used 9-week training program in preparation for the Groningen 4-Mile running event.During the follow up period participants registered their running exposure, other sporting activities and running related injuries in an Internet based running log. The primary outcome measure was the number of RRIs. RRI was defined as a musculoskeletal ailment or complaint of the lower extremities or back causing a restriction on running for at least three training sessions. The GRONORUN 2 study will add important information to the existing running science. The concept of preconditioning is easy to implement in existing training programs and will hopefully prevent RRIs especially in novice runners. The Netherlands National Trial Register NTR1906. The NTR is part of the WHO Primary Registries.
[Parallel virtual reality visualization of extreme large medical datasets].
Tang, Min
2010-04-01
On the basis of a brief description of grid computing, the essence and critical techniques of parallel visualization of extreme large medical datasets are discussed in connection with Intranet and common-configuration computers of hospitals. In this paper are introduced several kernel techniques, including the hardware structure, software framework, load balance and virtual reality visualization. The Maximum Intensity Projection algorithm is realized in parallel using common PC cluster. In virtual reality world, three-dimensional models can be rotated, zoomed, translated and cut interactively and conveniently through the control panel built on virtual reality modeling language (VRML). Experimental results demonstrate that this method provides promising and real-time results for playing the role in of a good assistant in making clinical diagnosis.
DEFF Research Database (Denmark)
Løfgren, Bo; Povlsen, Jonas Agerlund; Rasmussen, Lars Ege
2010-01-01
We have found that cardioprotection by l-glutamate mimics protection by classical ischaemic preconditioning (IPC). We investigated whether the effect of IPC involves amino acid transamination and whether IPC modulates myocardial glutamate metabolism. In a glucose-perfused, isolated rat heart model...... subjected to 40 min global no-flow ischaemia and 120 min reperfusion, the effects of IPC (2 cycles of 5 min ischaemia and 5 min reperfusion) and continuous glutamate (20 mm) administration during reperfusion on infarct size and haemodynamic recovery were studied. The effect of inhibiting amino acid...... transamination was evaluated by adding the amino acid transaminase inhibitor amino-oxyacetate (AOA; 0.025 mm) during reperfusion. Changes in coronary effluent, interstitial (microdialysis) and intracellular glutamate ([GLUT](i)) concentrations were measured. Ischaemic preconditioning and postischaemic glutamate...
Scheduling Parallel Jobs Using Migration and Consolidation in the Cloud
Directory of Open Access Journals (Sweden)
Xiaocheng Liu
2012-01-01
Full Text Available An increasing number of high performance computing parallel applications leverages the power of the cloud for parallel processing. How to schedule the parallel applications to improve the quality of service is the key to the successful host of parallel applications in the cloud. The large scale of the cloud makes the parallel job scheduling more complicated as even simple parallel job scheduling problem is NP-complete. In this paper, we propose a parallel job scheduling algorithm named MEASY. MEASY adopts migration and consolidation to enhance the most popular EASY scheduling algorithm. Our extensive experiments on well-known workloads show that our algorithm takes very good care of the quality of service. For two common parallel job scheduling objectives, our algorithm produces an up to 41.1% and an average of 23.1% improvement on the average response time; an up to 82.9% and an average of 69.3% improvement on the average slowdown. Our algorithm is robust even in terms that it allows inaccurate CPU usage estimation and high migration cost. Our approach involves trivial modification on EASY and requires no additional technique; it is practical and effective in the cloud environment.
Jeong, Yun-Mi; Sung, Young Kwan; Kim, Wang-Kyun; Kim, Ji Hye; Kwack, Mi Hee; Yoon, Insoo; Kim, Dae-Duk; Sung, Jong-Hyuk
2013-01-01
Hypoxia induces the survival and regenerative potential of adipose-derived stem cells (ASCs), but there are tremendous needs to find alternative methods for ASC preconditioning. Therefore, this work investigated: (1) the ability of low-dose ultraviolet B (UVB) radiation to stimulate the survival, migration, and tube-forming activity of ASCs in vitro; (2) the ability of UVB preconditioning to enhance the hair growth-promoting capacity of ASCs in vivo; and (3) the mechanism of action for ASC stimulation by UVB. Although high-dose UVB decreased the proliferation of ASCs, low-dose (10 or 20 mJ/cm(2)) treatment increased their survival, migration, and tube-forming activity. In addition, low-dose UVB upregulated the expression of ASC-derived growth factors, and a culture medium conditioned by UVB-irradiated ASCs increased the proliferation of dermal papilla and outer root sheet cells. Notably, injection of UVB-preconditioned ASCs into C(3)H/HeN mice significantly induced the telogen-to-anagen transition and increased new hair weight in vivo. UVB treatment significantly increased the generation of reactive oxygen species (ROS) in cultured ASCs, and inhibition of ROS generation by diphenyleneiodonium chloride (DPI) significantly attenuated UVB-induced ASC stimulation. Furthermore, NADPH oxidase 4 (Nox4) expression was induced in ASCs by UVB irradiation, and Nox4 silencing by small interfering RNA, like DPI, significantly reduced UVB-induced ROS generation. These results suggest that the primary involvement of ROS generation in UVB-mediated ASC stimulation occurs via the Nox4 enzyme. This is the first indication that a low dose of UVB radiation and/or the control of ROS generation could potentially be incorporated into a novel ASC preconditioning method for hair regeneration.
Valdé s, Felipe; Andriulli, Francesco P.; Bagci, Hakan; Michielssen, Eric
2011-01-01
A new regularized single source equation for analyzing scattering from homogeneous penetrable objects is presented. The proposed equation is a linear combination of a Calderón-preconditioned single source electric field integral equation and a
Ukraine Agricultural Land Market Formation Preconditions
Directory of Open Access Journals (Sweden)
Evgen Dankevych
2017-01-01
Full Text Available The theoretical land relations reforming principles were reviewed.Land relations in agriculture transformation process was studied. The land use features were detected and agricultural land use efficiency analysis was conducted.Ukraine land market formation research problems results have been shown. It was established that private land ownership institution ambiguous attitude, rent relations deformation, lack of the property rights ensure mechanism inhibit the land market development. Sociological research of Ukrainian Polesie region to determine the prerequisites for agricultural land marketformation preconditions has been conducted. 787 respondents from Zhytomyr, Rivne and Volyn regions were interviewed. Land shares owners age structure, their distribution by education level, their employment, land shares owners and agricultural enterprises executives to the agricultural land sale moratorium cancellation attitudes, land purchase financial resources, directions of Ukrainian Polissya region land shares use, shares owners land issues level of awareness have been determined during the research. Was substantiated that agricultural land market turnover includes not only land sale moratorium cancellation but also the adoption of the legislative framework and the appropriate infrastructure development, one of the key elements of which is land relations regulation specialized state agency – State Land Bank.
Parallel Algorithms for Graph Optimization using Tree Decompositions
Energy Technology Data Exchange (ETDEWEB)
Sullivan, Blair D [ORNL; Weerapurage, Dinesh P [ORNL; Groer, Christopher S [ORNL
2012-06-01
Although many $\\cal{NP}$-hard graph optimization problems can be solved in polynomial time on graphs of bounded tree-width, the adoption of these techniques into mainstream scientific computation has been limited due to the high memory requirements of the necessary dynamic programming tables and excessive runtimes of sequential implementations. This work addresses both challenges by proposing a set of new parallel algorithms for all steps of a tree decomposition-based approach to solve the maximum weighted independent set problem. A hybrid OpenMP/MPI implementation includes a highly scalable parallel dynamic programming algorithm leveraging the MADNESS task-based runtime, and computational results demonstrate scaling. This work enables a significant expansion of the scale of graphs on which exact solutions to maximum weighted independent set can be obtained, and forms a framework for solving additional graph optimization problems with similar techniques.
Preconditioning of two-by-two block matrix systems with square matrix blocks, with applications
Czech Academy of Sciences Publication Activity Database
Axelsson, Owe
2017-01-01
Roč. 62, č. 6 (2017), s. 537-559 ISSN 0862-7940. [SNA´17 - Seminar on numerical analysis. Ostrava, 30.01.2017-03.02.2017] Institutional support: RVO:68145535 Keywords : preconditioning * Schur complement * transformation * optimal control * implicit time integration Subject RIV: BA - General Mathematics OBOR OECD: Applied mathematics Impact factor: 0.618, year: 2016 http://articles.math.cas.cz/10.21136/AM.2017.0222-17/?type=F
Sharma, Ashish Kumar; Munajjam, Arshee; Vaishnav, Bhawna; Sharma, Richa; Sharma, Ashok; Kishore, Kunal; Sharma, Akash; Sharma, Divya; Kumari, Rita; Tiwari, Ashish; Singh, Santosh Kumar; Gaur, Samir; Jatav, Vijay Singh; Srinivasan, Barthu Parthi; Agarwal, Shyam Sunder
2012-01-01
The present study investigated the effect of garlic (Allium sativum Linn.) aqueous extracts on ischemic preconditioning and ischemia-reperfusion induced cardiac injury, as well as adenosine involvement in ischemic preconditioning and garlic extract induced cardioprotection. A model of ischemia-reperfusion injury was established using Langendorff apparatus. Aqueous extract of garlic dose was standardized (0.5%, 0.4%, 0.3%, 0.2%, 0.1%, 0.07%, 0.05%, 0.03%, 0.01%), and the 0.05% dose was found to be the most effective. Higher doses (more than 0.05%) were highly toxic, causing arrhythmia and cardiodepression, whereas the lower doses were ineffective. Garlic exaggerated the cardioprotective effect of ischemic preconditioning. The cardioprotective effect of ischemic preconditioning and garlic cardioprotection was significantly attenuated by theophylline (1,000 µmol/L) and 8-SPT (10 mg/kg, i.p.) and expressed by increased myocardial infarct size, increased LDH level, and reduced nitrite and adenosine levels. These findings suggest that adenosine is involved in the pharmacological and molecular mechanism of garlic induced cardioprotection and mediated by the modulation of nitric oxide. PMID:23554727
Parallel workflow tools to facilitate human brain MRI post-processing
Directory of Open Access Journals (Sweden)
Zaixu eCui
2015-05-01
Full Text Available Multi-modal magnetic resonance imaging (MRI techniques are widely applied in human brain studies. To obtain specific brain measures of interest from MRI datasets, a number of complex image post-processing steps are typically required. Parallel workflow tools have recently been developed, concatenating individual processing steps and enabling fully automated processing of raw MRI data to obtain the final results. These workflow tools are also designed to make optimal use of available computational resources and to support the parallel processing of different subjects or of independent processing steps for a single subject. Automated, parallel MRI post-processing tools can greatly facilitate relevant brain investigations and are being increasingly applied. In this review, we briefly summarize these parallel workflow tools and discuss relevant issues.
Small file aggregation in a parallel computing system
Faibish, Sorin; Bent, John M.; Tzelnic, Percy; Grider, Gary; Zhang, Jingwang
2014-09-02
Techniques are provided for small file aggregation in a parallel computing system. An exemplary method for storing a plurality of files generated by a plurality of processes in a parallel computing system comprises aggregating the plurality of files into a single aggregated file; and generating metadata for the single aggregated file. The metadata comprises an offset and a length of each of the plurality of files in the single aggregated file. The metadata can be used to unpack one or more of the files from the single aggregated file.
Node-based finite element method for large-scale adaptive fluid analysis in parallel environments
International Nuclear Information System (INIS)
Toshimitsu, Fujisawa; Genki, Yagawa
2003-01-01
In this paper, a FEM-based (finite element method) mesh free method with a probabilistic node generation technique is presented. In the proposed method, all computational procedures, from the mesh generation to the solution of a system of equations, can be performed fluently in parallel in terms of nodes. Local finite element mesh is generated robustly around each node, even for harsh boundary shapes such as cracks. The algorithm and the data structure of finite element calculation are based on nodes, and parallel computing is realized by dividing a system of equations by the row of the global coefficient matrix. In addition, the node-based finite element method is accompanied by a probabilistic node generation technique, which generates good-natured points for nodes of finite element mesh. Furthermore, the probabilistic node generation technique can be performed in parallel environments. As a numerical example of the proposed method, we perform a compressible flow simulation containing strong shocks. Numerical simulations with frequent mesh refinement, which are required for such kind of analysis, can effectively be performed on parallel processors by using the proposed method. (authors)
Node-based finite element method for large-scale adaptive fluid analysis in parallel environments
Energy Technology Data Exchange (ETDEWEB)
Toshimitsu, Fujisawa [Tokyo Univ., Collaborative Research Center of Frontier Simulation Software for Industrial Science, Institute of Industrial Science (Japan); Genki, Yagawa [Tokyo Univ., Department of Quantum Engineering and Systems Science (Japan)
2003-07-01
In this paper, a FEM-based (finite element method) mesh free method with a probabilistic node generation technique is presented. In the proposed method, all computational procedures, from the mesh generation to the solution of a system of equations, can be performed fluently in parallel in terms of nodes. Local finite element mesh is generated robustly around each node, even for harsh boundary shapes such as cracks. The algorithm and the data structure of finite element calculation are based on nodes, and parallel computing is realized by dividing a system of equations by the row of the global coefficient matrix. In addition, the node-based finite element method is accompanied by a probabilistic node generation technique, which generates good-natured points for nodes of finite element mesh. Furthermore, the probabilistic node generation technique can be performed in parallel environments. As a numerical example of the proposed method, we perform a compressible flow simulation containing strong shocks. Numerical simulations with frequent mesh refinement, which are required for such kind of analysis, can effectively be performed on parallel processors by using the proposed method. (authors)
A parallel algorithm for switch-level timing simulation on a hypercube multiprocessor
Rao, Hariprasad Nannapaneni
1989-01-01
The parallel approach to speeding up simulation is studied, specifically the simulation of digital LSI MOS circuitry on the Intel iPSC/2 hypercube. The simulation algorithm is based on RSIM, an event driven switch-level simulator that incorporates a linear transistor model for simulating digital MOS circuits. Parallel processing techniques based on the concepts of Virtual Time and rollback are utilized so that portions of the circuit may be simulated on separate processors, in parallel for as large an increase in speed as possible. A partitioning algorithm is also developed in order to subdivide the circuit for parallel processing.
Key cognitive preconditions for the evolution of language.
Donald, Merlin
2017-02-01
Languages are socially constructed systems of expression, generated interactively in social networks, which can be assimilated by the individual brain as it develops. Languages co-evolved with culture, reflecting the changing complexity of human culture as it acquired the properties of a distributed cognitive system. Two key preconditions set the stage for the evolution of such cultures: a very general ability to rehearse and refine skills (evident early in hominin evolution in toolmaking), and the emergence of material culture as an external (to the brain) memory record that could retain and accumulate knowledge across generations. The ability to practice and rehearse skill provided immediate survival-related benefits in that it expanded the physical powers of early hominins, but the same adaptation also provided the imaginative substrate for a system of "mimetic" expression, such as found in ritual and pantomime, and in proto-words, which performed an expressive function somewhat like the home signs of deaf non-signers. The hominid brain continued to adapt to the increasing importance and complexity of culture as human interactions with material culture became more complex; above all, this entailed a gradual expansion in the integrative systems of the brain, especially those involved in the metacognitive supervision of self-performances. This supported a style of embodied mimetic imagination that improved the coordination of shared activities such as fire tending, but also in rituals and reciprocal mimetic games. The time-depth of this mimetic adaptation, and its role in both the construction and acquisition of languages, explains the importance of mimetic expression in the media, religion, and politics. Spoken language evolved out of voco-mimesis, and emerged long after the more basic abilities needed to refine skill and share intentions, probably coinciding with the common ancestor of sapient humans. Self-monitoring and self-supervised practice were necessary
Parallel computers and three-dimensional computational electromagnetics
International Nuclear Information System (INIS)
Madsen, N.K.
1994-01-01
The authors have continued to enhance their ability to use new massively parallel processing computers to solve time-domain electromagnetic problems. New vectorization techniques have improved the performance of their code DSI3D by factors of 5 to 15, depending on the computer used. New radiation boundary conditions and far-field transformations now allow the computation of radar cross-section values for complex objects. A new parallel-data extraction code has been developed that allows the extraction of data subsets from large problems, which have been run on parallel computers, for subsequent post-processing on workstations with enhanced graphics capabilities. A new charged-particle-pushing version of DSI3D is under development. Finally, DSI3D has become a focal point for several new Cooperative Research and Development Agreement activities with industrial companies such as Lockheed Advanced Development Company, Varian, Hughes Electron Dynamics Division, General Atomic, and Cray
Nederlof, Rianne; Weber, Nina C.; Juffermans, Nicole P.; de Mol, Bas A. M. J.; Hollmann, Markus W.; Preckel, Benedikt; Zuurbier, Coert J.
2017-01-01
Remote ischemic preconditioning (RIPC) efficacy is debated. Possibly, because propofol, which has a RIPC-inhibiting action, is used in most RIPC trials. It has been suggested that clinical efficacy is, however, present with volatile anesthesia in the absence of propofol, although this is based on
Structured building model reduction toward parallel simulation
Energy Technology Data Exchange (ETDEWEB)
Dobbs, Justin R. [Cornell University; Hencey, Brondon M. [Cornell University
2013-08-26
Building energy model reduction exchanges accuracy for improved simulation speed by reducing the number of dynamical equations. Parallel computing aims to improve simulation times without loss of accuracy but is poorly utilized by contemporary simulators and is inherently limited by inter-processor communication. This paper bridges these disparate techniques to implement efficient parallel building thermal simulation. We begin with a survey of three structured reduction approaches that compares their performance to a leading unstructured method. We then use structured model reduction to find thermal clusters in the building energy model and allocate processing resources. Experimental results demonstrate faster simulation and low error without any interprocessor communication.
Parallel imaging with phase scrambling.
Zaitsev, Maxim; Schultz, Gerrit; Hennig, Juergen; Gruetter, Rolf; Gallichan, Daniel
2015-04-01
Most existing methods for accelerated parallel imaging in MRI require additional data, which are used to derive information about the sensitivity profile of each radiofrequency (RF) channel. In this work, a method is presented to avoid the acquisition of separate coil calibration data for accelerated Cartesian trajectories. Quadratic phase is imparted to the image to spread the signals in k-space (aka phase scrambling). By rewriting the Fourier transform as a convolution operation, a window can be introduced to the convolved chirp function, allowing a low-resolution image to be reconstructed from phase-scrambled data without prominent aliasing. This image (for each RF channel) can be used to derive coil sensitivities to drive existing parallel imaging techniques. As a proof of concept, the quadratic phase was applied by introducing an offset to the x(2) - y(2) shim and the data were reconstructed using adapted versions of the image space-based sensitivity encoding and GeneRalized Autocalibrating Partially Parallel Acquisitions algorithms. The method is demonstrated in a phantom (1 × 2, 1 × 3, and 2 × 2 acceleration) and in vivo (2 × 2 acceleration) using a 3D gradient echo acquisition. Phase scrambling can be used to perform parallel imaging acceleration without acquisition of separate coil calibration data, demonstrated here for a 3D-Cartesian trajectory. Further research is required to prove the applicability to other 2D and 3D sampling schemes. © 2014 Wiley Periodicals, Inc.
Enhanced nonlinear iterative techniques applied to a non-equilibrium plasma flow
Energy Technology Data Exchange (ETDEWEB)
Knoll, D.A.; McHugh, P.R. [Idaho National Engineering Lab., Idaho Falls, ID (United States)
1996-12-31
We study the application of enhanced nonlinear iterative methods to the steady-state solution of a system of two-dimensional convection-diffusion-reaction partial differential equations that describe the partially-ionized plasma flow in the boundary layer of a tokamak fusion reactor. This system of equations is characterized by multiple time and spatial scales, and contains highly anisotropic transport coefficients due to a strong imposed magnetic field. We use Newton`s method to linearize the nonlinear system of equations resulting from an implicit, finite volume discretization of the governing partial differential equations, on a staggered Cartesian mesh. The resulting linear systems are neither symmetric nor positive definite, and are poorly conditioned. Preconditioned Krylov iterative techniques are employed to solve these linear systems. We investigate both a modified and a matrix-free Newton-Krylov implementation, with the goal of reducing CPU cost associated with the numerical formation of the Jacobian. A combination of a damped iteration, one-way multigrid and a pseudo-transient continuation technique are used to enhance global nonlinear convergence and CPU efficiency. GMRES is employed as the Krylov method with Incomplete Lower-Upper(ILU) factorization preconditioning. The goal is to construct a combination of nonlinear and linear iterative techniques for this complex physical problem that optimizes trade-offs between robustness, CPU time, memory requirements, and code complexity. It is shown that a one-way multigrid implementation provides significant CPU savings for fine grid calculations. Performance comparisons of the modified Newton-Krylov and matrix-free Newton-Krylov algorithms will be presented.
Aerodynamic shape optimization using preconditioned conjugate gradient methods
Burgreen, Greg W.; Baysal, Oktay
1993-01-01
In an effort to further improve upon the latest advancements made in aerodynamic shape optimization procedures, a systematic study is performed to examine several current solution methodologies as applied to various aspects of the optimization procedure. It is demonstrated that preconditioned conjugate gradient-like methodologies dramatically decrease the computational efforts required for such procedures. The design problem investigated is the shape optimization of the upper and lower surfaces of an initially symmetric (NACA-012) airfoil in inviscid transonic flow and at zero degree angle-of-attack. The complete surface shape is represented using a Bezier-Bernstein polynomial. The present optimization method then automatically obtains supercritical airfoil shapes over a variety of freestream Mach numbers. Furthermore, the best optimization strategy examined resulted in a factor of 8 decrease in computational time as well as a factor of 4 decrease in memory over the most efficient strategies in current use.
Domain decomposition methods for solving an image problem
Energy Technology Data Exchange (ETDEWEB)
Tsui, W.K.; Tong, C.S. [Hong Kong Baptist College (Hong Kong)
1994-12-31
The domain decomposition method is a technique to break up a problem so that ensuing sub-problems can be solved on a parallel computer. In order to improve the convergence rate of the capacitance systems, pre-conditioned conjugate gradient methods are commonly used. In the last decade, most of the efficient preconditioners are based on elliptic partial differential equations which are particularly useful for solving elliptic partial differential equations. In this paper, the authors apply the so called covering preconditioner, which is based on the information of the operator under investigation. Therefore, it is good for various kinds of applications, specifically, they shall apply the preconditioned domain decomposition method for solving an image restoration problem. The image restoration problem is to extract an original image which has been degraded by a known convolution process and additive Gaussian noise.
Heuristic framework for parallel sorting computations | Nwanze ...
African Journals Online (AJOL)
Parallel sorting techniques have become of practical interest with the advent of new multiprocessor architectures. The decreasing cost of these processors will probably in the future, make the solutions that are derived thereof to be more appealing. Efficient algorithms for sorting scheme that are encountered in a number of ...
Efficient implementations of block sparse matrix operations on shared memory vector machines
International Nuclear Information System (INIS)
Washio, T.; Maruyama, K.; Osoda, T.; Doi, S.; Shimizu, F.
2000-01-01
In this paper, we propose vectorization and shared memory-parallelization techniques for block-type random sparse matrix operations in finite element (FEM) applications. Here, a block corresponds to unknowns on one node in the FEM mesh and we assume that the block size is constant over the mesh. First, we discuss some basic vectorization ideas (the jagged diagonal (JAD) format and the segmented scan algorithm) for the sparse matrix-vector product. Then, we extend these ideas to the shared memory parallelization. After that, we show that the techniques can be applied not only to the sparse matrix-vector product but also to the sparse matrix-matrix product, the incomplete or complete sparse LU factorization and preconditioning. Finally, we report the performance evaluation results obtained on an NEC SX-4 shared memory vector machine for linear systems in some FEM applications. (author)
Czech Academy of Sciences Publication Activity Database
Axelsson, Owe; Karátson, J.
2017-01-01
Roč. 210, January 2017 (2017), s. 155-164 ISSN 0377-0427 Institutional support: RVO:68145535 Keywords : finite difference method * error estimates * matrix splitting * preconditioning Subject RIV: BA - General Mathematics OBOR OECD: Applied mathematics Impact factor: 1.357, year: 2016 http://www. science direct.com/ science /article/pii/S0377042716301492?via%3Dihub