Use of the preconditioned conjugate gradient algorithm as a generic solver for mixed-model equations in animal breeding applications.

PubMed

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 essential.

CPDES3: A preconditioned conjugate gradient solver for linear asymmetric matrix equations arising from coupled partial differential equations in three dimensions

NASA Astrophysics Data System (ADS)

Anderson, D. V.; Koniges, A. E.; Shumaker, D. E.

1988-11-01

Many physical problems require the solution of coupled partial differential equations on three-dimensional domains. When the time scales of interest dictate an implicit discretization of the equations a rather complicated global matrix system needs solution. The exact form of the matrix depends on the choice of spatial grids and on the finite element or finite difference approximations employed. CPDES3 allows each spatial operator to have 7, 15, 19, or 27 point stencils and allows for general couplings between all of the component PDE's and it automatically generates the matrix structures needed to perform the algorithm. The resulting sparse matrix equation is solved by either the preconditioned conjugate gradient (CG) method or by the preconditioned biconjugate gradient (BCG) algorithm. An arbitrary number of component equations are permitted only limited by available memory. In the sub-band representation used, we generate an algorithm that is written compactly in terms of indirect induces which is vectorizable on some of the newer scientific computers.

CPDES2: A preconditioned conjugate gradient solver for linear asymmetric matrix equations arising from coupled partial differential equations in two dimensions

NASA Astrophysics Data System (ADS)

Anderson, D. V.; Koniges, A. E.; Shumaker, D. E.

1988-11-01

Many physical problems require the solution of coupled partial differential equations on two-dimensional domains. When the time scales of interest dictate an implicit discretization of the equations a rather complicated global matrix system needs solution. The exact form of the matrix depends on the choice of spatial grids and on the finite element or finite difference approximations employed. CPDES2 allows each spatial operator to have 5 or 9 point stencils and allows for general couplings between all of the component PDE's and it automatically generates the matrix structures needed to perform the algorithm. The resulting sparse matrix equation is solved by either the preconditioned conjugate gradient (CG) method or by the preconditioned biconjugate gradient (BCG) algorithm. An arbitrary number of component equations are permitted only limited by available memory. In the sub-band representation used, we generate an algorithm that is written compactly in terms of indirect indices which is vectorizable on some of the newer scientific computers.

Moving force identification based on modified preconditioned conjugate gradient method

NASA Astrophysics Data System (ADS)

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.

Preconditioned conjugate-gradient methods for low-speed flow calculations

NASA Technical Reports Server (NTRS)

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

NASA Technical Reports Server (NTRS)

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.

Liquid hydrogen turbopump rapid start program. [thermal preconditioning using coatings

NASA Technical Reports Server (NTRS)

Wong, G. S.

1973-01-01

This program was to analyze, test, and evaluate methods of achieving rapid-start of a liquid hydrogen feed system (inlet duct and turbopump) using a minimum of thermal preconditioning time and propellant. The program was divided into four tasks. Task 1 includes analytical studies of the testing conducted in the other three tasks. Task 2 describes the results from laboratory testing of coating samples and the successful adherence of a KX-635 coating to the internal surfaces of the feed system tested in Task 4. Task 3 presents results of testing an uncoated feed system. Tank pressure was varied to determine the effect of flowrate on preconditioning. The discharge volume and the discharge pressure which initiates opening of the discharge valve were varied to determine the effect on deadhead (no through-flow) start transients. Task 4 describes results of testing a similar, internally coated feed system and illustrates the savings in preconditioning time and propellant resulting from the coatings.

A new finite element and finite difference hybrid method for computing electrostatics of ionic solvated biomolecule

NASA Astrophysics Data System (ADS)

Ying, Jinyong; Xie, Dexuan

2015-10-01

The Poisson-Boltzmann equation (PBE) is one widely-used implicit solvent continuum model for calculating electrostatics of ionic solvated biomolecule. In this paper, a new finite element and finite difference hybrid method is presented to solve PBE efficiently based on a special seven-overlapped box partition with one central box containing the solute region and surrounded by six neighboring boxes. In particular, an efficient finite element solver is applied to the central box while a fast preconditioned conjugate gradient method using a multigrid V-cycle preconditioning is constructed for solving a system of finite difference equations defined on a uniform mesh of each neighboring box. Moreover, the PBE domain, the box partition, and an interface fitted tetrahedral mesh of the central box can be generated adaptively for a given PQR file of a biomolecule. This new hybrid PBE solver is programmed in C, Fortran, and Python as a software tool for predicting electrostatics of a biomolecule in a symmetric 1:1 ionic solvent. Numerical results on two test models with analytical solutions and 12 proteins validate this new software tool, and demonstrate its high performance in terms of CPU time and memory usage.

Limb remote-preconditioning protects against focal ischemia in rats and contradicts the dogma of therapeutic time windows for preconditioning

PubMed Central

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

Preconditioned conjugate gradient methods for the Navier-Stokes equations

NASA Technical Reports Server (NTRS)

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.

Scalable Parallel Computation for Extended MHD Modeling of Fusion Plasmas

NASA Astrophysics Data System (ADS)

Glasser, Alan H.

2008-11-01

Parallel solution of a linear system is scalable if simultaneously doubling the number of dependent variables and the number of processors results in little or no increase in the computation time to solution. Two approaches have this property for parabolic systems: multigrid and domain decomposition. Since extended MHD is primarily a hyperbolic rather than a parabolic system, additional steps must be taken to parabolize the linear system to be solved by such a method. Such physics-based preconditioning (PBP) methods have been pioneered by Chac'on, using finite volumes for spatial discretization, multigrid for solution of the preconditioning equations, and matrix-free Newton-Krylov methods for the accurate solution of the full nonlinear preconditioned equations. The work described here is an extension of these methods using high-order spectral element methods and FETI-DP domain decomposition. Application of PBP to a flux-source representation of the physics equations is discussed. The resulting scalability will be demonstrated for simple wave and for ideal and Hall MHD waves.

Preconditioning Strategies for Solving Elliptic Difference Equations on a Multiprocessor.

DTIC Science & Technology

1982-01-01

162, 1977. (MiGr8O] Mitchell, A., Griffiths, D., The Finite Difference Method in Partial Differential Equations , John Wiley & Sons, 1980. [Munk80...ADAL1b T35 AIR FO"CE INST OF TECH WRITG-PATTERSON AFS OH F/6 12/17PR CO ITIONIN STRATEGIES FOR SOLVING ELLIPTIC DIFFERENCE EWA-ETClU) 9UN S C K...TI TLE (ard S.tbr,,I) 5 TYPE OF REP’ORT & F IFIOD C_JVEFO Preconditioning Strategies for Solving Elliptic THESIS/VYYRY#YY0N Difference Equations on

On polynomial preconditioning for indefinite Hermitian matrices

NASA Technical Reports Server (NTRS)

Freund, Roland W.

1989-01-01

The minimal residual method is studied combined with polynomial preconditioning for solving large linear systems (Ax = b) with indefinite Hermitian coefficient matrices (A). The standard approach for choosing the polynomial preconditioners leads to preconditioned systems which are positive definite. Here, a different strategy is studied which leaves the preconditioned coefficient matrix indefinite. More precisely, the polynomial preconditioner is designed to cluster the positive, resp. negative eigenvalues of A around 1, resp. around some negative constant. In particular, it is shown that such indefinite polynomial preconditioners can be obtained as the optimal solutions of a certain two parameter family of Chebyshev approximation problems. Some basic results are established for these approximation problems and a Remez type algorithm is sketched for their numerical solution. The problem of selecting the parameters such that the resulting indefinite polynomial preconditioners speeds up the convergence of minimal residual method optimally is also addressed. An approach is proposed based on the concept of asymptotic convergence factors. Finally, some numerical examples of indefinite polynomial preconditioners are given.

Preconditioning of the background error covariance matrix in data assimilation for the Caspian Sea

NASA Astrophysics Data System (ADS)

Arcucci, Rossella; D'Amore, Luisa; Toumi, Ralf

2017-06-01

Data Assimilation (DA) is an uncertainty quantification technique used for improving numerical forecasted results by incorporating observed data into prediction models. As a crucial point into DA models is the ill conditioning of the covariance matrices involved, it is mandatory to introduce, in a DA software, preconditioning methods. Here we present first studies concerning the introduction of two different preconditioning methods in a DA software we are developing (we named S3DVAR) which implements a Scalable Three Dimensional Variational Data Assimilation model for assimilating sea surface temperature (SST) values collected into the Caspian Sea by using the Regional Ocean Modeling System (ROMS) with observations provided by the Group of High resolution sea surface temperature (GHRSST). We also present the algorithmic strategies we employ.

Comparison of Implicit Schemes for the Incompressible Navier-Stokes Equations

NASA Technical Reports Server (NTRS)

Rogers, Stuart E.

1995-01-01

For a computational flow simulation tool to be useful in a design environment, it must be very robust and efficient. To develop such a tool for incompressible flow applications, a number of different implicit schemes are compared for several two-dimensional flow problems in the current study. The schemes include Point-Jacobi relaxation, Gauss-Seidel line relaxation, incomplete lower-upper decomposition, and the generalized minimum residual method preconditioned with each of the three other schemes. The efficiency of the schemes is measured in terms of the computing time required to obtain a steady-state solution for the laminar flow over a backward-facing step, the flow over a NACA 4412 airfoil, and the flow over a three-element airfoil using overset grids. The flow solver used in the study is the INS2D code that solves the incompressible Navier-Stokes equations using the method of artificial compressibility and upwind differencing of the convective terms. The results show that the generalized minimum residual method preconditioned with the incomplete lower-upper factorization outperforms all other methods by at least a factor of 2.

The Role of Ionospheric Outflow Preconditioning in Determining Storm Geoeffectiveness

NASA Astrophysics Data System (ADS)

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 outflow greatly influences the geoeffectiveness of magnetospheric storms.

40 CFR 80.52 - Vehicle preconditioning.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 17 2013-07-01 2013-07-01 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...

40 CFR 80.52 - Vehicle preconditioning.

Code of Federal Regulations, 2010 CFR

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...

40 CFR 80.52 - Vehicle preconditioning.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 17 2014-07-01 2014-07-01 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...

40 CFR 80.52 - Vehicle preconditioning.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 17 2012-07-01 2012-07-01 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...

40 CFR 80.52 - Vehicle preconditioning.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 16 2011-07-01 2011-07-01 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...

Solving large test-day models by iteration on data and preconditioned conjugate gradient.

PubMed

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.

On adaptive weighted polynomial preconditioning for Hermitian positive definite matrices

NASA Technical Reports Server (NTRS)

Fischer, Bernd; Freund, Roland W.

1992-01-01

The conjugate gradient algorithm for solving Hermitian positive definite linear systems is usually combined with preconditioning in order to speed up convergence. In recent years, there has been a revival of polynomial preconditioning, motivated by the attractive features of the method on modern architectures. Standard techniques for choosing the preconditioning polynomial are based only on bounds for the extreme eigenvalues. Here a different approach is proposed, which aims at adapting the preconditioner to the eigenvalue distribution of the coefficient matrix. The technique is based on the observation that good estimates for the eigenvalue distribution can be derived after only a few steps of the Lanczos process. This information is then used to construct a weight function for a suitable Chebyshev approximation problem. The solution of this problem yields the polynomial preconditioner. In particular, we investigate the use of Bernstein-Szego weights.

Preconditioned alternating direction method of multipliers for inverse problems with constraints

NASA Astrophysics Data System (ADS)

Jiao, Yuling; Jin, Qinian; Lu, Xiliang; Wang, Weijie

2017-02-01

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.

Development and acceleration of unstructured mesh-based cfd solver

NASA Astrophysics Data System (ADS)

Emelyanov, V.; Karpenko, A.; Volkov, K.

2017-06-01

The study was undertaken as part of a larger effort to establish a common computational fluid dynamics (CFD) code for simulation of internal and external flows and involves some basic validation studies. The governing equations are solved with ¦nite volume code on unstructured meshes. The computational procedure involves reconstruction of the solution in each control volume and extrapolation of the unknowns to find the flow variables on the faces of control volume, solution of Riemann problem for each face of the control volume, and evolution of the time step. The nonlinear CFD solver works in an explicit time-marching fashion, based on a three-step Runge-Kutta stepping procedure. Convergence to a steady state is accelerated by the use of geometric technique and by the application of Jacobi preconditioning for high-speed flows, with a separate low Mach number preconditioning method for use with low-speed flows. The CFD code is implemented on graphics processing units (GPUs). Speedup of solution on GPUs with respect to solution on central processing units (CPU) is compared with the use of different meshes and different methods of distribution of input data into blocks. The results obtained provide promising perspective for designing a GPU-based software framework for applications in CFD.

Solving large mixed linear models using preconditioned conjugate gradient iteration.

PubMed

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.

Hybrid preconditioning for iterative diagonalization of ill-conditioned generalized eigenvalue problems in electronic structure calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cai, Yunfeng, E-mail: yfcai@math.pku.edu.cn; Department of Computer Science, University of California, Davis 95616; Bai, Zhaojun, E-mail: bai@cs.ucdavis.edu

2013-12-15

The iterative diagonalization of a sequence of large ill-conditioned generalized eigenvalue problems is a computational bottleneck in quantum mechanical methods employing a nonorthogonal basis for ab initio electronic structure calculations. We propose a hybrid preconditioning scheme to effectively combine global and locally accelerated preconditioners for rapid iterative diagonalization of such eigenvalue problems. In partition-of-unity finite-element (PUFE) pseudopotential density-functional calculations, employing a nonorthogonal basis, we show that the hybrid preconditioned block steepest descent method is a cost-effective eigensolver, outperforming current state-of-the-art global preconditioning schemes, and comparably efficient for the ill-conditioned generalized eigenvalue problems produced by PUFE as the locally optimal blockmore » preconditioned conjugate-gradient method for the well-conditioned standard eigenvalue problems produced by planewave methods.« less

Preconditioned characteristic boundary conditions based on artificial compressibility method for solution of incompressible flows

NASA Astrophysics Data System (ADS)

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.

Algorithms for the Euler and Navier-Stokes equations for supercomputers

NASA Technical Reports Server (NTRS)

Turkel, E.

1985-01-01

The steady state Euler and Navier-Stokes equations are considered for both compressible and incompressible flow. Methods are found for accelerating the convergence to a steady state. This acceleration is based on preconditioning the system so that it is no longer time consistent. In order that the acceleration technique be scheme-independent, this preconditioning is done at the differential equation level. Applications are presented for very slow flows and also for the incompressible equations.

Condition number estimation of preconditioned matrices.

PubMed

Kushida, Noriyuki

2015-01-01

The present paper introduces a condition number estimation method for preconditioned matrices. The newly developed method provides reasonable results, while the conventional method which is based on the Lanczos connection gives meaningless results. The Lanczos connection based method provides the condition numbers of coefficient matrices of systems of linear equations with information obtained through the preconditioned conjugate gradient method. Estimating the condition number of preconditioned matrices is sometimes important when describing the effectiveness of new preconditionerers or selecting adequate preconditioners. Operating a preconditioner on a coefficient matrix is the simplest method of estimation. However, this is not possible for large-scale computing, especially if computation is performed on distributed memory parallel computers. This is because, the preconditioned matrices become dense, even if the original matrices are sparse. Although the Lanczos connection method can be used to calculate the condition number of preconditioned matrices, it is not considered to be applicable to large-scale problems because of its weakness with respect to numerical errors. Therefore, we have developed a robust and parallelizable method based on Hager's method. The feasibility studies are curried out for the diagonal scaling preconditioner and the SSOR preconditioner with a diagonal matrix, a tri-daigonal matrix and Pei's matrix. As a result, the Lanczos connection method contains around 10% error in the results even with a simple problem. On the other hand, the new method contains negligible errors. In addition, the newly developed method returns reasonable solutions when the Lanczos connection method fails with Pei's matrix, and matrices generated with the finite element method.

Boundary conditions in Chebyshev and Legendre methods

NASA Technical Reports Server (NTRS)

Canuto, C.

1984-01-01

Two different ways of treating non-Dirichlet boundary conditions in Chebyshev and Legendre collocation methods are discussed for second order differential problems. An error analysis is provided. The effect of preconditioning the corresponding spectral operators by finite difference matrices is also investigated.

Investigation of Reperfusion Injury and Ischemic Preconditioning in Microsurgry

PubMed Central

Wang, Wei Zhong

2008-01-01

Ischemia/reperfusion (I/R) is inevitable in many vascular and musculoskeletal traumas, diseases, free tissue transfers, and during time-consuming reconstructive surgeries in the extremities. Salvage of a prolonged ischemic extremity or flap still remains a challenge for the microvascular surgeon. One of the common complications after microsurgery is I/R-induced tissue death or I/R injury. Twenty years after the discovery, ischemic preconditioning (IPC) has emerged as a powerful method for attenuating I/R injury in a variety of organs or tissues. However, its therapeutic expectations still need to be fulfilled. In this article, the author reviews some important experimental evidences of I/R injury as well as preconditioning-induced protection in the fields relevant to microsurgery. PMID:18946882

Three-dimensional unstructured grid Euler computations using a fully-implicit, upwind method

NASA Technical Reports Server (NTRS)

Whitaker, David L.

1993-01-01

A method has been developed to solve the Euler equations on a three-dimensional unstructured grid composed of tetrahedra. The method uses an upwind flow solver with a linearized, backward-Euler time integration scheme. Each time step results in a sparse linear system of equations which is solved by an iterative, sparse matrix solver. Local-time stepping, switched evolution relaxation (SER), preconditioning and reuse of the Jacobian are employed to accelerate the convergence rate. Implicit boundary conditions were found to be extremely important for fast convergence. Numerical experiments have shown that convergence rates comparable to that of a multigrid, central-difference scheme are achievable on the same mesh. Results are presented for several grids about an ONERA M6 wing.

Preconditioned conjugate gradient methods for the compressible Navier-Stokes equations

NASA Technical Reports Server (NTRS)

Venkatakrishnan, V.

1990-01-01

The compressible Navier-Stokes equations are solved for a variety of two-dimensional inviscid and viscous problems by preconditioned conjugate gradient-like algorithms. Roe's flux difference splitting technique is used to discretize the inviscid fluxes. The viscous terms are discretized by using central differences. An algebraic turbulence model is also incorporated. The system of linear equations which arises out of the linearization of a fully implicit scheme is solved iteratively by the well known methods of GMRES (Generalized Minimum Residual technique) and Chebyschev iteration. Incomplete LU factorization and block diagonal factorization are used as preconditioners. The resulting algorithm is competitive with the best current schemes, but has wide applications in parallel computing and unstructured mesh computations.

Efficient spectral computation of the stationary states of rotating Bose-Einstein condensates by preconditioned nonlinear conjugate gradient methods

NASA Astrophysics Data System (ADS)

Antoine, Xavier; Levitt, Antoine; Tang, Qinglin

2017-08-01

We propose a preconditioned nonlinear conjugate gradient method coupled with a spectral spatial discretization scheme for computing the ground states (GS) of rotating Bose-Einstein condensates (BEC), modeled by the Gross-Pitaevskii Equation (GPE). We first start by reviewing the classical gradient flow (also known as imaginary time (IMT)) method which considers the problem from the PDE standpoint, leading to numerically solve a dissipative equation. Based on this IMT equation, we analyze the forward Euler (FE), Crank-Nicolson (CN) and the classical backward Euler (BE) schemes for linear problems and recognize classical power iterations, allowing us to derive convergence rates. By considering the alternative point of view of minimization problems, we propose the preconditioned steepest descent (PSD) and conjugate gradient (PCG) methods for the GS computation of the GPE. We investigate the choice of the preconditioner, which plays a key role in the acceleration of the convergence process. The performance of the new algorithms is tested in 1D, 2D and 3D. We conclude that the PCG method outperforms all the previous methods, most particularly for 2D and 3D fast rotating BECs, while being simple to implement.

Multiple solution of linear algebraic systems by an iterative method with recomputed preconditioner in the analysis of microstrip structures

NASA Astrophysics Data System (ADS)

Ahunov, Roman R.; Kuksenko, Sergey P.; Gazizov, Talgat R.

2016-06-01

A multiple solution of linear algebraic systems with dense matrix by iterative methods is considered. To accelerate the process, the recomputing of the preconditioning matrix is used. A priory condition of the recomputing based on change of the arithmetic mean of the current solution time during the multiple solution is proposed. To confirm the effectiveness of the proposed approach, the numerical experiments using iterative methods BiCGStab and CGS for four different sets of matrices on two examples of microstrip structures are carried out. For solution of 100 linear systems the acceleration up to 1.6 times, compared to the approach without recomputing, is obtained.

The U.S. Geological Survey Modular Ground-Water Model - PCGN: A Preconditioned Conjugate Gradient Solver with Improved Nonlinear Control

USGS Publications Warehouse

Naff, Richard L.; Banta, Edward R.

2008-01-01

The preconditioned conjugate gradient with improved nonlinear control (PCGN) package provides addi-tional means by which the solution of nonlinear ground-water flow problems can be controlled as compared to existing solver packages for MODFLOW. Picard iteration is used to solve nonlinear ground-water flow equations by iteratively solving a linear approximation of the nonlinear equations. The linear solution is provided by means of the preconditioned conjugate gradient algorithm where preconditioning is provided by the modi-fied incomplete Cholesky algorithm. The incomplete Cholesky scheme incorporates two levels of fill, 0 and 1, in which the pivots can be modified so that the row sums of the preconditioning matrix and the original matrix are approximately equal. A relaxation factor is used to implement the modified pivots, which determines the degree of modification allowed. The effects of fill level and degree of pivot modification are briefly explored by means of a synthetic, heterogeneous finite-difference matrix; results are reported in the final section of this report. The preconditioned conjugate gradient method is coupled with Picard iteration so as to efficiently solve the nonlinear equations associated with many ground-water flow problems. The description of this coupling of the linear solver with Picard iteration is a primary concern of this document.

Condition Number Estimation of Preconditioned Matrices

PubMed Central

Kushida, Noriyuki

2015-01-01

The present paper introduces a condition number estimation method for preconditioned matrices. The newly developed method provides reasonable results, while the conventional method which is based on the Lanczos connection gives meaningless results. The Lanczos connection based method provides the condition numbers of coefficient matrices of systems of linear equations with information obtained through the preconditioned conjugate gradient method. Estimating the condition number of preconditioned matrices is sometimes important when describing the effectiveness of new preconditionerers or selecting adequate preconditioners. Operating a preconditioner on a coefficient matrix is the simplest method of estimation. However, this is not possible for large-scale computing, especially if computation is performed on distributed memory parallel computers. This is because, the preconditioned matrices become dense, even if the original matrices are sparse. Although the Lanczos connection method can be used to calculate the condition number of preconditioned matrices, it is not considered to be applicable to large-scale problems because of its weakness with respect to numerical errors. Therefore, we have developed a robust and parallelizable method based on Hager’s method. The feasibility studies are curried out for the diagonal scaling preconditioner and the SSOR preconditioner with a diagonal matrix, a tri-daigonal matrix and Pei’s matrix. As a result, the Lanczos connection method contains around 10% error in the results even with a simple problem. On the other hand, the new method contains negligible errors. In addition, the newly developed method returns reasonable solutions when the Lanczos connection method fails with Pei’s matrix, and matrices generated with the finite element method. PMID:25816331

Block Preconditioning to Enable Physics-Compatible Implicit Multifluid Plasma Simulations

NASA Astrophysics Data System (ADS)

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.

Fully Implicit, Nonlinear 3D Extended Magnetohydrodynamics

NASA Astrophysics Data System (ADS)

Chacon, Luis; Knoll, Dana

2003-10-01

Extended magnetohydrodynamics (XMHD) includes nonideal effects such as nonlinear, anisotropic transport and two-fluid (Hall) effects. XMHD supports multiple, separate time scales that make explicit time differencing approaches extremely inefficient. While a fully implicit implementation promises efficiency without sacrificing numerical accuracy,(D. A. Knoll et al., phJ. Comput. Phys.) 185 (2), 583-611 (2003) the nonlinear nature of the XMHD system and the numerical stiffness associated with the fast waves make this endeavor difficult. Newton-Krylov methods are, however, ideally suited for such a task. These synergistically combine Newton's method for nonlinear convergence, and Krylov techniques to solve the associated Jacobian (linear) systems. Krylov methods can be implemented Jacobian-free and can be preconditioned for efficiency. Successful preconditioning strategies have been developed for 2D incompressible resistive(L. Chacón et al., phJ. Comput. Phys). 178 (1), 15- 36 (2002) and Hall(L. Chacón and D. A. Knoll, phJ. Comput. Phys.), 188 (2), 573-592 (2003) MHD models. These are based on ``physics-based'' ideas, in which knowledge of the physics is exploited to derive well-conditioned (diagonally-dominant) approximations to the original system that are amenable to optimal solver technologies (multigrid). In this work, we will describe the status of the extension of the 2D preconditioning ideas for a 3D compressible, single-fluid XMHD model.

Improved preconditioned conjugate gradient algorithm and application in 3D inversion of gravity-gradiometry data

NASA Astrophysics Data System (ADS)

Wang, Tai-Han; Huang, Da-Nian; Ma, Guo-Qing; Meng, Zhao-Hai; Li, Ye

2017-06-01

With the continuous development of full tensor gradiometer (FTG) measurement techniques, three-dimensional (3D) inversion of FTG data is becoming increasingly used in oil and gas exploration. In the fast processing and interpretation of large-scale high-precision data, the use of the graphics processing unit process unit (GPU) and preconditioning methods are very important in the data inversion. In this paper, an improved preconditioned conjugate gradient algorithm is proposed by combining the symmetric successive over-relaxation (SSOR) technique and the incomplete Choleksy decomposition conjugate gradient algorithm (ICCG). Since preparing the preconditioner requires extra time, a parallel implement based on GPU is proposed. The improved method is then applied in the inversion of noisecontaminated synthetic data to prove its adaptability in the inversion of 3D FTG data. Results show that the parallel SSOR-ICCG algorithm based on NVIDIA Tesla C2050 GPU achieves a speedup of approximately 25 times that of a serial program using a 2.0 GHz Central Processing Unit (CPU). Real airborne gravity-gradiometry data from Vinton salt dome (southwest Louisiana, USA) are also considered. Good results are obtained, which verifies the efficiency and feasibility of the proposed parallel method in fast inversion of 3D FTG data.

On coupling fluid plasma and kinetic neutral physics models

DOE PAGES

Joseph, I.; Rensink, M. E.; Stotler, D. P.; ...

2017-03-01

The coupled fluid plasma and kinetic neutral physics equations are analyzed through theory and simulation of benchmark cases. It is shown that coupling methods that do not treat the coupling rates implicitly are restricted to short time steps for stability. Fast charge exchange, ionization and recombination coupling rates exist, even after constraining the solution by requiring that the neutrals are at equilibrium. For explicit coupling, the present implementation of Monte Carlo correlated sampling techniques does not allow for complete convergence in slab geometry. For the benchmark case, residuals decay with particle number and increase with grid size, indicating that theymore » scale in a manner that is similar to the theoretical prediction for nonlinear bias error. Progress is reported on implementation of a fully implicit Jacobian-free Newton–Krylov coupling scheme. The present block Jacobi preconditioning method is still sensitive to time step and methods that better precondition the coupled system are under investigation.« less

Higher Order Time Integration Schemes for the Unsteady Navier-Stokes Equations on Unstructured Meshes

NASA Technical Reports Server (NTRS)

Jothiprasad, Giridhar; Mavriplis, Dimitri J.; Caughey, David A.; Bushnell, Dennis M. (Technical Monitor)

2002-01-01

The efficiency gains obtained using higher-order implicit Runge-Kutta schemes as compared with the second-order accurate backward difference schemes for the unsteady Navier-Stokes equations are investigated. Three different algorithms for solving the nonlinear system of equations arising at each timestep are presented. The first algorithm (NMG) is a pseudo-time-stepping scheme which employs a non-linear full approximation storage (FAS) agglomeration multigrid method to accelerate convergence. The other two algorithms are based on Inexact Newton's methods. The linear system arising at each Newton step is solved using iterative/Krylov techniques and left preconditioning is used to accelerate convergence of the linear solvers. One of the methods (LMG) uses Richardson's iterative scheme for solving the linear system at each Newton step while the other (PGMRES) uses the Generalized Minimal Residual method. Results demonstrating the relative superiority of these Newton's methods based schemes are presented. Efficiency gains as high as 10 are obtained by combining the higher-order time integration schemes with the more efficient nonlinear solvers.

Hypoxic preconditioning facilitates acclimatization to hypobaric hypoxia in rat heart.

PubMed

Singh, Mrinalini; Shukla, Dhananjay; Thomas, Pauline; Saxena, Saurabh; Bansal, Anju

2010-12-01

Acute systemic hypoxia induces delayed cardioprotection against ischaemia-reperfusion injury in the heart. As cobalt chloride (CoCl₂) is known to elicit hypoxia-like responses, it was hypothesized that this chemical would mimic the preconditioning effect and facilitate acclimatization to hypobaric hypoxia in rat heart. Male Sprague-Dawley rats treated with distilled water or cobalt chloride (12.5 mg Co/kg for 7 days) were exposed to simulated altitude at 7622 m for different time periods (1, 2, 3 and 5 days). Hypoxic preconditioning with cobalt appreciably attenuated hypobaric hypoxia-induced oxidative damage as observed by a decrease in free radical (reactive oxygen species) generation, oxidation of lipids and proteins. Interestingly, the observed effect was due to increased expression of the antioxidant proteins hemeoxygenase and metallothionein, as no significant change was observed in antioxidant enzyme activity. Hypoxic preconditioning with cobalt increased hypoxia-inducible factor 1α (HIF-1α) expression as well as HIF-1 DNA binding activity, which further resulted in increased expression of HIF-1 regulated genes such as erythropoietin, vascular endothelial growth factor and glucose transporter. A significant decrease was observed in lactate dehydrogenase activity and lactate levels in the heart of preconditioned animals compared with non-preconditioned animals exposed to hypoxia. The results showed that hypoxic preconditioning with cobalt induces acclimatization by up-regulation of hemeoxygenase 1 and metallothionein 1 via HIF-1 stabilization. © 2010 The Authors. JPP © 2010 Royal Pharmaceutical Society of Great Britain.

Choice of Variables and Preconditioning for Time Dependent Problems

NASA Technical Reports Server (NTRS)

Turkel, Eli; Vatsa, Verr N.

2003-01-01

We consider the use of low speed preconditioning for time dependent problems. These are solved using a dual time step approach. We consider the effect of this dual time step on the parameter of the low speed preconditioning. In addition, we compare the use of two sets of variables, conservation and primitive variables, to solve the system. We show the effect of these choices on both the convergence to a steady state and the accuracy of the numerical solutions for low Mach number steady state and time dependent flows.

Using Chebyshev polynomials and approximate inverse triangular factorizations for preconditioning the conjugate gradient method

NASA Astrophysics Data System (ADS)

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.

Brain Injury Lesion Imaging Using Preconditioned Quantitative Susceptibility Mapping without Skull Stripping.

PubMed

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; they were worse on preconditioned quantitative susceptibility mapping. Preconditioned quantitative susceptibility mapping MR imaging can bring the benefits of quantitative susceptibility mapping imaging to clinical practice without the limitations of mask-based quantitative susceptibility mapping, especially for evaluating cerebral microhemorrhage-associated pathologies, such as traumatic brain injury. © 2018 by American Journal of Neuroradiology.

Time integration algorithms for the two-dimensional Euler equations on unstructured meshes

NASA Technical Reports Server (NTRS)

Slack, David C.; Whitaker, D. L.; Walters, Robert W.

1994-01-01

Explicit and implicit time integration algorithms for the two-dimensional Euler equations on unstructured grids are presented. Both cell-centered and cell-vertex finite volume upwind schemes utilizing Roe's approximate Riemann solver are developed. For the cell-vertex scheme, a four-stage Runge-Kutta time integration, a fourstage Runge-Kutta time integration with implicit residual averaging, a point Jacobi method, a symmetric point Gauss-Seidel method and two methods utilizing preconditioned sparse matrix solvers are presented. For the cell-centered scheme, a Runge-Kutta scheme, an implicit tridiagonal relaxation scheme modeled after line Gauss-Seidel, a fully implicit lower-upper (LU) decomposition, and a hybrid scheme utilizing both Runge-Kutta and LU methods are presented. A reverse Cuthill-McKee renumbering scheme is employed for the direct solver to decrease CPU time by reducing the fill of the Jacobian matrix. A comparison of the various time integration schemes is made for both first-order and higher order accurate solutions using several mesh sizes, higher order accuracy is achieved by using multidimensional monotone linear reconstruction procedures. The results obtained for a transonic flow over a circular arc suggest that the preconditioned sparse matrix solvers perform better than the other methods as the number of elements in the mesh increases.

Remote ischemic preconditioning and endothelial function in patients with acute myocardial infarction and primary PCI.

PubMed

Manchurov, Vladimir; Ryazankina, Nadezda; Khmara, Tatyana; Skrypnik, Dmitry; Reztsov, Roman; Vasilieva, Elena; Shpektor, Alexander

2014-07-01

Remote ischemic preconditioning by transient limb ischemia reduces myocardial ischemia-reperfusion injury in patients undergoing percutaneous coronary intervention. The aim of the study we report here was to assess the effect of remote ischemic preconditioning on endothelial function in patients with acute myocardial infarction who underwent primary percutaneous coronary intervention. Forty-eight patients with acute myocardial infarction were enrolled. All participants were randomly divided into 2 groups. In Group I (n = 23), remote ischemic preconditioning was performed before primary percutaneous coronary intervention (intermittent arm ischemia-reperfusion through 4 cycles of 5-minute inflation and 5-minute deflation of a blood-pressure cuff to 200 mm Hg). In Group II (n = 25), standard percutaneous coronary intervention without preconditioning was performed. We assessed endothelial function using the flow-mediated dilation test on baseline, then within 1-3 hours after percutaneous coronary intervention, and again on days 2 and 7 after percutaneous coronary intervention. The brachial artery flow-mediated dilation results were significantly higher on the first day after primary percutaneous coronary intervention in the preconditioning group (Group I) than in the control group (Group II) (12.1% vs 0.0%, P = .03, and 11.1% vs 6.3%, P = .016, respectively), and this difference remained on the seventh day (12.3% vs 7.4%, P = .0005, respectively). We demonstrated for the first time that remote ischemic preconditioning before primary percutaneous coronary intervention significantly improves endothelial function in patients with acute myocardial infarction, and this effect remains constant for at least a week. We suppose that the improvement of endothelial function may be one of the possible explanations of the effect of remote ischemic preconditioning. Copyright © 2014 Elsevier Inc. All rights reserved.

Preconditioned steepest descent methods for some nonlinear elliptic equations involving p-Laplacian terms

DOE Office of Scientific and Technical Information (OSTI.GOV)

Feng, Wenqiang, E-mail: wfeng1@vols.utk.edu; Salgado, Abner J., E-mail: asalgad1@utk.edu; Wang, Cheng, E-mail: cwang1@umassd.edu

We describe and analyze preconditioned steepest descent (PSD) solvers for fourth and sixth-order nonlinear elliptic equations that include p-Laplacian terms on periodic domains in 2 and 3 dimensions. The highest and lowest order terms of the equations are constant-coefficient, positive linear operators, which suggests a natural preconditioning strategy. Such nonlinear elliptic equations often arise from time discretization of parabolic equations that model various biological and physical phenomena, in particular, liquid crystals, thin film epitaxial growth and phase transformations. The analyses of the schemes involve the characterization of the strictly convex energies associated with the equations. We first give a generalmore » framework for PSD in Hilbert spaces. Based on certain reasonable assumptions of the linear pre-conditioner, a geometric convergence rate is shown for the nonlinear PSD iteration. We then apply the general theory to the fourth and sixth-order problems of interest, making use of Sobolev embedding and regularity results to confirm the appropriateness of our pre-conditioners for the regularized p-Lapacian problems. Our results include a sharper theoretical convergence result for p-Laplacian systems compared to what may be found in existing works. We demonstrate rigorously how to apply the theory in the finite dimensional setting using finite difference discretization methods. Numerical simulations for some important physical application problems – including thin film epitaxy with slope selection and the square phase field crystal model – are carried out to verify the efficiency of the scheme.« less

Preconditioned steepest descent methods for some nonlinear elliptic equations involving p-Laplacian terms

NASA Astrophysics Data System (ADS)

Feng, Wenqiang; Salgado, Abner J.; Wang, Cheng; Wise, Steven M.

2017-04-01

We describe and analyze preconditioned steepest descent (PSD) solvers for fourth and sixth-order nonlinear elliptic equations that include p-Laplacian terms on periodic domains in 2 and 3 dimensions. The highest and lowest order terms of the equations are constant-coefficient, positive linear operators, which suggests a natural preconditioning strategy. Such nonlinear elliptic equations often arise from time discretization of parabolic equations that model various biological and physical phenomena, in particular, liquid crystals, thin film epitaxial growth and phase transformations. The analyses of the schemes involve the characterization of the strictly convex energies associated with the equations. We first give a general framework for PSD in Hilbert spaces. Based on certain reasonable assumptions of the linear pre-conditioner, a geometric convergence rate is shown for the nonlinear PSD iteration. We then apply the general theory to the fourth and sixth-order problems of interest, making use of Sobolev embedding and regularity results to confirm the appropriateness of our pre-conditioners for the regularized p-Lapacian problems. Our results include a sharper theoretical convergence result for p-Laplacian systems compared to what may be found in existing works. We demonstrate rigorously how to apply the theory in the finite dimensional setting using finite difference discretization methods. Numerical simulations for some important physical application problems - including thin film epitaxy with slope selection and the square phase field crystal model - are carried out to verify the efficiency of the scheme.

Seismic waveform inversion best practices: regional, global and exploration test cases

NASA Astrophysics Data System (ADS)

Modrak, Ryan; Tromp, Jeroen

2016-09-01

Reaching the global minimum of a waveform misfit function requires careful choices about the nonlinear optimization, preconditioning and regularization methods underlying an inversion. Because waveform inversion problems are susceptible to erratic convergence associated with strong nonlinearity, one or two test cases are not enough to reliably inform such decisions. We identify best practices, instead, using four seismic near-surface problems, one regional problem and two global problems. To make meaningful quantitative comparisons between methods, we carry out hundreds of inversions, varying one aspect of the implementation at a time. Comparing nonlinear optimization algorithms, we find that limited-memory BFGS provides computational savings over nonlinear conjugate gradient methods in a wide range of test cases. Comparing preconditioners, we show that a new diagonal scaling derived from the adjoint of the forward operator provides better performance than two conventional preconditioning schemes. Comparing regularization strategies, we find that projection, convolution, Tikhonov regularization and total variation regularization are effective in different contexts. Besides questions of one strategy or another, reliability and efficiency in waveform inversion depend on close numerical attention and care. Implementation details involving the line search and restart conditions have a strong effect on computational cost, regardless of the chosen nonlinear optimization algorithm.

Nested Conjugate Gradient Algorithm with Nested Preconditioning for Non-linear Image Restoration.

PubMed

Skariah, Deepak G; Arigovindan, Muthuvel

2017-06-19

We develop a novel optimization algorithm, which we call Nested Non-Linear Conjugate Gradient algorithm (NNCG), for image restoration based on quadratic data fitting and smooth non-quadratic regularization. The algorithm is constructed as a nesting of two conjugate gradient (CG) iterations. The outer iteration is constructed as a preconditioned non-linear CG algorithm; the preconditioning is performed by the inner CG iteration that is linear. The inner CG iteration, which performs preconditioning for outer CG iteration, itself is accelerated by an another FFT based non-iterative preconditioner. We prove that the method converges to a stationary point for both convex and non-convex regularization functionals. We demonstrate experimentally that proposed method outperforms the well-known majorization-minimization method used for convex regularization, and a non-convex inertial-proximal method for non-convex regularization functional.

The mechanism of protection from 5 (N-ethyl-N-isopropyl)amiloride differs from that of ischemic preconditioning in rabbit heart.

PubMed

Sato, H; Miki, T; Vallabhapurapu, R P; Wang, P; Liu, G S; Cohen, M V; Downey, J M

1997-10-01

We investigated the effects of 5-(N-ethyl-N-isopropyl)amiloride (EIPA) on infarction in isolated rabbit hearts and cardiomyocytes. Thirty min of regional ischemia caused 29.6 +/- 2.8% of the risk zone to infarct in untreated Krebs buffer-perfused hearts. Treatment with EIPA (1 microM) for 20 min starting either 15 min before ischemia or 15 min after the onset of ischemia significantly reduced infarction to 5.4 +/- 2.0% and 7.0 +/- 1.0%, respectively (p < 0.01 versus untreated hearts). In both cases salvage was very similar to that seen with ischemic preconditioning (PC) (7.1 +/- 1.5% infarction). Unlike the case with ischemic preconditioning, however, protection from EIPA was not blocked by 50 microM polymyxin B, a PKC inhibitor, or 1 microM glibenclamide, a KATP channel blocker. Forty-five min of regional ischemia caused 51.0 +/- 2.9% infarction in untreated hearts. Ischemic preconditioning reduced infarction to 23.4 +/- 3.1% (p < 0.001 versus untreated hearts). In these hearts with longer periods of ischemia pretreatment with EIPA reduced infarction similarly to 28.8 +/- 2.1% (p < 0.01 versus untreated hearts). However, when EIPA was combined with ischemic PC, no further reduction in infarction was seen (23.8 +/- 3.5% infarction). To further elucidate the mechanism of EIPA's cardioprotective effect, this agent was also examined in isolated rabbit cardiomyocytes. Preconditioning caused a delay of about 30 min in the progressive increase in osmotic fragility that occurs during simulated ischemia. In contrast, EIPA had no effect on the time course of ischemia-induced osmotic fragility. Furthermore, EIPA treatment did not alter the salutary effect of ischemic preconditioning when the two were combined in this model. We conclude that Na+/H+ exchange inhibition limits myocardial infarction in the isolated rabbit heart by a mechanism which is quite different from that of ischemic preconditioning. Despite the apparently divergent mechanisms, EIPA's cardioprotective effect could not be added to that of ischemic or metabolic preconditioning in these models.

Comparison results on preconditioned SOR-type iterative method for Z-matrices linear systems

NASA Astrophysics Data System (ADS)

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.

The role of hypoxia-inducible factor-1α and vascular endothelial growth factor in late-phase preconditioning with xenon, isoflurane and levosimendan in rat cardiomyocytes

PubMed Central

Goetzenich, Andreas; Hatam, Nima; Preuss, Stephanie; Moza, Ajay; Bleilevens, Christian; Roehl, Anna B.; Autschbach, Rüdiger; Bernhagen, Jürgen; Stoppe, Christian

2014-01-01

OBJECTIVES The protective effects of late-phase preconditioning can be triggered by several stimuli. Unfortunately, the transfer from bench to bedside still represents a challenge, as concomitant medication or diseases influence the complex signalling pathways involved. In an established model of primary neonatal rat cardiomyocytes, we analysed the cardioprotective effects of three different stimulating pharmaceuticals of clinical relevance. The effect of additional β-blocker treatment was studied as these were previously shown to negatively influence preconditioning. METHODS Twenty-four hours prior to hypoxia, cells pre-treated with or without metoprolol (0.55 µg/ml) were preconditioned with isoflurane, levosimendan or xenon. The influences of these stimuli on hypoxia-inducible factor-1α (HIF-1α), vascular endothelial growth factor (VEGF) as well as inducible and endothelial nitric synthase (iNOS/eNOS) and cyclooxygenase-2 (COX-2) were analysed by polymerase chain reaction and western blotting. The preconditioning was proved by trypan blue cell counts following 5 h of hypoxia and confirmed by fluorescence staining. RESULTS Five hours of hypoxia reduced cell survival in unpreconditioned control cells to 44 ± 4%. Surviving cell count was significantly higher in cells preconditioned either by 2 × 15 min isoflurane (70 ± 16%; P = 0.005) or by xenon (59 ± 8%; P = 0.049). Xenon-preconditioned cells showed a significantly elevated content of VEGF (0.025 ± 0.010 IDV [integrated density values when compared with GAPDH] vs 0.003 ± 0.006 IDV in controls; P = 0.0003). The protein expression of HIF-1α was increased both by levosimendan (0.563 ± 0.175 IDV vs 0.142 ± 0.042 IDV in controls; P = 0.0289) and by xenon (0.868 ± 0.222 IDV; P < 0.0001) pretreatment. A significant elevation of mRNA expression of iNOS was measureable following preconditioning by xenon but not by the other chosen stimuli. eNOS mRNA expression was found to be suppressed by β-blocker treatment for all stimuli. In our model, independently of the chosen stimulus, β-blocker treatment had no significant effect on cell survival. CONCLUSIONS We found that the stimulation of late-phase preconditioning involves several distinct pathways that are variably addressed by the different stimuli. In contrast to isoflurane treatment, xenon-induced preconditioning does not lead to an increase in COX-2 gene transcription but to a significant increase in HIF-1α and subsequently VEGF. PMID:24351506

Fetal asphyctic preconditioning modulates the acute cytokine response thereby protecting against perinatal asphyxia in neonatal rats

PubMed Central

2013-01-01

Background Perinatal asphyxia (PA) is a major cause of brain damage and neurodevelopmental impairment in infants. Recent investigations have shown that experimental sublethal fetal asphyxia (FA preconditioning) protects against a subsequent more severe asphyctic insult at birth. The molecular mechanisms of this protection have, however, not been elucidated. Evidence implicates that inflammatory cytokines play a protective role in the induction of ischemic tolerance in the adult brain. Accordingly, we hypothesize that FA preconditioning leads to changes in the fetal cytokine response, thereby protecting the newborn against a subsequent asphyctic insult. Methods In rats, FA preconditioning was induced at embryonic day 17 by clamping the uterine vasculature for 30 min. At term birth, global PA was induced by placing the uterine horns, containing the pups, in a saline bath for 19 min. We assessed, at different time points after FA and PA, mRNA and protein expression of several cytokines and related receptor mRNA levels in total hemispheres of fetal and neonatal brains. Additionally, we measured pSTAT3/STAT3 levels to investigate cellular responses to these cytokines. Results Prenatally, FA induced acute downregulation in IL-1β, TNF-α and IL-10 mRNA levels. At 96 h post FA, IL-6 mRNA and IL-10 protein expression were increased in FA brains compared with controls. Two hours after birth, all proinflammatory cytokines and pSTAT3/STAT3 levels decreased in pups that experienced FA and/or PA. Interestingly, IL-10 and IL-6 mRNA levels increased after PA. When pups were FA preconditioned, however, IL-10 and IL-6 mRNA levels were comparable to those in controls. Conclusions FA leads to prenatal changes in the neuroinflammatory response. This modulation of the cytokine response probably results in the protective inflammatory phenotype seen when combining FA and PA and may have significant implications for preventing post-asphyctic perinatal encephalopathy. PMID:23351591

40 CFR 86.1232-96 - Vehicle preconditioning.

Code of Federal Regulations, 2013 CFR

2013-07-01

... awaiting testing, to prevent unusual loading of the canisters. During this time care must be taken to... vehicles with multiple canisters in a series configuration, the set of canisters must be preconditioned as... designed for vapor load or purge steps, the service port shall be used during testing to precondition the...

[The relationship between ischemic preconditioning-induced infarction size limitation and duration of test myocardial ischemia].

PubMed

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.

On linearization and preconditioning for radiation diffusion coupled to material thermal conduction equations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Feng, Tao, E-mail: fengtao2@mail.ustc.edu.cn; Graduate School of China Academy Engineering Physics, Beijing 100083; An, Hengbin, E-mail: an_hengbin@iapcm.ac.cn

2013-03-01

Jacobian-free Newton–Krylov (JFNK) method is an effective algorithm for solving large scale nonlinear equations. One of the most important advantages of JFNK method is that there is no necessity to form and store the Jacobian matrix of the nonlinear system when JFNK method is employed. However, an approximation of the Jacobian is needed for the purpose of preconditioning. In this paper, JFNK method is employed to solve a class of non-equilibrium radiation diffusion coupled to material thermal conduction equations, and two preconditioners are designed by linearizing the equations in two methods. Numerical results show that the two preconditioning methods canmore » improve the convergence behavior and efficiency of JFNK method.« less

Techniques and Software for Monolithic Preconditioning of Moderately-sized Geodynamic Stokes Flow Problems

NASA Astrophysics Data System (ADS)

Sanan, Patrick; May, Dave A.; Schenk, Olaf; Bollhöffer, Matthias

2017-04-01

Geodynamics simulations typically involve the repeated solution of saddle-point systems arising from the Stokes equations. These computations often dominate the time to solution. Direct solvers are known for their robustness and ``black box'' properties, yet exhibit superlinear memory requirements and time to solution. More complex multilevel-preconditioned iterative solvers have been very successful for large problems, yet their use can require more effort from the practitioner in terms of setting up a solver and choosing its parameters. We champion an intermediate approach, based on leveraging the power of modern incomplete factorization techniques for indefinite symmetric matrices. These provide an interesting alternative in situations in between the regimes where direct solvers are an obvious choice and those where complex, scalable, iterative solvers are an obvious choice. That is, much like their relatives for definite systems, ILU/ICC-preconditioned Krylov methods and ILU/ICC-smoothed multigrid methods, the approaches demonstrated here provide a useful addition to the solver toolkit. We present results with a simple, PETSc-based, open-source Q2-Q1 (Taylor-Hood) finite element discretization, in 2 and 3 dimensions, with the Stokes and Lamé (linear elasticity) saddle point systems. Attention is paid to cases in which full-operator incomplete factorization gives an improvement in time to solution over direct solution methods (which may not even be feasible due to memory limitations), without the complication of more complex (or at least, less-automatic) preconditioners or smoothers. As an important factor in the relevance of these tools is their availability in portable software, we also describe open-source PETSc interfaces to the factorization routines.

Coral thermal tolerance: tuning gene expression to resist thermal stress.

PubMed

Bellantuono, Anthony J; Granados-Cifuentes, Camila; Miller, David J; Hoegh-Guldberg, Ove; Rodriguez-Lanetty, Mauricio

2012-01-01

The acclimatization capacity of corals is a critical consideration in the persistence of coral reefs under stresses imposed by global climate change. The stress history of corals plays a role in subsequent response to heat stress, but the transcriptomic changes associated with these plastic changes have not been previously explored. In order to identify host transcriptomic changes associated with acquired thermal tolerance in the scleractinian coral Acropora millepora, corals preconditioned to a sub-lethal temperature of 3°C below bleaching threshold temperature were compared to both non-preconditioned corals and untreated controls using a cDNA microarray platform. After eight days of hyperthermal challenge, conditions under which non-preconditioned corals bleached and preconditioned corals (thermal-tolerant) maintained Symbiodinium density, a clear differentiation in the transcriptional profiles was revealed among the condition examined. Among these changes, nine differentially expressed genes separated preconditioned corals from non-preconditioned corals, with 42 genes differentially expressed between control and preconditioned treatments, and 70 genes between non-preconditioned corals and controls. Differentially expressed genes included components of an apoptotic signaling cascade, which suggest the inhibition of apoptosis in preconditioned corals. Additionally, lectins and genes involved in response to oxidative stress were also detected. One dominant pattern was the apparent tuning of gene expression observed between preconditioned and non-preconditioned treatments; that is, differences in expression magnitude were more apparent than differences in the identity of genes differentially expressed. Our work revealed a transcriptomic signature underlying the tolerance associated with coral thermal history, and suggests that understanding the molecular mechanisms behind physiological acclimatization would be critical for the modeling of reefs in impending climate change scenarios.

Coral Thermal Tolerance: Tuning Gene Expression to Resist Thermal Stress

PubMed Central

Bellantuono, Anthony J.; Granados-Cifuentes, Camila; Miller, David J.; Hoegh-Guldberg, Ove; Rodriguez-Lanetty, Mauricio

2012-01-01

The acclimatization capacity of corals is a critical consideration in the persistence of coral reefs under stresses imposed by global climate change. The stress history of corals plays a role in subsequent response to heat stress, but the transcriptomic changes associated with these plastic changes have not been previously explored. In order to identify host transcriptomic changes associated with acquired thermal tolerance in the scleractinian coral Acropora millepora, corals preconditioned to a sub-lethal temperature of 3°C below bleaching threshold temperature were compared to both non-preconditioned corals and untreated controls using a cDNA microarray platform. After eight days of hyperthermal challenge, conditions under which non-preconditioned corals bleached and preconditioned corals (thermal-tolerant) maintained Symbiodinium density, a clear differentiation in the transcriptional profiles was revealed among the condition examined. Among these changes, nine differentially expressed genes separated preconditioned corals from non-preconditioned corals, with 42 genes differentially expressed between control and preconditioned treatments, and 70 genes between non-preconditioned corals and controls. Differentially expressed genes included components of an apoptotic signaling cascade, which suggest the inhibition of apoptosis in preconditioned corals. Additionally, lectins and genes involved in response to oxidative stress were also detected. One dominant pattern was the apparent tuning of gene expression observed between preconditioned and non-preconditioned treatments; that is, differences in expression magnitude were more apparent than differences in the identity of genes differentially expressed. Our work revealed a transcriptomic signature underlying the tolerance associated with coral thermal history, and suggests that understanding the molecular mechanisms behind physiological acclimatization would be critical for the modeling of reefs in impending climate change scenarios. PMID:23226355

Morphine Preconditioning Downregulates MicroRNA-134 Expression Against Oxygen-Glucose Deprivation Injuries in Cultured Neurons of Mice.

PubMed

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.

The time dependence of the effect of ischemic preconditioning on successive sprint swimming performance.

PubMed

Lisbôa, Felipe D; Turnes, Tiago; Cruz, Rogério S O; Raimundo, João A G; Pereira, Gustavo S; Caputo, Fabrizio

2017-05-01

The present study aimed to determine the effects of ischemic preconditioning on performance in three successive 50-m swimming trials and to measure stroke rate, stroke length and blood lactate accumulation. Counterbalanced, repeated-measures cross-over study. On two separate days, eleven competitive male swimmers (20±3 years, 182±5cm, 77±5kg) performed three successive 50-m trials in a 50-m swimming pool, preceded by intermittent bilateral cuff inflation (4× 5-min of blood flow restriction+5-min of cuff deflation) at either 220 for thighs and 180mmHg for arms (ischemic preconditioning) or 20mmHg for both limbs (control-treatment). The 50-m trials were conducted 1-, 2-, and 8-h after the procedure. While no ergogenic effect of ischemic preconditioning was observed for 1-h (0.4%, 95% confidence limits of ±0.6%, p=0.215), there were clear beneficial effects of ischemic preconditioning on 2- and 8-h (1.0% and 1.2%, respectively; 95% confidence limits of ±0.6% in both cases, p≤0.002). Furthermore, ischemic preconditioning increased blood lactate accumulation in 2-(p<0.001) and 8-h (p=0.010) and stroke rate for 2- and 8-h in specific 10-m segments (p<0.05). These findings suggest a time-dependent effect of ischemic preconditioning on 50-m swimming performance for competitive athletes, with the time window of the beneficial effect starting after about 2-h and lasting for at least 8-h after ischemic preconditioning. This change in performance was accompanied by an increase in blood lactate accumulation and faster strokes in front crawl. Copyright © 2016 Sports Medicine Australia. Published by Elsevier Ltd. All rights reserved.

Incomplete Sparse Approximate Inverses for Parallel Preconditioning

DOE PAGES

Anzt, Hartwig; Huckle, Thomas K.; Bräckle, Jürgen; ...

2017-10-28

In this study, we propose a new preconditioning method that can be seen as a generalization of block-Jacobi methods, or as a simplification of the sparse approximate inverse (SAI) preconditioners. The “Incomplete Sparse Approximate Inverses” (ISAI) is in particular efficient in the solution of sparse triangular linear systems of equations. Those arise, for example, in the context of incomplete factorization preconditioning. ISAI preconditioners can be generated via an algorithm providing fine-grained parallelism, which makes them attractive for hardware with a high concurrency level. Finally, in a study covering a large number of matrices, we identify the ISAI preconditioner as anmore » attractive alternative to exact triangular solves in the context of incomplete factorization preconditioning.« less

Preconditioning Provides Neuroprotection in Models of CNS Disease: Paradigms and Clinical Significance

PubMed Central

Stetler, R. Anne; Leak, Rehana K.; Gan, Yu; Li, Peiying; Hu, Xiaoming; Jing, Zheng; Chen, Jun; Zigmond, Michael J.; Gao, Yanqin

2014-01-01

Preconditioning is a phenomenon in which brief episodes of a sublethal insult induce robust protection against subsequent lethal injuries. Preconditioning has been observed in multiple organisms and can occur in the brain as well as other tissues. Extensive animal studies suggest that the brain can be preconditioned to resist acute injuries, such as ischemic stroke, neonatal hypoxia/ischemia, trauma, and agents that are used in models of neurodegenerative diseases, such as Parkinson’s disease and Alzheimer’s disease. Effective preconditioning stimuli are numerous and diverse, ranging from transient ischemia, hypoxia, hyperbaric oxygen, hypothermia and hyperthermia, to exposure to neurotoxins and pharmacological agents. The phenomenon of “cross-tolerance,” in which a sublethal stress protects against a different type of injury, suggests that different preconditioning stimuli may confer protection against a wide range of injuries. Research conducted over the past few decades indicates that brain preconditioning is complex, involving multiple effectors such as metabolic inhibition, activation of extra- and intracellular defense mechanisms, a shift in the neuronal excitatory/inhibitory balance, and reduction in inflammatory sequelae. An improved understanding of brain preconditioning should help us identify innovative therapeutic strategies that prevent or at least reduce neuronal damage in susceptible patients. In this review, we focus on the experimental evidence of preconditioning in the brain and systematically survey the models used to develop paradigms for neuroprotection, and then discuss the clinical potential of brain preconditioning. In a subsequent components of this two-part series, we will discuss the cellular and molecular events that are likely to underlie these phenomena. PMID:24389580

Exercise-induced ischemia initiates the second window of protection in humans independent of collateral recruitment.

PubMed

Lambiase, Pier D; Edwards, Richard J; Cusack, Michael R; Bucknall, Clifford A; Redwood, Simon R; Marber, Michael S

2003-04-02

This study was designed to examine if exercise-induced ischemia initiated late preconditioning in humans that becomes manifest during subsequent exercise and serial balloon occlusion of the left anterior descending coronary artery (LAD). The existence of late preconditioning in humans is controversial. We therefore compared myocardial responses to exercise-induced and intracoronary balloon inflation-induced ischemia in two groups of patients subjected to different temporal patterns of ischemia. Thirty patients with stable angina secondary to single-vessel LAD disease underwent percutaneous coronary intervention (PCI) after two separate exercise tolerance test (ETT) protocols designed to investigate isolated early preconditioning (IEP) alone or the second window of protection (SWOP). The IEP subjects underwent three sequential ETTs at least two weeks before PCI. The SWOP subjects underwent five sequential ETTs commencing 24 h before PCI. During PCI there was no significant difference in intracoronary pressure-derived collateral flow index (CFI) between groups (IEP = 0.15 +/- 0.13, SWOP = 0.19 +/- 0.15). In SWOP patients, compared with the initial ETT, the ETT performed 24 h later had a 40% (p < 0.001) increase in time to 0.1-mV ST depression and a 60% (p < 0.05) decrease in ventricular ectopic frequency. During the first balloon inflation, peak ST elevation was reduced by 49% (p < 0.05) in the SWOP versus the IEP group, and the dependence on CFI observed in the IEP group was abolished (analysis of covariance, p < 0.05). The significant attenuation of ST elevation (47%, p < 0.005) seen at the time of the second inflation in the IEP patients was not seen in the SWOP patients. Exercise-induced ischemia triggers late preconditioning in humans, which becomes manifest during exercise and PCI. This is the first evidence that ischemia induced by coronary occlusion is attenuated in humans by a late preconditioning effect induced by exercise.

The survey of preconditioners used for accelerating the rate of convergence in the Gauss-Seidel method

NASA Astrophysics Data System (ADS)

Niki, Hiroshi; Harada, Kyouji; Morimoto, Munenori; Sakakihara, Michio

2004-03-01

Several preconditioned iterative methods reported in the literature have been used for improving the convergence rate of the Gauss-Seidel method. In this article, on the basis of nonnegative matrix, comparisons between some splittings for such preconditioned matrices are derived. Simple numerical examples are also given.

Numerical Treatment of Degenerate Diffusion Equations via Feller's Boundary Classification, and Applications

NASA Technical Reports Server (NTRS)

Cacio, Emanuela; Cohn, Stephen E.; Spigler, Renato

2011-01-01

A numerical method is devised to solve a class of linear boundary-value problems for one-dimensional parabolic equations degenerate at the boundaries. Feller theory, which classifies the nature of the boundary points, is used to decide whether boundary conditions are needed to ensure uniqueness, and, if so, which ones they are. The algorithm is based on a suitable preconditioned implicit finite-difference scheme, grid, and treatment of the boundary data. Second-order accuracy, unconditional stability, and unconditional convergence of solutions of the finite-difference scheme to a constant as the time-step index tends to infinity are further properties of the method. Several examples, pertaining to financial mathematics, physics, and genetics, are presented for the purpose of illustration.

Blended learning in CME: the perception of GP trainers.

PubMed

Te Pas, E; Meinema, J G; Visser, M R M; van Dijk, N

2016-05-01

Blended learning (the combination of electronic methods with traditional teaching methods) has the potential to combine the best of traditional education with the best of computer-mediated training. We chose to develop such an intervention for GP trainers who were undertaking a Continuing Medical Education (CME) course in evidence-based medicine (EBM). This study reports on our experience and investigated the factors influencing the perception on usefulness and logistics of blended learning for learners in CME. In total, 170 GP trainers participated in the intervention. We used questionnaires, observations during the four face-to-face meetings and evaluations in the e-course over one year. Additionally we organised focus groups to gain insight in some of the outcomes of the questionnaires and interpretations of the observations. The GP trainers found the design and the educational method (e-course in combination with meetings) attractive, instructive and complementary. Factors influencing their learning were (1) educational design, (2) educational method, (3) topic of the intervention, (4) time (planning), (5) time (intervention), (6) learning style, (7) technical issues, (8) preconditions and (9) level of difficulty. A close link between daily practice and the educational intervention was considered an important precondition for the success of the intervention in this group of learners. GP trainers were positive about blended learning: they found e-learning a useful way to gain knowledge and the meetings a pleasant way of transferring the knowledge into practice. Although some preconditions should be taken into consideration during its development and implementation, they would participate in similarly designed learning in the future.

A preconditioned formulation of the Cauchy-Riemann equations

NASA Technical Reports Server (NTRS)

Phillips, T. N.

1983-01-01

A preconditioning of the Cauchy-Riemann equations which results in a second-order system is described. This system is shown to have a unique solution if the boundary conditions are chosen carefully. This choice of boundary condition enables the solution of the first-order system to be retrieved. A numerical solution of the preconditioned equations is obtained by the multigrid method.

Preconditioning, postconditioning and their application to clinical cardiology.

PubMed

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.

An M-step preconditioned conjugate gradient method for parallel computation

NASA Technical Reports Server (NTRS)

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.

Stimulus-triggered enhancement of chilling tolerance in zebrafish embryos

PubMed Central

Szabó, Katalin; Budai, Csilla; Losonczi, Eszter; Bernáth, Gergely; Csenki-Bakos, Zsolt; Urbányi, Béla; Pribenszky, Csaba; Horváth, Ákos; Cserepes, Judit

2017-01-01

Background Cryopreservation of zebrafish embryos is still an unsolved problem despite market demand and massive efforts to preserve genetic variation among numerous existing lines. Chilled storage of embryos might be a step towards developing successful cryopreservation, but no methods to date have worked. Methods In the present study, we applied a novel strategy to improve the chilling tolerance of zebrafish embryos by introducing a preconditioning hydrostatic pressure treatment to the embryos. In our experiments, 26-somites and Prim-5 stage zebrafish embryos were chilled at 0°C for 24 hours after preconditioning. Embryo survival rate, ability to reach maturation and fertilizing capacity were tested. Results Our results indicate that applied preconditioning technology made it possible for the chilled embryos to develop normally until maturity, and to produce healthy offspring as normal, thus passing on their genetic material successfully. Treated embryos had a significantly higher survival and better developmental rate, moreover the treated group had a higher ratio of normal morphology during continued development. While all controls from chilled embryos died by 30 day-post-fertilization, the treated group reached maturity (~90–120 days) and were able to reproduce, resulting in offspring in expected quantity and quality. Conclusions Based on our results, we conclude that the preconditioning technology represents a significant improvement in zebrafish embryo chilling tolerance, thus enabling a long-time survival. Furthermore, as embryonic development is arrested during chilled storage this technology also provides a solution to synchronize or delay the development. PMID:28166301

Ischemic preconditioning inhibits over-expression of arginyl-tRNA synthetase gene Rars in ischemia-injured neurons.

PubMed

Shen, Yin; Zhao, Hong-Yang; Wang, Hai-Jun; Wang, Wen-Liang; Zhang, Li-Zhi; Fu, Rong

2016-08-01

The expression changes of Rars gene in ischemia-injured neurons were investigated by detecting its translational product arginyl-tRNA synthetase (ArgRS), and the inhibitory effects of ischemic preconditioning (IPC) on Rars gene were explored. Both IPC model and prolonged ischemia (PI) model were established by using the classic oxygen glucose deprivation (OGD) method. The primary cultured neurons were assigned into the following groups: the experimental group (IPC+PI group), undergoing PI after a short period of IPC; the conditional control group (PI control group), subjected to PI without IPC; blank control group, the normally cultured neurons. The Rars transcriptional activities and ArgRS expression levels were measured at different time points after re-oxygenation (3 h/6 h/12 h/24 h). Data were collected and statistically analyzed. Compared to the blank control group, the Rars activities and ArgRS levels were significantly increased in PI control group, peaking at the time point of 6 h after re-oxygenation. Rars activities and ArgRS levels were significantly lower in the experimental group than in the PI control group at different time points after re-oxygenation. PI insult can induce an escalating activity of Rars and lead to ArgRS over-expression in primary cultured neurons. IPC can inhibit the increased Rars activity and down-regulate ArgRS expression of ischemia-insulted neurons. This mechanism may confer ischemic tolerance on neurons.

Eigenmode Analysis of Boundary Conditions for One-Dimensional Preconditioned Euler Equations

NASA Technical Reports Server (NTRS)

Darmofal, David L.

1998-01-01

An analysis of the effect of local preconditioning on boundary conditions for the subsonic, one-dimensional Euler equations is presented. Decay rates for the eigenmodes of the initial boundary value problem are determined for different boundary conditions. Riemann invariant boundary conditions based on the unpreconditioned Euler equations are shown to be reflective with preconditioning, and, at low Mach numbers, disturbances do not decay. Other boundary conditions are investigated which are non-reflective with preconditioning and numerical results are presented confirming the analysis.

Real-time monitoring of the solution concentration variation during the crystallization process of protein-lysozyme by using digital holographic interferometry.

PubMed

Zhang, Yanyan; Zhao, Jianlin; Di, Jianglei; Jiang, Hongzhen; Wang, Qian; Wang, Jun; Guo, Yunzhu; Yin, Dachuan

2012-07-30

We report a real-time measurement method of the solution concentration variation during the growth of protein-lysozyme crystals based on digital holographic interferometry. A series of holograms containing the information of the solution concentration variation in the whole crystallization process is recorded by CCD. Based on the principle of double-exposure holographic interferometry and the relationship between the phase difference of the reconstructed object wave and the solution concentration, the solution concentration variation with time for arbitrary point in the solution can be obtained, and then the two-dimensional concentration distribution of the solution during crystallization process can also be figured out under the precondition which the refractive index is constant through the light propagation direction. The experimental results turns out that it is feasible to in situ, full-field and real-time monitor the crystal growth process by using this method.

Preconditioning 2D Integer Data for Fast Convex Hull Computations.

PubMed

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.

Interactions of GSK-3β with mitochondrial permeability transition pore modulators during preconditioning: age-associated differences.

PubMed

Zhu, Jiang; Rebecchi, Mario J; Glass, Peter S A; Brink, Peter R; Liu, Lixin

2013-04-01

Anesthetic preconditioning (APC) and ischemic preconditioning (IPC) are lost with normal aging. Here, we investigated age-related difference between phosphoglycogen synthase kinase-3beta (pGSK-3β) and pGSK-3β with modulators of mitochondrial permeability transition pore, including adenine nucleotide translocase (ANT), cyclophilin-D, or voltage-dependent anion channel. APC or IPC significantly increased pGSK-3β in the young groups in both the cytosol and the mitochondria and also significantly increased pGSK-3β in co-immunoprecipitates with ANT. Importantly, the level of cyclophilin-D in co-immunoprecipitates with ANT was significantly decreased in the young APC and IPC groups, but not in old rats. We also found that APC or IPC significantly prolonged mitochondrial permeability transition pore opening time in the young cardiomyocytes under oxidative stress, but not in the elderly. Attenuation of APC or IPC protection in the aging heart is associated with failure to reduce ANT-cyclophilin-D interactions and to decreased pGSK-3β responsiveness of ANT, critical modulators of mitochondrial permeability transition pore.

[Effect of electroacupuncture and moxibustion preconditioning on blood endothelin and creatine kinase contents and myocardial HSP 70 expression in rabbits with myocardial ischemia-reperfusion injury].

PubMed

Wang, Chao; Xie, Wen-juan; Liu, Mi; Yan, Jie; Zhang, Jia-li; Liu, Zhao; Guo, Li-na

2014-10-01

To observe the effect of electroacupuncture (EA) and moxibustion (Moxi) preconditioning of bi- lateral "Neiguan" (PC 6) on plasma endothelin (ET) and serum creatine kinase (CK) contents and myocardial hot shock protein 70 (HSP 70) expression in myocardial ischemia-reperfusion injury (MIRI) rabbits, so as to revel their mechanisms underlying prevention of myocardial ischemia. A total of 72 New Zealand rabbits were randomly divided into sham operation, MIRI model, EA preconditioning and Moxi preconditioning groups (n = 18/group). Each group was further divided into 0 h, 24 h and 48 h (time-point) subgroups (n=6 in each subgroup). The MIRI model was established by occlusion of the anterior descending branch of the left coronary artery for 40 min and reperfusion for 60 min. The contents of plasma ET and serum CK were detected by ELISA, and myocardial HSP 70 expression was detected by immunohistochemistry. EA and Moxi preconditioning were respectively applied to bilateral PC 6 for 20 min, once daily for 5 days. Following MIRI, contents of plasma ET and serum CK contents were significantly increased at 0 h, 24 h and 48 h in comparison with the sham group (P<0.01, P<0.05), while myo- cardial HSP 70 expression at the 3 time-points was moderately increased (P>0.05). Compared with the model groups, plasma ET contents at both 24 h and 48 h in the EA preconditioning group and at 48 h in the Moxi preconditioning group, CK contents at both 24 h and 48 h only in the EA preconditioning group were significantly down-regulated (P<0.01, P<0.05). Myocardial HSP 70 expression levels in the EA and Moxi preconditioning groups were considerably up-regulated at the three time-points in comparison with the model group(P<0.05, P<0.01). Acupuncture and moxibustion pretreatment may suppress MIRI-induced increase of plasma ET and serum CK and up-regulate myocardial HSP 70 protein expression in MIRI rabbits, suggesting a preventive protection action on ischemic myocardium.

The multigrid preconditioned conjugate gradient method

NASA Technical Reports Server (NTRS)

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.

Documentation of a numerical code for the simulation of variable density ground-water flow in three dimensions

USGS Publications Warehouse

Kuiper, L.K.

1985-01-01

A numerical code is documented for the simulation of variable density time dependent groundwater flow in three dimensions. The groundwater density, although variable with distance, is assumed to be constant in time. The Integrated Finite Difference grid elements in the code follow the geologic strata in the modeled area. If appropriate, the determination of hydraulic head in confining beds can be deleted to decrease computation time. The strongly implicit procedure (SIP), successive over-relaxation (SOR), and eight different preconditioned conjugate gradient (PCG) methods are used to solve the approximating equations. The use of the computer program that performs the calculations in the numerical code is emphasized. Detailed instructions are given for using the computer program, including input data formats. An example simulation and the Fortran listing of the program are included. (USGS)

40 CFR 86.132-96 - Vehicle preconditioning.

Code of Federal Regulations, 2013 CFR

2013-07-01

... outdoors awaiting testing, to prevent unusual loading of the canisters. During this time care must be taken... idle again for 1 minute. (H) After the vehicle is turned off the last time, it may be tested for... preconditioned according to the following procedure. For vehicles with multiple canisters in a series...

M-step preconditioned conjugate gradient methods

NASA Technical Reports Server (NTRS)

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.

Low-Rank Correction Methods for Algebraic Domain Decomposition Preconditioners

DOE PAGES

Li, Ruipeng; Saad, Yousef

2017-08-01

This study presents a parallel preconditioning method for distributed sparse linear systems, based on an approximate inverse of the original matrix, that adopts a general framework of distributed sparse matrices and exploits domain decomposition (DD) and low-rank corrections. The DD approach decouples the matrix and, once inverted, a low-rank approximation is applied by exploiting the Sherman--Morrison--Woodbury formula, which yields two variants of the preconditioning methods. The low-rank expansion is computed by the Lanczos procedure with reorthogonalizations. Numerical experiments indicate that, when combined with Krylov subspace accelerators, this preconditioner can be efficient and robust for solving symmetric sparse linear systems. Comparisonsmore » with pARMS, a DD-based parallel incomplete LU (ILU) preconditioning method, are presented for solving Poisson's equation and linear elasticity problems.« less

Low-Rank Correction Methods for Algebraic Domain Decomposition Preconditioners

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Ruipeng; Saad, Yousef

This study presents a parallel preconditioning method for distributed sparse linear systems, based on an approximate inverse of the original matrix, that adopts a general framework of distributed sparse matrices and exploits domain decomposition (DD) and low-rank corrections. The DD approach decouples the matrix and, once inverted, a low-rank approximation is applied by exploiting the Sherman--Morrison--Woodbury formula, which yields two variants of the preconditioning methods. The low-rank expansion is computed by the Lanczos procedure with reorthogonalizations. Numerical experiments indicate that, when combined with Krylov subspace accelerators, this preconditioner can be efficient and robust for solving symmetric sparse linear systems. Comparisonsmore » with pARMS, a DD-based parallel incomplete LU (ILU) preconditioning method, are presented for solving Poisson's equation and linear elasticity problems.« less

Krylov subspace methods on supercomputers

NASA Technical Reports Server (NTRS)

Saad, Youcef

1988-01-01

A short survey of recent research on Krylov subspace methods with emphasis on implementation on vector and parallel computers is presented. Conjugate gradient methods have proven very useful on traditional scalar computers, and their popularity is likely to increase as three-dimensional models gain importance. A conservative approach to derive effective iterative techniques for supercomputers has been to find efficient parallel/vector implementations of the standard algorithms. The main source of difficulty in the incomplete factorization preconditionings is in the solution of the triangular systems at each step. A few approaches consisting of implementing efficient forward and backward triangular solutions are described in detail. Polynomial preconditioning as an alternative to standard incomplete factorization techniques is also discussed. Another efficient approach is to reorder the equations so as to improve the structure of the matrix to achieve better parallelism or vectorization. An overview of these and other ideas and their effectiveness or potential for different types of architectures is given.

Orderings for conjugate gradient preconditionings

NASA Technical Reports Server (NTRS)

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.

Efficient geostatistical inversion of transient groundwater flow using preconditioned nonlinear conjugate gradients

NASA Astrophysics Data System (ADS)

Klein, Ole; Cirpka, Olaf A.; Bastian, Peter; Ippisch, Olaf

2017-04-01

In the geostatistical inverse problem of subsurface hydrology, continuous hydraulic parameter fields, in most cases hydraulic conductivity, are estimated from measurements of dependent variables, such as hydraulic heads, under the assumption that the parameter fields are autocorrelated random space functions. Upon discretization, the continuous fields become large parameter vectors with O (104 -107) elements. While cokriging-like inversion methods have been shown to be efficient for highly resolved parameter fields when the number of measurements is small, they require the calculation of the sensitivity of each measurement with respect to all parameters, which may become prohibitive with large sets of measured data such as those arising from transient groundwater flow. We present a Preconditioned Conjugate Gradient method for the geostatistical inverse problem, in which a single adjoint equation needs to be solved to obtain the gradient of the objective function. Using the autocovariance matrix of the parameters as preconditioning matrix, expensive multiplications with its inverse can be avoided, and the number of iterations is significantly reduced. We use a randomized spectral decomposition of the posterior covariance matrix of the parameters to perform a linearized uncertainty quantification of the parameter estimate. The feasibility of the method is tested by virtual examples of head observations in steady-state and transient groundwater flow. These synthetic tests demonstrate that transient data can reduce both parameter uncertainty and time spent conducting experiments, while the presented methods are able to handle the resulting large number of measurements.

HMC algorithm with multiple time scale integration and mass preconditioning

NASA Astrophysics Data System (ADS)

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.

Projection methods for line radiative transfer in spherical media.

NASA Astrophysics Data System (ADS)

Anusha, L. S.; Nagendra, K. N.

An efficient numerical method called the Preconditioned Bi-Conjugate Gradient (Pre-BiCG) method is presented for the solution of radiative transfer equation in spherical geometry. A variant of this method called Stabilized Preconditioned Bi-Conjugate Gradient (Pre-BiCG-STAB) is also presented. These methods are based on projections on the subspaces of the n dimensional Euclidean space mathbb {R}n called Krylov subspaces. The methods are shown to be faster in terms of convergence rate compared to the contemporary iterative methods such as Jacobi, Gauss-Seidel and Successive Over Relaxation (SOR).

Aerodynamic shape optimization using preconditioned conjugate gradient methods

NASA Technical Reports Server (NTRS)

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.

Preconditioning 2D Integer Data for Fast Convex Hull Computations

PubMed Central

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. PMID:26938221

Bundle block adjustment of large-scale remote sensing data with Block-based Sparse Matrix Compression combined with Preconditioned Conjugate Gradient

NASA Astrophysics Data System (ADS)

Zheng, Maoteng; Zhang, Yongjun; Zhou, Shunping; Zhu, Junfeng; Xiong, Xiaodong

2016-07-01

In recent years, new platforms and sensors in photogrammetry, remote sensing and computer vision areas have become available, such as Unmanned Aircraft Vehicles (UAV), oblique camera systems, common digital cameras and even mobile phone cameras. Images collected by all these kinds of sensors could be used as remote sensing data sources. These sensors can obtain large-scale remote sensing data which consist of a great number of images. Bundle block adjustment of large-scale data with conventional algorithm is very time and space (memory) consuming due to the super large normal matrix arising from large-scale data. In this paper, an efficient Block-based Sparse Matrix Compression (BSMC) method combined with the Preconditioned Conjugate Gradient (PCG) algorithm is chosen to develop a stable and efficient bundle block adjustment system in order to deal with the large-scale remote sensing data. The main contribution of this work is the BSMC-based PCG algorithm which is more efficient in time and memory than the traditional algorithm without compromising the accuracy. Totally 8 datasets of real data are used to test our proposed method. Preliminary results have shown that the BSMC method can efficiently decrease the time and memory requirement of large-scale data.

Hyperbaric oxygen therapy and preconditioning for ischemic and hemorrhagic stroke.

PubMed

Hu, Sheng-Li; Feng, Hua; Xi, Guo-Hua

2016-01-01

To date, the therapeutic methods for ischemic and hemorrhagic stroke are still limited. The lack of oxygen supply is critical for brain injury following stroke. Hyperbaric oxygen (HBO), an approach through a process in which patients breathe in 100% pure oxygen at over 101 kPa, has been shown to facilitate oxygen delivery and increase oxygen supply. Hence, HBO possesses the potentials to produce beneficial effects on stroke. Actually, accumulated basic and clinical evidences have demonstrated that HBO therapy and preconditioning could induce neuroprotective functions via different mechanisms. Nevertheless, the lack of clinical translational study limits the application of HBO. More translational studies and clinical trials are needed in the future to develop effective HBO protocols.

Preserving Symmetry in Preconditioned Krylov Subspace Methods

NASA Technical Reports Server (NTRS)

Chan, Tony F.; Chow, E.; Saad, Y.; Yeung, M. C.

1996-01-01

We consider the problem of solving a linear system Ax = b when A is nearly symmetric and when the system is preconditioned by a symmetric positive definite matrix M. In the symmetric case, one can recover symmetry by using M-inner products in the conjugate gradient (CG) algorithm. This idea can also be used in the nonsymmetric case, and near symmetry can be preserved similarly. Like CG, the new algorithms are mathematically equivalent to split preconditioning, but do not require M to be factored. Better robustness in a specific sense can also be observed. When combined with truncated versions of iterative methods, tests show that this is more effective than the common practice of forfeiting near-symmetry altogether.

miR-21 Contributes to Xenon-conferred Amelioration of Renal Ischemia–Reperfusion Injury in Mice

PubMed Central

Jia, Ping; Teng, Jie; Zou, Jianzhou; Fang, Yi; Zhang, Xiaoyan; Bosnjak, Zeljko J.; Liang, Mingyu; Ding, Xiaoqiang

2015-01-01

Background MicroRNAs participate in the regulation of numerous physiological and disease processes. The in vivo role of microRNAs in anesthetics-conferred organoprotection is unknown. Methods Mice were exposed for 2 h to either 70% xenon, or 70% nitrogen, 24 h before the induction of renal ischemia-reperfusion injury. The role of microRNA, miR-21, in renal protection conferred by the delayed xenon preconditioning was examined using in vivo knockdown of miR-21 and analysis of miR-21 target pathways. Results Xenon preconditioning provided morphologic and functional protection against renal ischemia-reperfusion injury (n = 6), characterized by attenuation of renal tubular damage, apoptosis, and oxidative stress. Xenon preconditioning significantly increased the expression of miR-21 in the mouse kidney. A locked nucleic acid-modified anti–miR-21, given before xenon preconditioning, knocked down miR-21 effectively, and exacerbated subsequent renal ischemia-reperfusion injury. Mice treated with anti–miR-21 and ischemia-reperfusion injury showed significantly higher serum creatinine than antiscrambled oligonucleotides-treated mice, 24 h after ischemia-reperfusion (1.37 ± 0.28 vs. 0.81 ± 0.14 mg/dl; n = 5; P < 0.05). Knockdown of miR-21 induced significant up-regulation of programmed cell death protein 4 and phosphatase and tensin homolog deleted on chromosome 10, two proapoptotic target effectors of miR-21, and resulted in significant down-regulation of phosphorylated protein kinase B and increased tubular cell apoptosis. In addition, xenon preconditioning up-regulated hypoxia-inducible factor-1α and its downstream effector vascular endothelial growth factor in a time-dependent manner. Knockdown of miR-21 resulted in a significant decrease of hypoxia-inducible factor-1α. Conclusions These results indicate that miR-21 contributes to the renoprotective effect of xenon preconditioning. PMID:23681145

Electrical Resistivity Tomography using a finite element based BFGS algorithm with algebraic multigrid preconditioning

NASA Astrophysics Data System (ADS)

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.

Beneficial effects of remote organ ischemic preconditioning on micro-rheological parameters during liver ischemia-reperfusion in the rat.

PubMed

Magyar, Zsuzsanna; Mester, Anita; Nadubinszky, Gabor; Varga, Gabor; Ghanem, Souleiman; Somogyi, Viktoria; Tanczos, Bence; Deak, Adam; Bidiga, Laszlo; Oltean, Mihai; Peto, Katalin; Nemeth, Norbert

2018-04-14

Remote ischemic preconditioning (RIPC) can be protective against the damage. However, there is no consensus on the optimal amount of tissue, the number and duration of the ischemic cycles, and the timing of the preconditioning. The hemorheological background of the process is also unknown. To investigate the effects of remote organ ischemic preconditioning on micro-rheological parameters during liver ischemia-reperfusion in rats. In anesthetized rats 60-minute partial liver ischemia was induced with 120-minute reperfusion (Control, n = 7). In the preconditioned groups a tourniquet was applied on the left thigh for 3×10 minutes 1 hour (RIPC-1, n = 7) or 24 hours (RIPC-24, n = 7) prior to the liver ischemia. Blood samples were taken before the operation and during the reperfusion. Acid-base, hematological parameters, erythrocyte aggregation and deformability were tested. Lactate concentration significantly increased by the end of the reperfusion. Erythrocyte deformability was improved in the RIPC-1 group, erythrocyte aggregation increased during the reperfusion, particularly in the RIPC-24 group. RIPC alleviated several hemorheological changes caused by the liver I/R. However, the optimal timing of the RIPC cannot be defined based on these results.

Effects of preconditioning the rhizosphere of different plant species on biotic methane oxidation kinetics.

PubMed

Ndanga, Éliane M; Lopera, Carolina B; Bradley, Robert L; Cabral, Alexandre R

2016-09-01

The rhizosphere is known as the most active biogeochemical layer of the soil. Therefore, it could be a beneficial environment for biotic methane oxidation. The aim of this study was to document - by means of batch incubation tests - the kinetics of CH4 oxidation in rhizosphere soils that were previously exposed to methane. Soils from three pre-exposure to CH4 zones were sampled: the never-before pre-exposed (NEX), the moderately pre-exposed (MEX) and the very pre-exposed (VEX). For each pre-exposure zone, the rhizosphere of several plant species was collected, pre-incubated, placed in glass vials and submitted to CH4 concentrations varying from 0.5% to 10%. The time to the beginning of CH4 consumption and the CH4 oxidation rate were recorded. The results showed that the fastest CH4 consumption occurred for the very pre-exposed rhizosphere. Specifically, a statistically significant difference in CH4 oxidation half-life was found between the rhizosphere of the VEX vegetated with a mixture of different plants and the NEX vegetated with ryegrass. This difference was attributed to the combined effect of the preconditioning level and plant species as well as to the organic matter content. Regardless of the preconditioning level, the oxidation rate values obtained in this study were comparable to those reported in the reviewed literature for mature compost. Copyright © 2016 Elsevier Ltd. All rights reserved.

Modeling of frequency-domain scalar wave equation with the average-derivative optimal scheme based on a multigrid-preconditioned iterative solver

NASA Astrophysics Data System (ADS)

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.

Exercise and Cardiac Preconditioning Against Ischemia Reperfusion Injury

PubMed Central

Quindry, John C; Hamilton, Karyn L

2013-01-01

Cardiovascular disease (CVD), including ischemia reperfusion (IR) injury, remains a major cause of morbidity and mortality in industrialized nations. Ongoing research is aimed at uncovering therapeutic interventions against IR injury. Regular exercise participation is recognized as an important lifestyle intervention in the prevention and treatment of CVD and IR injury. More recent understanding reveals that moderate intensity aerobic exercise is also an important experimental model for understanding the cellular mechanisms of cardioprotection against IR injury. An important discovery in this regard was the observation that one-to-several days of exercise will attenuate IR injury. This phenomenon has been observed in young and old hearts of both sexes. Due to the short time course of exercise induced protection, IR injury prevention must be mediated by acute biochemical alterations within the myocardium. Research over the last decade reveals that redundant mechanisms account for exercise induced cardioprotection against IR. While much is now known about exercise preconditioning against IR injury, many questions remain. Perhaps most pressing, is what mechanisms mediate cardioprotection in aged hearts and what sex-dependent differences exist. Given that that exercise preconditioning is a polygenic effect, it is likely that multiple mediators of exercise induced cardioprotection have yet to be uncovered. Also unknown, is whether post translational modifications due to exercise are responsible for IR injury prevention. This review will provide an overview the major mechanisms of IR injury and exercise preconditioning. The discussion highlights many promising avenues for further research and describes how exercise preconditioning may continue to be an important scientific paradigm in the translation of cardioprotection research to the clinic. PMID:23909636

The Galvanotactic Migration of Keratinocytes is Enhanced by Hypoxic Preconditioning

PubMed Central

Guo, Xiaowei; Jiang, Xupin; Ren, Xi; Sun, Huanbo; Zhang, Dongxia; Zhang, Qiong; Zhang, Jiaping; Huang, Yuesheng

2015-01-01

The endogenous electric field (EF)-directed migration of keratinocytes (galvanotaxis) into wounds is an essential step in wound re-epithelialization. Hypoxia, which occurs immediately after injury, acts as an early stimulus to initiate the healing process; however, the mechanisms for this effect, remain elusive. We show here that the galvanotactic migration of keratinocytes was enhanced by hypoxia preconditioning as a result of the increased directionality rather than the increased motility of keratinocytes. This enhancement was both oxygen tension- and preconditioning time-dependent, with the maximum effects achieved using 2% O2 preconditioning for 6 hours. Hypoxic preconditioning (2% O2, 6 hours) decreased the threshold voltage of galvanotaxis to < 25 mV/mm, whereas this value was between 25 and 50 mV/mm in the normal culture control. In a scratch-wound monolayer assay in which the applied EF was in the default healing direction, hypoxic preconditioning accelerated healing by 1.38-fold compared with the control conditions. Scavenging of the induced ROS by N-acetylcysteine (NAC) abolished the enhanced galvanotaxis and the accelerated healing by hypoxic preconditioning. Our data demonstrate a novel and unsuspected role of hypoxia in supporting keratinocyte galvanotaxis. Enhancing the galvanotactic response of cells might therefore be a clinically attractive approach to induce improved wound healing. PMID:25988491

Preconditioning for the Navier-Stokes equations with finite-rate chemistry

NASA Technical Reports Server (NTRS)

Godfrey, Andrew G.; Walters, Robert W.; Van Leer, Bram

1993-01-01

The preconditioning procedure for generalized finite-rate chemistry and the proper preconditioning for the one-dimensional Navier-Stokes equations are presented. Eigenvalue stiffness is resolved and convergence-rate acceleration is demonstrated over the entire Mach-number range from the incompressible to the hypersonic. Specific benefits are realized at low and transonic flow speeds. The extended preconditioning matrix accounts for thermal and chemical non-equilibrium and its implementation is explained for both explicit and implicit time marching. The effect of higher-order spatial accuracy and various flux splittings is investigated. Numerical analysis reveals the possible theoretical improvements from using proconditioning at all Mach numbers. Numerical results confirm the expectations from the numerical analysis. Representative test cases include flows with previously troublesome embedded high-condition-number regions.

Leg ischaemia before circulatory arrest alters brain leucocyte count and respiratory chain redox state.

PubMed

Yannopoulos, Fredrik S; Arvola, Oiva; Haapanen, Henri; Herajärvi, Johanna; Miinalainen, Ilkka; Jensen, Hanna; Kiviluoma, Kai; Juvonen, Tatu

2014-03-01

Remote ischaemic preconditioning and its neuroprotective abilities are currently under investigation and the method has shown significant effects in several small and large animal studies. In our previous studies, leucocyte filtration during cardiopulmonary bypass reduced cerebrocortical adherent leucocyte count and mitigated cerebral damage after hypothermic circulatory arrest (HCA) in piglets. This study aimed to obtain and assess direct visual data of leucocyte behaviour in cerebral vessels after hypothermic circulatory arrest following remote ischaemic preconditioning. Twelve native stock piglets were randomized into a remote ischaemic preconditioning group (n = 6) and a control group (n = 6). The intervention group underwent hind-leg ischaemia, whereas the control group received a sham-treatment before a 60-min period of hypothermic circulatory arrest. An intravital microscope was used to obtain measurements from the cerebrocortical vessel in vivo. It included three sets of filters: a violet filter to visualize microvascular perfusion and vessel diameter, a green filter for visualization of rhodamine-labelled leucocytes and an ultraviolet filter for reduced nicotinamide adenine dinucleotide (NADH) analysis. The final magnification on the microscope was 400. After the experiment, cerebral and cerebellar biopsies were collected and analysed with transmission electron microscope by a blinded analyst. In the transmission electron microscope analysis, the entire intervention group had normal, unaffected rough endoplasmic reticulum's in their cerebellar tissue, whereas the control group had a mean score of 1.06 (standard deviation 0.41) (P = 0.026). The measured amount of adherent leucocytes was lower in the remote ischaemic preconditioning group. The difference was statistically significant at 5, 15 and 45 min after circulatory arrest. Statistically significant differences were seen also in the recovery phase at 90 and 120 min after reperfusion. Nicotinamide adenine dinucleotide autofluorescence had statistically significant differences at 10 min after cooling and at 120 and 180 min after hypothermic circulatory arrest. Remote ischaemic preconditioning seems to provide better mitochondrial respiratory chain function as indicated by the higher NADH content. It simultaneously provides a reduction of adherent leucocytes in cerebral vessels after hypothermic circulatory arrest. Additionally, it might provide some degree of cellular organ preservation as implied by the electron microscopy results.

Finding Chemical Reaction Paths with a Multilevel Preconditioning Protocol

PubMed Central

2015-01-01

Finding transition paths for chemical reactions can be computationally costly owing to the level of quantum-chemical theory needed for accuracy. Here, we show that a multilevel preconditioning scheme that was recently introduced (Tempkin et al. J. Chem. Phys.2014, 140, 184114) can be used to accelerate quantum-chemical string calculations. We demonstrate the method by finding minimum-energy paths for two well-characterized reactions: tautomerization of malonaldehyde and Claissen rearrangement of chorismate to prephanate. For these reactions, we show that preconditioning density functional theory (DFT) with a semiempirical method reduces the computational cost for reaching a converged path that is an optimum under DFT by several fold. The approach also shows promise for free energy calculations when thermal noise can be controlled. PMID:25516726

Monolithic multigrid methods for two-dimensional resistive magnetohydrodynamics

DOE PAGES

Adler, James H.; Benson, Thomas R.; Cyr, Eric C.; ...

2016-01-06

Magnetohydrodynamic (MHD) representations are used to model a wide range of plasma physics applications and are characterized by a nonlinear system of partial differential equations that strongly couples a charged fluid with the evolution of electromagnetic fields. The resulting linear systems that arise from discretization and linearization of the nonlinear problem are generally difficult to solve. In this paper, we investigate multigrid preconditioners for this system. We consider two well-known multigrid relaxation methods for incompressible fluid dynamics: Braess--Sarazin relaxation and Vanka relaxation. We first extend these to the context of steady-state one-fluid viscoresistive MHD. Then we compare the two relaxationmore » procedures within a multigrid-preconditioned GMRES method employed within Newton's method. To isolate the effects of the different relaxation methods, we use structured grids, inf-sup stable finite elements, and geometric interpolation. Furthermore, we present convergence and timing results for a two-dimensional, steady-state test problem.« less

Multigrid one shot methods for optimal control problems: Infinite dimensional control

NASA Technical Reports Server (NTRS)

Arian, Eyal; Taasan, Shlomo

1994-01-01

The multigrid one shot method for optimal control problems, governed by elliptic systems, is introduced for the infinite dimensional control space. ln this case, the control variable is a function whose discrete representation involves_an increasing number of variables with grid refinement. The minimization algorithm uses Lagrange multipliers to calculate sensitivity gradients. A preconditioned gradient descent algorithm is accelerated by a set of coarse grids. It optimizes for different scales in the representation of the control variable on different discretization levels. An analysis which reduces the problem to the boundary is introduced. It is used to approximate the two level asymptotic convergence rate, to determine the amplitude of the minimization steps, and the choice of a high pass filter to be used when necessary. The effectiveness of the method is demonstrated on a series of test problems. The new method enables the solutions of optimal control problems at the same cost of solving the corresponding analysis problems just a few times.

Efficient Parallel Formulations of Hierarchical Methods and Their Applications

NASA Astrophysics Data System (ADS)

Grama, Ananth Y.

1996-01-01

Hierarchical methods such as the Fast Multipole Method (FMM) and Barnes-Hut (BH) are used for rapid evaluation of potential (gravitational, electrostatic) fields in particle systems. They are also used for solving integral equations using boundary element methods. The linear systems arising from these methods are dense and are solved iteratively. Hierarchical methods reduce the complexity of the core matrix-vector product from O(n^2) to O(n log n) and the memory requirement from O(n^2) to O(n). We have developed highly scalable parallel formulations of a hybrid FMM/BH method that are capable of handling arbitrarily irregular distributions. We apply these formulations to astrophysical simulations of Plummer and Gaussian galaxies. We have used our parallel formulations to solve the integral form of the Laplace equation. We show that our parallel hierarchical mat-vecs yield high efficiency and overall performance even on relatively small problems. A problem containing approximately 200K nodes takes under a second to compute on 256 processors and yet yields over 85% efficiency. The efficiency and raw performance is expected to increase for bigger problems. For the 200K node problem, our code delivers about 5 GFLOPS of performance on a 256 processor T3D. This is impressive considering the fact that the problem has floating point divides and roots, and very little locality resulting in poor cache performance. A dense matrix-vector product of the same dimensions would require about 0.5 TeraBytes of memory and about 770 TeraFLOPS of computing speed. Clearly, if the loss in accuracy resulting from the use of hierarchical methods is acceptable, our code yields significant savings in time and memory. We also study the convergence of a GMRES solver built around this mat-vec. We accelerate the convergence of the solver using three preconditioning techniques: diagonal scaling, block-diagonal preconditioning, and inner-outer preconditioning. We study the performance and parallel efficiency of these preconditioned solvers. Using this solver, we solve dense linear systems with hundreds of thousands of unknowns. Solving a 105K unknown problem takes about 10 minutes on a 64 processor T3D. Until very recently, boundary element problems of this magnitude could not even be generated, let alone solved.

Generalized Preconditioned Locally Harmonic Residual Eigensolver (GPLHR) v0.1

DOE Office of Scientific and Technical Information (OSTI.GOV)

VECHARYNSKI, EUGENE; YANG, CHAO

The software contains a MATLAB implementation of the Generalized Preconditioned Locally Harmonic Residual (GPLHR) method for solving standard and generalized non-Hermitian eigenproblems. The method is particularly useful for computing a subset of eigenvalues, and their eigen- or Schur vectors, closest to a given shift. The proposed method is based on block iterations and can take advantage of a preconditioner if it is available. It does not need to perform exact shift-and-invert transformation. Standard and generalized eigenproblems are handled in a unified framework.

Parallel iterative methods for sparse linear and nonlinear equations

NASA Technical Reports Server (NTRS)

Saad, Youcef

1989-01-01

As three-dimensional models are gaining importance, iterative methods will become almost mandatory. Among these, preconditioned Krylov subspace methods have been viewed as the most efficient and reliable, when solving linear as well as nonlinear systems of equations. There has been several different approaches taken to adapt iterative methods for supercomputers. Some of these approaches are discussed and the methods that deal more specifically with general unstructured sparse matrices, such as those arising from finite element methods, are emphasized.

Domain decomposition methods for the parallel computation of reacting flows

NASA Technical Reports Server (NTRS)

Keyes, David E.

1988-01-01

Domain decomposition is a natural route to parallel computing for partial differential equation solvers. Subdomains of which the original domain of definition is comprised are assigned to independent processors at the price of periodic coordination between processors to compute global parameters and maintain the requisite degree of continuity of the solution at the subdomain interfaces. In the domain-decomposed solution of steady multidimensional systems of PDEs by finite difference methods using a pseudo-transient version of Newton iteration, the only portion of the computation which generally stands in the way of efficient parallelization is the solution of the large, sparse linear systems arising at each Newton step. For some Jacobian matrices drawn from an actual two-dimensional reacting flow problem, comparisons are made between relaxation-based linear solvers and also preconditioned iterative methods of Conjugate Gradient and Chebyshev type, focusing attention on both iteration count and global inner product count. The generalized minimum residual method with block-ILU preconditioning is judged the best serial method among those considered, and parallel numerical experiments on the Encore Multimax demonstrate for it approximately 10-fold speedup on 16 processors.

Implicit-Explicit Time Integration Methods for Non-hydrostatic Atmospheric Models

NASA Astrophysics Data System (ADS)

Gardner, D. J.; Guerra, J. E.; Hamon, F. P.; Reynolds, D. R.; Ullrich, P. A.; Woodward, C. S.

2016-12-01

The Accelerated Climate Modeling for Energy (ACME) project is developing a non-hydrostatic atmospheric dynamical core for high-resolution coupled climate simulations on Department of Energy leadership class supercomputers. An important factor in computational efficiency is avoiding the overly restrictive time step size limitations of fully explicit time integration methods due to the stiffest modes present in the model (acoustic waves). In this work we compare the accuracy and performance of different Implicit-Explicit (IMEX) splittings of the non-hydrostatic equations and various Additive Runge-Kutta (ARK) time integration methods. Results utilizing the Tempest non-hydrostatic atmospheric model and the ARKode package show that the choice of IMEX splitting and ARK scheme has a significant impact on the maximum stable time step size as well as solution quality. Horizontally Explicit Vertically Implicit (HEVI) approaches paired with certain ARK methods lead to greatly improved runtimes. With effective preconditioning IMEX splittings that incorporate some implicit horizontal dynamics can be competitive with HEVI results. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344. LLNL-ABS-699187

Active Focal Zone Sharpening for High-Precision Treatment Using Histotripsy

PubMed Central

Wang, Tzu-Yin; Xu, Zhen; Hall, Timothy L.; Fowlkes, J. Brian; Roberts, William W.; Cain, Charles A.

2011-01-01

The goal of this study is to develop a focal zone sharpening strategy that produces more precise lesions for pulsed cavitational ultrasound therapy, or histotripsy. Precise and well-confined lesions were produced by locally suppressing cavitation in the periphery of the treatment focus without affecting cavitation in the center. The local suppression of cavitation was achieved using cavitation nuclei preconditioning pulses to actively control cavitation in the periphery of the focus. A 1-MHz 513-element therapeutic array was used to generate both the therapy and the nuclei preconditioning pulses. For therapy, 10-cycle bursts at 100-Hz pulse repetition frequency with P−/P+ pressure of 21/76 MPa were delivered to the geometric focus of the therapeutic array. For nuclei preconditioning, a different pulse was delivered to an annular region immediately surrounding the focus before each therapy pulse. A parametric study on the effective pressure, pulse duration, and delivery time of the preconditioning pulse was conducted in red blood cell-gel phantoms, where cavitational damage was indicated by the color change resulting from local cell lysis. Results showed that a short-duration (20 µs) preconditioning pulse at a medium pressure (P−/P+ pressure of 7.2/13.6 MPa) delivered shortly before (30 µs) the therapy pulse substantially suppressed the peripheral damage by 77 ± 13% while complete fractionation in the focal center was maintained. High-speed imaging of the bubble cloud showed a substantial decrease in the maximum width of the bubble cloud by 48 ± 24% using focal zone sharpening. Experiments in ex vivo livers confirmed that highly confined lesions were produced in real tissues as well as in the phantoms. This study demonstrated the feasibility of active focal zone sharpening using cavitation nuclei preconditioning, allowing for increased treatment precision compared with the natural focal width of the therapy transducer. PMID:21342816

Active focal zone sharpening for high-precision treatment using histotripsy.

PubMed

Wang, Tzu-Yin; Xu, Zhen; Hall, Timothy; Fowlkes, J; Roberts, William; Cain, Charles

2011-02-01

The goal of this study is to develop a focal zone sharpening strategy that produces more precise lesions for pulsed cavitational ultrasound therapy, or histotripsy. Precise and well-confined lesions were produced by locally suppressing cavitation in the periphery of the treatment focus without affecting cavitation in the center. The local suppression of cavitation was achieved using cavitation nuclei preconditioning pulses to actively control cavitation in the periphery of the focus. A 1-MHz 513-element therapeutic array was used to generate both the therapy and the nuclei preconditioning pulses. For therapy, 10-cycle bursts at 100-Hz pulse repetition frequency with P-/P+ pressure of 21/76 MPa were delivered to the geometric focus of the therapeutic array. For nuclei preconditioning, a different pulse was delivered to an annular region immediately surrounding the focus before each therapy pulse. A parametric study on the effective pressure, pulse duration, and delivery time of the preconditioning pulse was conducted in red blood cell-gel phantoms, where cavitational damage was indicated by the color change resulting from local cell lysis. Results showed that a short-duration (20 μs) preconditioning pulse at a medium pressure (P-/P+ pressure of 7.2/13.6 MPa) delivered shortly before (30 μs) the therapy pulse substantially suppressed the peripheral damage by 77 ± 13% while complete fractionation in the focal center was maintained. High-speed imaging of the bubble cloud showed a substantial decrease in the maximum width of the bubble cloud by 48 ± 24% using focal zone sharpening. Experiments in ex vivo livers confirmed that highly confined lesions were produced in real tissues as well as in the phantoms. This study demonstrated the feasibility of active focal zone sharpening using cavitation nuclei preconditioning, allowing for increased treatment precision compared with the natural focal width of the therapy transducer.

Role of Phosphatidylinositol-3 Kinase Pathway in NMDA Preconditioning: Different Mechanisms for Seizures and Hippocampal Neuronal Degeneration Induced by Quinolinic Acid.

PubMed

Constantino, Leandra C; Binder, Luisa B; Vandresen-Filho, Samuel; Viola, Giordano G; Ludka, Fabiana K; Lopes, Mark W; Leal, Rodrigo B; Tasca, Carla I

2018-04-20

N-methyl D-aspartate (NMDA) preconditioning is evoked by the administration of a subtoxic dose of NMDA and is protective against neuronal excitotoxicity. This effect may involve a diversity of targets and cell signaling cascades associated to neuroprotection. Phosphatidylinositol-3 kinase/protein kinase B (PI3K/Akt) and mitogen-activated protein kinases (MAPKs) such as extracellular regulated protein kinase 1/2 (ERK1/2) and p38 MAPK pathways play a major role in neuroprotective mechanisms. However, their involvement in NMDA preconditioning was not yet fully investigated. The present study aimed to evaluate the effect of NMDA preconditioning on PI3K/Akt, ERK1/2, and p38 MAPK pathways in the hippocampus of mice and characterize the involvement of PI3K on NMDA preconditioning-evoked prevention of seizures and hippocampal cell damage induced by quinolinic acid (QA). Thus, mice received wortmannin (a PI3K inhibitor) and 15 min later a subconvulsant dose of NMDA (preconditioning) or saline. After 24 h of this treatment, an intracerebroventricular QA infusion was administered. Phosphorylation levels and total content of Akt, glycogen synthase protein kinase-3β (GSK-3β), ERK1/2, and p38 MAPK were not altered after 24 h of NMDA preconditioning with or without wortmmanin pretreatment. Moreover, after QA administration, behavioral seizures, hippocampal neuronal degeneration, and Akt activation were evaluated. Inhibition of PI3K pathway was effective in abolishing the protective effect of NMDA preconditioning against QA-induced seizures, but did not modify neuronal protection promoted by preconditioning as evaluated by Fluoro-Jade B staining. The study confirms that PI3K participates in the mechanism of protection induced by NMDA preconditioning against QA-induced seizures. Conversely, NMDA preconditioning-evoked protection against neuronal degeneration is not altered by PI3K signaling pathway inhibition. These results point to differential mechanisms regarding protection against a behavioral and cellular manifestation of neural damage.

Age-related reduction of cerebral ischemic preconditioning: myth or reality?

PubMed Central

Della-Morte, David; Cacciatore, Francesco; Salsano, Elisa; Pirozzi, Gilda; Genio, Maria Teresa Del; D’Antonio, Iole; Gargiulo, Gaetano; Palmirotta, Raffaele; Guadagni, Fiorella; Rundek, Tatjana; Abete, Pasquale

2013-01-01

Stroke is one of the leading causes of death in industrialized countries for people older than 65 years of age. The reasons are still unclear. A reduction of endogenous mechanisms against ischemic insults has been proposed to explain this phenomenon. The “cerebral” ischemic preconditioning mechanism is characterized by a brief episode of ischemia that renders the brain more resistant against subsequent longer ischemic events. This ischemic tolerance has been shown in numerous experimental models of cerebral ischemia. This protective mechanism seems to be reduced with aging both in experimental and clinical studies. Alterations of mediators released and/or intracellular pathways may be responsible for age-related ischemic preconditioning reduction. Agents able to mimic the “cerebral” preconditioning effect may represent a new powerful tool for the treatment of acute ischemic stroke in the elderly. In this article, animal and human cerebral ischemic preconditioning, its age-related difference, and its potential therapeutical applications are discussed. PMID:24204128

Preconditioning to Reduce Decompression Stress in Scuba Divers.

PubMed

Germonpré, Peter; Balestra, Costantino

2017-02-01

Using ultrasound imaging, vascular gas emboli (VGE) are observed after asymptomatic scuba dives and are considered a key element in the potential development of decompression sickness (DCS). Diving is also accompanied with vascular dysfunction, as measured by flow-mediated dilation (FMD). Previous studies showed significant intersubject variability to VGE for the same diving exposure and demonstrated that VGE can be reduced with even a single pre-dive intervention. Several preconditioning methods have been reported recently, seemingly acting either on VGE quantity or on endothelial inflammatory markers. Nine male divers who consistently showed VGE postdive performed a standardized deep pool dive (33 m/108 ft, 20 min in 33°C water temperature) to investigate the effect of three different preconditioning interventions: heat exposure (a 30-min session of dry infrared sauna), whole-body vibration (a 30-min session on a vibration mattress), and dark chocolate ingestion (30 g of chocolate containing 86% cocoa). Dives were made one day per week and interventions were administered in a randomized order. These interventions were shown to selectively reduce VGE, FMD, or both compared to control dives. Vibration had an effect on VGE (39.54%, SEM 16.3%) but not on FMD postdive. Sauna had effects on both parameters (VGE: 26.64%, SEM 10.4%; FMD: 102.7%, SEM 2.1%), whereas chocolate only improved FMD (102.5%, SEM 1.7%). This experiment, which had the same subjects perform all control and preconditioning dives in wet but completely standardized diving conditions, demonstrates that endothelial dysfunction appears to not be solely related to VGE.Germonpré P, Balestra C. Preconditioning to reduce decompression stress in scuba divers. Aerosp Med Hum Perform. 2017; 88(2):114-120.

Finding Chemical Reaction Paths with a Multilevel Preconditioning Protocol

DOE PAGES

Kale, Seyit; Sode, Olaseni; Weare, Jonathan; ...

2014-11-07

Finding transition paths for chemical reactions can be computationally costly owing to the level of quantum-chemical theory needed for accuracy. Here, we show that a multilevel preconditioning scheme that was recently introduced (Tempkin et al. J. Chem. Phys. 2014, 140, 184114) can be used to accelerate quantum-chemical string calculations. We demonstrate the method by finding minimum-energy paths for two well-characterized reactions: tautomerization of malonaldehyde and Claissen rearrangement of chorismate to prephanate. For these reactions, we show that preconditioning density functional theory (DFT) with a semiempirical method reduces the computational cost for reaching a converged path that is an optimum undermore » DFT by several fold. In conclusion, the approach also shows promise for free energy calculations when thermal noise can be controlled.« less

Wetting properties of Au/Sn solders for microelectronics

NASA Astrophysics Data System (ADS)

Peterson, K. A.; Williams, C. B.

Hermetic sealing of microelectronic packages with Au/Sn solder is critically dependent upon good wetting. In studying specific problems in hermetic sealing, a solderability test based on ASTM standard F-357-78 has proven useful. The test has helped isolate and quantify the effects of contamination due to epoxy die attach and related handling, thermal preconditioning of packages, gold plating thickness, time and temperature during sealing, and solder alloy composition as they affect wetting. Some differences in hardware have been documented between manufacturing lots, but the overriding factors have been contamination which occurs during packaging process flows and thermal preconditioning during processing. The paper includes a review of metallurgical aspects of soldering to a non-inert surface and an examination of microstructural differences in seal joints. The results also quantify the conventional wisdom that alloys which are on the tin-rich side of the eutectic composition offer superior wetting properties.

Flap preconditioning by pressure-controlled cupping in a rat model.

PubMed

Koh, Kyung S; Park, Sung Woo; Oh, Tae Suk; Choi, Jong Woo

2016-08-01

Flap survival is essential for the success of soft-tissue reconstruction. Accordingly, various surgical and medical methods aim to increase flap survival. Because flap survival is affected by the innate vascular supply, traditional preconditioning methods mainly target vasodilatation or vascular reorientation to increase blood flow to the tissue. External stress on the skin, such as an external volume expander or cupping, induces vascular remodeling, and these approaches have been used in the fat grafting field and in traditional Asian medicine. In the present study, we used a rat random-pattern dorsal flap model to study the effectiveness of preconditioning with an externally applied device (cupping) at the flap site that directly applied negative pressure to the skin. The device, the pressure-controlled cupping, is connected to negative pressure vacuum device providing accurate pressure control from 0 mm Hg to -200 mm Hg. Flap surgery was performed after preconditioning under -25 mm Hg suction pressure for 30 min a day for 5 d, followed by 9 d of postoperative observation. Flap survival was assessed as the area of viable tissue and was compared between the preconditioned group and a control group. The preconditioned group showed absolute percentage increase of flap viability relative to the entire flap by 19.0± 7.6% (average 70.1% versus 51.0%). Tissue perfusion of entire flap, evaluated by laser Doppler imaging system, was improved with absolute percentage increase by 24.2± 10.4% (average 77.4% versus 53.1%). Histologic analysis of hematoxylin and eosin, CD31, and Masson-trichrome staining showed increased vascular density in the subdermal plexus and more organized collagen production with hypertrophy of the attached muscle. Our study suggests that flap preconditioning caused by controlled noninvasive suction induces vascular remodeling that increases tissue perfusion and improves flap survival in a rat model. Copyright © 2016 Elsevier Inc. All rights reserved.

IMPLEMENTATION AND VALIDATION OF A FULLY IMPLICIT ACCUMULATOR MODEL IN RELAP-7

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhao, Haihua; Zou, Ling; Zhang, Hongbin

2016-01-01

This paper presents the implementation and validation of an accumulator model in RELAP-7 under the framework of preconditioned Jacobian free Newton Krylov (JFNK) method, based on the similar model used in RELAP5. RELAP-7 is a new nuclear reactor system safety analysis code being developed at the Idaho National Laboratory (INL). RELAP-7 is a fully implicit system code. The JFNK and preconditioning methods used in RELAP-7 is briefly discussed. The slightly modified accumulator model is summarized for completeness. The implemented model was validated with LOFT L3-1 test and benchmarked with RELAP5 results. RELAP-7 and RELAP5 had almost identical results for themore » accumulator gas pressure and water level, although there were some minor difference in other parameters such as accumulator gas temperature and tank wall temperature. One advantage of the JFNK method is its easiness to maintain and modify models due to fully separation of numerical methods from physical models. It would be straightforward to extend the current RELAP-7 accumulator model to simulate the advanced accumulator design.« less

Accelerating nuclear configuration interaction calculations through a preconditioned block iterative eigensolver

NASA Astrophysics Data System (ADS)

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.

A highly accurate boundary integral equation method for surfactant-laden drops in 3D

NASA Astrophysics Data System (ADS)

Sorgentone, Chiara; Tornberg, Anna-Karin

2018-05-01

The presence of surfactants alters the dynamics of viscous drops immersed in an ambient viscous fluid. This is specifically true at small scales, such as in applications of droplet based microfluidics, where the interface dynamics become of increased importance. At such small scales, viscous forces dominate and inertial effects are often negligible. Considering Stokes flow, a numerical method based on a boundary integral formulation is presented for simulating 3D drops covered by an insoluble surfactant. The method is able to simulate drops with different viscosities and close interactions, automatically controlling the time step size and maintaining high accuracy also when substantial drop deformation appears. To achieve this, the drop surfaces as well as the surfactant concentration on each surface are represented by spherical harmonics expansions. A novel reparameterization method is introduced to ensure a high-quality representation of the drops also under deformation, specialized quadrature methods for singular and nearly singular integrals that appear in the formulation are evoked and the adaptive time stepping scheme for the coupled drop and surfactant evolution is designed with a preconditioned implicit treatment of the surfactant diffusion.

Shape reanalysis and sensitivities utilizing preconditioned iterative boundary solvers

NASA Technical Reports Server (NTRS)

Guru Prasad, K.; Kane, J. H.

1992-01-01

The computational advantages associated with the utilization of preconditined iterative equation solvers are quantified for the reanalysis of perturbed shapes using continuum structural boundary element analysis (BEA). Both single- and multi-zone three-dimensional problems are examined. Significant reductions in computer time are obtained by making use of previously computed solution vectors and preconditioners in subsequent analyses. The effectiveness of this technique is demonstrated for the computation of shape response sensitivities required in shape optimization. Computer times and accuracies achieved using the preconditioned iterative solvers are compared with those obtained via direct solvers and implicit differentiation of the boundary integral equations. It is concluded that this approach employing preconditioned iterative equation solvers in reanalysis and sensitivity analysis can be competitive with if not superior to those involving direct solvers.

Electrochemical models for the discharge characteristics of the nickel cadmium cell

NASA Technical Reports Server (NTRS)

Spritzer, M. S.

1981-01-01

The potential time characteristics of a preconditioned fully charged cell discharge at constant current was studied. Electrochemical principles applied to the sealed nickel cadmium cell and its behavior and to predict operating characteristics were described. A thermodynamic approach to arrive at several related but different equations and its discharge are reported.

Efficient Preconditioning for the p-Version Finite Element Method in Two Dimensions

DTIC Science & Technology

1989-10-01

paper, we study fast parallel preconditioners for systems of equations arising from the p-version finite element method. The p-version finite element...computations and the solution of a relatively small global auxiliary problem. We study two different methods. In the first (Section 3), the global...20], will be studied in the next section. Problem (3.12) is obviously much more easily solved than the original problem ,nd the procedure is highly

An iterative method for the Helmholtz equation

NASA Technical Reports Server (NTRS)

Bayliss, A.; Goldstein, C. I.; Turkel, E.

1983-01-01

An iterative algorithm for the solution of the Helmholtz equation is developed. The algorithm is based on a preconditioned conjugate gradient iteration for the normal equations. The preconditioning is based on an SSOR sweep for the discrete Laplacian. Numerical results are presented for a wide variety of problems of physical interest and demonstrate the effectiveness of the algorithm.

The Crank Nicolson Time Integrator for EMPHASIS.

DOE Office of Scientific and Technical Information (OSTI.GOV)

McGregor, Duncan Alisdair Odum; Love, Edward; Kramer, Richard Michael Jack

2018-03-01

We investigate the use of implicit time integrators for finite element time domain approxi- mations of Maxwell's equations in vacuum. We discretize Maxwell's equations in time using Crank-Nicolson and in 3D space using compatible finite elements. We solve the system by taking a single step of Newton's method and inverting the Eddy-Current Schur complement allowing for the use of standard preconditioning techniques. This approach also generalizes to more complex material models that can include the Unsplit PML. We present verification results and demonstrate performance at CFL numbers up to 1000.

Neuron specific metabolic adaptations following multi-day exposures to oxygen glucose deprivation.

PubMed

Zeiger, Stephanie L H; McKenzie, Jennifer R; Stankowski, Jeannette N; Martin, Jacob A; Cliffel, David E; McLaughlin, BethAnn

2010-11-01

Prior exposure to sub toxic insults can induce a powerful endogenous neuroprotective program known as ischemic preconditioning. Current models typically rely on a single stress episode to induce neuroprotection whereas the clinical reality is that patients may experience multiple transient ischemic attacks (TIAs) prior to suffering a stroke. We sought to develop a neuron-enriched preconditioning model using multiple oxygen glucose deprivation (OGD) episodes to assess the endogenous protective mechanisms neurons implement at the metabolic and cellular level. We found that neurons exposed to a five minute period of glucose deprivation recovered oxygen utilization and lactate production using novel microphysiometry techniques. Using the non-toxic and energetically favorable five minute exposure, we developed a preconditioning paradigm where neurons are exposed to this brief OGD for three consecutive days. These cells experienced a 45% greater survival following an otherwise lethal event and exhibited a longer lasting window of protection in comparison to our previous in vitro preconditioning model using a single stress. As in other models, preconditioned cells exhibited mild caspase activation, an increase in oxidized proteins and a requirement for reactive oxygen species for neuroprotection. Heat shock protein 70 was upregulated during preconditioning, yet the majority of this protein was released extracellularly. We believe coupling this neuron-enriched multi-day model with microphysiometry will allow us to assess neuronal specific real-time metabolic adaptations necessary for preconditioning. Copyright © 2010 Elsevier B.V. All rights reserved.

Algorithmic Enhancements for Unsteady Aerodynamics and Combustion Applications

NASA Technical Reports Server (NTRS)

Venkateswaran, Sankaran; Olsen, Michael (Technical Monitor)

2001-01-01

Research in the FY01 focused on the analysis and development of enhanced algorithms for unsteady aerodynamics and chemically reacting flowfields. The research was performed in support of NASA Ames' efforts to improve the capabilities of the in-house computational fluid dynamics code, OVERFLOW. Specifically, the research was focused on the four areas: (1) investigation of stagnation region effects; (2) unsteady preconditioning dual-time procedures; (3) dissipation formulation for combustion; and (4) time-stepping methods for combustion.

Cardioprotective Effects of Transfusion of Late-Phase Preconditioned Plasma May Be Induced by Activating the Reperfusion Injury Salvage Kinase Pathway but Not the Survivor Activating Factor Enhancement Pathway in Rats.

PubMed

Zhao, Yang; Zheng, Zhi-Nan; Pi, Yan-Na; Liang, Xue; Jin, San-Qing

2017-01-01

A previous study in our laboratory demonstrated that transfusion of plasma collected at the late phase of remote ischemic preconditioning (RIPC) could reduce myocardial infarct size. Here, we tested whether the reperfusion injury salvage kinase (RISK) and survivor activating factor enhancement (SAFE) pathways are involved in transferring protection. In a two-part study, donor rats ( n = 3) donated plasma 48 hours after RIPC (preconditioned plasma) or control (nonpreconditioned plasma). Normal (part 1) or ischemic (part 2) myocardia were collected from recipients ( n = 6) 24 hours after receiving normal saline, nonpreconditioned plasma, and preconditioned plasma or after further suffering ischemia reperfusion. Western blot was performed to analyze STAT3, Akt, and Erk1/2 phosphorylation in normal and ischemic myocardium (central area and border area). In normal myocardia, preconditioned plasma increased Akt and Erk1/2 phosphorylation significantly compared to nonpreconditioned plasma and normal saline; no STAT3 phosphorylation was detected. In ischemic myocardia, preconditioned plasma increased Akt and Erk1/2 phosphorylation significantly in both central and border areas compared to other fluids; no significant difference in STAT3 phosphorylation occurred among groups. Transfusion of preconditioned plasma collected at the late phase of RIPC could activate the RISK but not SAFE pathway, suggesting that RISK pathway may be involved in transferring protection.

Neuroprotective Effects of Peptides during Ischemic Preconditioning.

PubMed

Zarubina, I V; Shabanov, P D

2016-02-01

Experiments on rats showed that neurospecific protein preparations reduce the severity of neurological deficit, restore the structure of individual behavior of the animals with different hypoxia tolerance, and exert antioxidant action during chronic ischemic damage to the brain unfolding during the early and late phases of ischemic preconditioning.

Effect of non-invasive remote ischemic preconditioning on intra-renal perfusion in volunteers.

PubMed

Robert, René; Vinet, Mathieu; Jamet, Angéline; Coudroy, Rémi

2017-06-01

Remote ischemic preconditioning may attenuate renal injury and protect the kidney during subsequent inflammatory or ischemic stress. However, the mechanism of such a protection is not well understood. The aim of this study was to investigate the impact of remote ischemic preconditioning on renal resistivity index (RRI) in nine healthy volunteers. In six volunteers, four cycles of 4-min inflation of a blood pressure cuff were applied to one upper arm, followed by 4-min reperfusion with the cuff deflated. RRI was determined using Doppler echography during each cuff deflated period. Measures were also performed in three volunteers without preconditioning. The median value of RRI significantly decreased progressively from 0.59 [0.53-0.62] before the remote conditioning (baseline) to 0.49 [0.46-0.53] at the end of the experiment (p < 0.001) whereas there was no change in controls. In this study, for the first time, we have clearly shown in a small group of subjects that remote ischemic preconditioning can induce a significantly decrease in RRI through increased intra-renal perfusion.

Toll-like receptor 3 pre-conditioning increases the therapeutic efficacy of umbilical cord mesenchymal stromal cells in a dextran sulfate sodium-induced colitis model.

PubMed

Fuenzalida, Patricia; Kurte, Mónica; Fernández-O'ryan, Catalina; Ibañez, Cristina; Gauthier-Abeliuk, Melanie; Vega-Letter, Ana María; Gonzalez, Paz; Irarrázabal, Carlos; Quezada, Nataly; Figueroa, Fernando; Carrión, Flavio

2016-05-01

Immunomodulatory properties of human umbilical cord-derived mesenchymal stromal cells (UCMSCs) can be differentially modulated by toll-like receptors (TLR) agonists. Here, the therapeutic efficacy of short TLR3 and TLR4 pre-conditioning of UCMSCs was evaluated in a dextran sulfate sodium (DSS)-induced colitis in mice. The novelty of this study is that although modulation of human MSCs activity by TLRs is not a new concept, this is the first time that short TLR pre-conditioning has been carried out in a murine inflammatory model of acute colitis. C57BL/6 mice were exposed to 2.5% dextran sulfate sodium (DSS) in drinking water ad libitum for 7 days. At days 1 and 3, mice were injected intraperitoneally with 1 × 10(6) UCMSCs untreated or TLR3 and TLR4 pre-conditioned UCMSCs. UCMSCs were pre-conditioned with poly(I:C) for TLR3 and LPS for TLR4 for 1 h at 37°C and 5% CO2. We evaluated clinical signs of disease and body weights daily. At the end of the experiment, colon length and histological changes were assessed. poly(I:C) pre-conditioned UCMSCs significantly ameliorated the clinical and histopathological severity of DSS-induced colitis compared with UCMSCs or LPS pre-conditioned UCMSCs. In contrast, infusion of LPS pre-conditioned UCMSCs significantly increased clinical signs of disease, colon shortening and histological disease index in DSS-induced colitis. These results show that short in vitro TLR3 pre-conditioning with poly(I:C) enhances the therapeutic efficacy of UCMSCs, which is a major breakthrough for developing improved treatments to patients with inflammatory bowel disease. Copyright © 2016 International Society for Cellular Therapy. Published by Elsevier Inc. All rights reserved.

Between Culture and Cultural Heritage: Curriculum Historical Preconditions as Constitutive for Cultural Relations--The Swedish Case

ERIC Educational Resources Information Center

Brantefors, Lotta

2015-01-01

The aim here is to describe and discuss how different cultural meanings, offered in education, can contribute to unjust cultural relations such as othering and xenophobia. By analysing the cultural and discursive content in curricula using a (neo)pragmatic curriculum theory research method, dominating ideas, values and discourses between 1948 and…

The role of hypoxia-inducible factor-1α and vascular endothelial growth factor in late-phase preconditioning with xenon, isoflurane and levosimendan in rat cardiomyocytes.

PubMed

Goetzenich, Andreas; Hatam, Nima; Preuss, Stephanie; Moza, Ajay; Bleilevens, Christian; Roehl, Anna B; Autschbach, Rüdiger; Bernhagen, Jürgen; Stoppe, Christian

2014-03-01

The protective effects of late-phase preconditioning can be triggered by several stimuli. Unfortunately, the transfer from bench to bedside still represents a challenge, as concomitant medication or diseases influence the complex signalling pathways involved. In an established model of primary neonatal rat cardiomyocytes, we analysed the cardioprotective effects of three different stimulating pharmaceuticals of clinical relevance. The effect of additional β-blocker treatment was studied as these were previously shown to negatively influence preconditioning. Twenty-four hours prior to hypoxia, cells pre-treated with or without metoprolol (0.55 µg/ml) were preconditioned with isoflurane, levosimendan or xenon. The influences of these stimuli on hypoxia-inducible factor-1α (HIF-1α), vascular endothelial growth factor (VEGF) as well as inducible and endothelial nitric synthase (iNOS/eNOS) and cyclooxygenase-2 (COX-2) were analysed by polymerase chain reaction and western blotting. The preconditioning was proved by trypan blue cell counts following 5 h of hypoxia and confirmed by fluorescence staining. Five hours of hypoxia reduced cell survival in unpreconditioned control cells to 44 ± 4%. Surviving cell count was significantly higher in cells preconditioned either by 2 × 15 min isoflurane (70 ± 16%; P = 0.005) or by xenon (59 ± 8%; P = 0.049). Xenon-preconditioned cells showed a significantly elevated content of VEGF (0.025 ± 0.010 IDV [integrated density values when compared with GAPDH] vs 0.003 ± 0.006 IDV in controls; P = 0.0003). The protein expression of HIF-1α was increased both by levosimendan (0.563 ± 0.175 IDV vs 0.142 ± 0.042 IDV in controls; P = 0.0289) and by xenon (0.868 ± 0.222 IDV; P < 0.0001) pretreatment. A significant elevation of mRNA expression of iNOS was measureable following preconditioning by xenon but not by the other chosen stimuli. eNOS mRNA expression was found to be suppressed by β-blocker treatment for all stimuli. In our model, independently of the chosen stimulus, β-blocker treatment had no significant effect on cell survival. We found that the stimulation of late-phase preconditioning involves several distinct pathways that are variably addressed by the different stimuli. In contrast to isoflurane treatment, xenon-induced preconditioning does not lead to an increase in COX-2 gene transcription but to a significant increase in HIF-1α and subsequently VEGF.

AZTEC: A parallel iterative package for the solving linear systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hutchinson, S.A.; Shadid, J.N.; Tuminaro, R.S.

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.

Geometric multigrid for an implicit-time immersed boundary method

DOE Office of Scientific and Technical Information (OSTI.GOV)

Guy, Robert D.; Philip, Bobby; Griffith, Boyce E.

2014-10-12

The immersed boundary (IB) method is an approach to fluid-structure interaction that uses Lagrangian variables to describe the deformations and resulting forces of the structure and Eulerian variables to describe the motion and forces of the fluid. Explicit time stepping schemes for the IB method require solvers only for Eulerian equations, for which fast Cartesian grid solution methods are available. Such methods are relatively straightforward to develop and are widely used in practice but often require very small time steps to maintain stability. Implicit-time IB methods permit the stable use of large time steps, but efficient implementations of such methodsmore » require significantly more complex solvers that effectively treat both Lagrangian and Eulerian variables simultaneously. Moreover, several different approaches to solving the coupled Lagrangian-Eulerian equations have been proposed, but a complete understanding of this problem is still emerging. This paper presents a geometric multigrid method for an implicit-time discretization of the IB equations. This multigrid scheme uses a generalization of box relaxation that is shown to handle problems in which the physical stiffness of the structure is very large. Numerical examples are provided to illustrate the effectiveness and efficiency of the algorithms described herein. Finally, these tests show that using multigrid as a preconditioner for a Krylov method yields improvements in both robustness and efficiency as compared to using multigrid as a solver. They also demonstrate that with a time step 100–1000 times larger than that permitted by an explicit IB method, the multigrid-preconditioned implicit IB method is approximately 50–200 times more efficient than the explicit method.« less

High-Order/Low-Order methods for ocean modeling

DOE PAGES

Newman, Christopher; Womeldorff, Geoff; Chacón, Luis; ...

2015-06-01

In this study, we examine a High Order/Low Order (HOLO) approach for a z-level ocean model and show that the traditional semi-implicit and split-explicit methods, as well as a recent preconditioning strategy, can easily be cast in the framework of HOLO methods. The HOLO formulation admits an implicit-explicit method that is algorithmically scalable and second-order accurate, allowing timesteps much larger than the barotropic time scale. We show how HOLO approaches, in particular the implicit-explicit method, can provide a solid route for ocean simulation to heterogeneous computing and exascale environments.

[The effect of hypoxia preconditioning no binding activity of HIF-1 on the HRE with EPO in the hippocampus of mice].

PubMed

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.

Differentiation Practices in Grade 2 and 3: Variations in Teacher Behavior in Mathematics and Reading Comprehension Lessons

ERIC Educational Resources Information Center

Ritzema, Evelien S.; Deunk, Marjolein I.; Bosker, Roel J.

2016-01-01

This study focused on the differentiation practices of second- and third-grade teachers in mathematics and reading comprehension lessons. Preconditions for differentiation, classroom organization, and how teachers dealt with students of different ability levels were investigated through observations, using a time-sampling instrument. Data of 43…

Unsteady Computations of a Jet in a Crossflow with Ground Effect

NASA Technical Reports Server (NTRS)

Pandya, Shishir; Murman, Scott; Venkateswaran, Sankaran; Kwak, Dochan (Technical Monitor)

2002-01-01

A numerical study of a jet in crossflow with ground effect is conducted using OVERFLOW with dual time-stepping and low Mach number preconditioning. The results of the numerical study are compared to an experiment to show that the numerical methods are capable of capturing the dominant features of the flow field as well as the unsteadiness associated with the ground vortex.

The visual stress model—A psycho-physiological method for the evaluation of operational reliability of pilots and cosmonauts

NASA Astrophysics Data System (ADS)

Kammel, H.; Haase, H.

An experimental psycho-physiological method is presented for the evaluation of visual-cognitive performance preconditions and operational reliability of pilots and cosmonauts. As visual-cognitive stress are used tachistoscopically presented instrument symbols under conditions of individual speed of work and time pressure. The results of the compared extreme groups consisting of pilots with good and insufficient flight performance showed that the pilots with impairments to the quality of flight activity differ already before the test in their individual habitual characteristics and actual motivation, during the stress in their operational parameters, in the dimensions of their cardiorespiratory activation as well as in their efficiency and after the stress in their subjective experience of the stress. Conclusions are drawn for the evaluation of the aptitude of pilots and cosmonauts.

A numerical solution for the diffusion equation in hydrogeologic systems

USGS Publications Warehouse

Ishii, A.L.; Healy, R.W.; Striegl, Robert G.

1989-01-01

The documentation of a computer code for the numerical solution of the linear diffusion equation in one or two dimensions in Cartesian or cylindrical coordinates is presented. Applications of the program include molecular diffusion, heat conduction, and fluid flow in confined systems. The flow media may be anisotropic and heterogeneous. The model is formulated by replacing the continuous linear diffusion equation by discrete finite-difference approximations at each node in a block-centered grid. The resulting matrix equation is solved by the method of preconditioned conjugate gradients. The conjugate gradient method does not require the estimation of iteration parameters and is guaranteed convergent in the absence of rounding error. The matrixes are preconditioned to decrease the steps to convergence. The model allows the specification of any number of boundary conditions for any number of stress periods, and the output of a summary table for selected nodes showing flux and the concentration of the flux quantity for each time step. The model is written in a modular format for ease of modification. The model was verified by comparison of numerical and analytical solutions for cases of molecular diffusion, two-dimensional heat transfer, and axisymmetric radial saturated fluid flow. Application of the model to a hypothetical two-dimensional field situation of gas diffusion in the unsaturated zone is demonstrated. The input and output files are included as a check on program installation. The definition of variables, input requirements, flow chart, and program listing are included in the attachments. (USGS)

A Semi-Implicit, Three-Dimensional Model for Estuarine Circulation

USGS Publications Warehouse

Smith, Peter E.

2006-01-01

A semi-implicit, finite-difference method for the numerical solution of the three-dimensional equations for circulation in estuaries is presented and tested. The method uses a three-time-level, leapfrog-trapezoidal scheme that is essentially second-order accurate in the spatial and temporal numerical approximations. The three-time-level scheme is shown to be preferred over a two-time-level scheme, especially for problems with strong nonlinearities. The stability of the semi-implicit scheme is free from any time-step limitation related to the terms describing vertical diffusion and the propagation of the surface gravity waves. The scheme does not rely on any form of vertical/horizontal mode-splitting to treat the vertical diffusion implicitly. At each time step, the numerical method uses a double-sweep method to transform a large number of small tridiagonal equation systems and then uses the preconditioned conjugate-gradient method to solve a single, large, five-diagonal equation system for the water surface elevation. The governing equations for the multi-level scheme are prepared in a conservative form by integrating them over the height of each horizontal layer. The layer-integrated volumetric transports replace velocities as the dependent variables so that the depth-integrated continuity equation that is used in the solution for the water surface elevation is linear. Volumetric transports are computed explicitly from the momentum equations. The resulting method is mass conservative, efficient, and numerically accurate.

Fetal asphyctic preconditioning alters the transcriptional response to perinatal asphyxia.

PubMed

Cox-Limpens, Kimberly E M; Vles, Johan S H; LA van den Hove, Daniel; Zimmermann, Luc J I; Gavilanes, Antonio W D

2014-05-29

Genomic reprogramming is thought to be, at least in part, responsible for the protective effect of brain preconditioning. Unraveling mechanisms of this endogenous neuroprotection, activated by preconditioning, is an important step towards new clinical strategies for treating asphyctic neonates.Therefore, we investigated whole-genome transcriptional changes in the brain of rats which underwent perinatal asphyxia (PA), and rats where PA was preceded by fetal asphyctic preconditioning (FAPA). Offspring were sacrificed 6 h and 96 h after birth, and whole-genome transcription was investigated using the Affymetrix Gene1.0ST chip. Microarray data were analyzed with the Bioconductor Limma package. In addition to univariate analysis, we performed Gene Set Enrichment Analysis (GSEA) in order to derive results with maximum biological relevance. We observed minimal, 25% or less, overlap of differentially regulated transcripts across different experimental groups which leads us to conclude that the transcriptional phenotype of these groups is largely unique. In both the PA and FAPA group we observe an upregulation of transcripts involved in cellular stress. Contrastingly, transcripts with a function in the cell nucleus were mostly downregulated in PA animals, while we see considerable upregulation in the FAPA group. Furthermore, we observed that histone deacetylases (HDACs) are exclusively regulated in FAPA animals. This study is the first to investigate whole-genome transcription in the neonatal brain after PA alone, and after perinatal asphyxia preceded by preconditioning (FAPA). We describe several genes/pathways, such as ubiquitination and proteolysis, which were not previously linked to preconditioning-induced neuroprotection. Furthermore, we observed that the majority of upregulated genes in preconditioned animals have a function in the cell nucleus, including several epigenetic players such as HDACs, which suggests that epigenetic mechanisms are likely to play a role in preconditioning-induced neuroprotection.

Fetal asphyctic preconditioning alters the transcriptional response to perinatal asphyxia

PubMed Central

2014-01-01

Background Genomic reprogramming is thought to be, at least in part, responsible for the protective effect of brain preconditioning. Unraveling mechanisms of this endogenous neuroprotection, activated by preconditioning, is an important step towards new clinical strategies for treating asphyctic neonates. Therefore, we investigated whole-genome transcriptional changes in the brain of rats which underwent perinatal asphyxia (PA), and rats where PA was preceded by fetal asphyctic preconditioning (FAPA). Offspring were sacrificed 6 h and 96 h after birth, and whole-genome transcription was investigated using the Affymetrix Gene1.0ST chip. Microarray data were analyzed with the Bioconductor Limma package. In addition to univariate analysis, we performed Gene Set Enrichment Analysis (GSEA) in order to derive results with maximum biological relevance. Results We observed minimal, 25% or less, overlap of differentially regulated transcripts across different experimental groups which leads us to conclude that the transcriptional phenotype of these groups is largely unique. In both the PA and FAPA group we observe an upregulation of transcripts involved in cellular stress. Contrastingly, transcripts with a function in the cell nucleus were mostly downregulated in PA animals, while we see considerable upregulation in the FAPA group. Furthermore, we observed that histone deacetylases (HDACs) are exclusively regulated in FAPA animals. Conclusions This study is the first to investigate whole-genome transcription in the neonatal brain after PA alone, and after perinatal asphyxia preceded by preconditioning (FAPA). We describe several genes/pathways, such as ubiquitination and proteolysis, which were not previously linked to preconditioning-induced neuroprotection. Furthermore, we observed that the majority of upregulated genes in preconditioned animals have a function in the cell nucleus, including several epigenetic players such as HDACs, which suggests that epigenetic mechanisms are likely to play a role in preconditioning-induced neuroprotection. PMID:24885038

Tensor-product preconditioners for higher-order space-time discontinuous Galerkin methods

NASA Astrophysics Data System (ADS)

Diosady, Laslo T.; Murman, Scott M.

2017-02-01

A space-time discontinuous-Galerkin spectral-element discretization is presented for direct numerical simulation of the compressible Navier-Stokes equations. An efficient solution technique based on a matrix-free Newton-Krylov method is developed in order to overcome the stiffness associated with high solution order. The use of tensor-product basis functions is key to maintaining efficiency at high-order. Efficient preconditioning methods are presented which can take advantage of the tensor-product formulation. A diagonalized Alternating-Direction-Implicit (ADI) scheme is extended to the space-time discontinuous Galerkin discretization. A new preconditioner for the compressible Euler/Navier-Stokes equations based on the fast-diagonalization method is also presented. Numerical results demonstrate the effectiveness of these preconditioners for the direct numerical simulation of subsonic turbulent flows.

Tensor-Product Preconditioners for Higher-Order Space-Time Discontinuous Galerkin Methods

NASA Technical Reports Server (NTRS)

Diosady, Laslo T.; Murman, Scott M.

2016-01-01

space-time discontinuous-Galerkin spectral-element discretization is presented for direct numerical simulation of the compressible Navier-Stokes equat ions. An efficient solution technique based on a matrix-free Newton-Krylov method is developed in order to overcome the stiffness associated with high solution order. The use of tensor-product basis functions is key to maintaining efficiency at high order. Efficient preconditioning methods are presented which can take advantage of the tensor-product formulation. A diagonalized Alternating-Direction-Implicit (ADI) scheme is extended to the space-time discontinuous Galerkin discretization. A new preconditioner for the compressible Euler/Navier-Stokes equations based on the fast-diagonalization method is also presented. Numerical results demonstrate the effectiveness of these preconditioners for the direct numerical simulation of subsonic turbulent flows.

Some methodological aspects of ethics committees' expertise: the Ukrainian example.

PubMed

Pustovit, Svitlana V

2006-01-01

Today local, national and international ethics committees have become an effective means of social regulation in many European countries. Science itself is an important precondition for the development of bioethical knowledge and ethics expertise. Cultural, social, historical and religious preconditions can facilitate different forms and methods of ethics expertise in each country. Ukrainian ethics expertise has some methodological problems connected with its socio-cultural, historical, science and philosophy development particularities. In this context, clarification of some common legitimacies or methodological approaches to ethics committee (EC) phenomena such as globalization, scientization and the prioritization of an ethics paradigm are very important. On the other hand, elaborate study and critical analysis of international experience by Ukraine and other Eastern European countries will provide the integration of their local and national ethics expertises into a world bioethics ethos.

Time-derivative preconditioning for viscous flows

NASA Technical Reports Server (NTRS)

Choi, Yunho; Merkle, Charles L.

1991-01-01

A time-derivative preconditioning algorithm that is effective over a wide range of flow conditions from inviscid to very diffusive flows and from low speed to supersonic flows was developed. This algorithm uses a viscous set of primary dependent variables to introduce well-conditioned eigenvalues and to avoid having a nonphysical time reversal for viscous flow. The resulting algorithm also provides a mechanism for controlling the inviscid and viscous time step parameters to be of order one for very diffusive flows, thereby ensuring rapid convergence at very viscous flows as well as for inviscid flows. Convergence capabilities are demonstrated through computation of a wide variety of problems.

A New Coarsening Operator for the Optimal Preconditioning of the Dual and Primal Domain Decomposition Methods: Application to Problems with Severe Coefficient Jumps

NASA Technical Reports Server (NTRS)

Farhat, Charbel; Rixen, Daniel

1996-01-01

We present an optimal preconditioning algorithm that is equally applicable to the dual (FETI) and primal (Balancing) Schur complement domain decomposition methods, and which successfully addresses the problems of subdomain heterogeneities including the effects of large jumps of coefficients. The proposed preconditioner is derived from energy principles and embeds a new coarsening operator that propagates the error globally and accelerates convergence. The resulting iterative solver is illustrated with the solution of highly heterogeneous elasticity problems.

Multigrid and Krylov Subspace Methods for the Discrete Stokes Equations

NASA Technical Reports Server (NTRS)

Elman, Howard C.

1996-01-01

Discretization of the Stokes equations produces a symmetric indefinite system of linear equations. For stable discretizations, a variety of numerical methods have been proposed that have rates of convergence independent of the mesh size used in the discretization. In this paper, we compare the performance of four such methods: variants of the Uzawa, preconditioned conjugate gradient, preconditioned conjugate residual, and multigrid methods, for solving several two-dimensional model problems. The results indicate that where it is applicable, multigrid with smoothing based on incomplete factorization is more efficient than the other methods, but typically by no more than a factor of two. The conjugate residual method has the advantage of being both independent of iteration parameters and widely applicable.

The European 2015 drought from a hydrological perspective

NASA Astrophysics Data System (ADS)

Laaha, Gregor; Gauster, Tobias; Tallaksen, Lena M.; Vidal, Jean-Philippe; Stahl, Kerstin; Prudhomme, Christel; Heudorfer, Benedikt; Vlnas, Radek; Ionita, Monica; Van Lanen, Henny A. J.; Adler, Mary-Jeanne; Caillouet, Laurie; Delus, Claire; Fendekova, Miriam; Gailliez, Sebastien; Hannaford, Jamie; Kingston, Daniel; Van Loon, Anne F.; Mediero, Luis; Osuch, Marzena; Romanowicz, Renata; Sauquet, Eric; Stagge, James H.; Wong, Wai K.

2017-06-01

In 2015 large parts of Europe were affected by drought. In this paper, we analyze the hydrological footprint (dynamic development over space and time) of the drought of 2015 in terms of both severity (magnitude) and spatial extent and compare it to the extreme drought of 2003. Analyses are based on a range of low flow and hydrological drought indices derived for about 800 streamflow records across Europe, collected in a community effort based on a common protocol. We compare the hydrological footprints of both events with the meteorological footprints, in order to learn from similarities and differences of both perspectives and to draw conclusions for drought management. The region affected by hydrological drought in 2015 differed somewhat from the drought of 2003, with its center located more towards eastern Europe. In terms of low flow magnitude, a region surrounding the Czech Republic was the most affected, with summer low flows that exhibited return intervals of 100 years and more. In terms of deficit volumes, the geographical center of the event was in southern Germany, where the drought lasted a particularly long time. A detailed spatial and temporal assessment of the 2015 event showed that the particular behavior in these regions was partly a result of diverging wetness preconditions in the studied catchments. Extreme droughts emerged where preconditions were particularly dry. In regions with wet preconditions, low flow events developed later and tended to be less severe. For both the 2003 and 2015 events, the onset of the hydrological drought was well correlated with the lowest flow recorded during the event (low flow magnitude), pointing towards a potential for early warning of the severity of streamflow drought. Time series of monthly drought indices (both streamflow- and climate-based indices) showed that meteorological and hydrological events developed differently in space and time, both in terms of extent and severity (magnitude). These results emphasize that drought is a hazard which leaves different footprints on the various components of the water cycle at different spatial and temporal scales. The difference in the dynamic development of meteorological and hydrological drought also implies that impacts on various water-use sectors and river ecology cannot be informed by climate indices alone. Thus, an assessment of drought impacts on water resources requires hydrological data in addition to drought indices based solely on climate data. The transboundary scale of the event also suggests that additional efforts need to be undertaken to make timely pan-European hydrological assessments more operational in the future.

Accelerating nuclear configuration interaction calculations through a preconditioned block iterative eigensolver

DOE PAGES

Shao, Meiyue; Aktulga, H.  Metin; Yang, Chao; ...

2017-09-14

In this paper, 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. Themore » 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. Finally, 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.« less

Accelerating nuclear configuration interaction calculations through a preconditioned block iterative eigensolver

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shao, Meiyue; Aktulga, H.  Metin; Yang, Chao

In this paper, 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. Themore » 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. Finally, 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.« less

Analysis of Preconditioning and Relaxation Operators for the Discontinuous Galerkin Method Applied to Diffusion

NASA Technical Reports Server (NTRS)

Atkins, H. L.; Shu, Chi-Wang

2001-01-01

The explicit stability constraint of the discontinuous Galerkin method applied to the diffusion operator decreases dramatically as the order of the method is increased. Block Jacobi and block Gauss-Seidel preconditioner operators are examined for their effectiveness at accelerating convergence. A Fourier analysis for methods of order 2 through 6 reveals that both preconditioner operators bound the eigenvalues of the discrete spatial operator. Additionally, in one dimension, the eigenvalues are grouped into two or three regions that are invariant with order of the method. Local relaxation methods are constructed that rapidly damp high frequencies for arbitrarily large time step.

A Block Preconditioned Conjugate Gradient-type Iterative Solver for Linear Systems in Thermal Reservoir Simulation

NASA Astrophysics Data System (ADS)

Betté, Srinivas; Diaz, Julio C.; Jines, William R.; Steihaug, Trond

1986-11-01

A preconditioned residual-norm-reducing iterative solver is described. Based on a truncated form of the generalized-conjugate-gradient method for nonsymmetric systems of linear equations, the iterative scheme is very effective for linear systems generated in reservoir simulation of thermal oil recovery processes. As a consequence of employing an adaptive implicit finite-difference scheme to solve the model equations, the number of variables per cell-block varies dynamically over the grid. The data structure allows for 5- and 9-point operators in the areal model, 5-point in the cross-sectional model, and 7- and 11-point operators in the three-dimensional model. Block-diagonal-scaling of the linear system, done prior to iteration, is found to have a significant effect on the rate of convergence. Block-incomplete-LU-decomposition (BILU) and block-symmetric-Gauss-Seidel (BSGS) methods, which result in no fill-in, are used as preconditioning procedures. A full factorization is done on the well terms, and the cells are ordered in a manner which minimizes the fill-in in the well-column due to this factorization. The convergence criterion for the linear (inner) iteration is linked to that of the nonlinear (Newton) iteration, thereby enhancing the efficiency of the computation. The algorithm, with both BILU and BSGS preconditioners, is evaluated in the context of a variety of thermal simulation problems. The solver is robust and can be used with little or no user intervention.

Exercise preconditioning improves behavioral functions following transient cerebral ischemia induced by 4-vessel occlusion (4-VO) in rats.

PubMed

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 < 0.05) and exercise preconditioning improved it in ischemic animals. In the passive avoidance 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 < 0.001). In the adhesive removal test, latency to touch and remove the sticky labels from forepaw was increased following induction of ischemia (all P < 0.001) and exercise preconditioning decreased these indices compared to the ischemic group (all P < 0.001). In the ledged 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.

Mechanical preconditioning enables electrophysiologic coupling of skeletal myoblast cells to myocardium

PubMed Central

Treskes, Philipp; Cowan, Douglas B.; Stamm, Christof; Rubach, Martin; Adelmann, Roland; Wittwer, Thorsten; Wahlers, Thorsten

2015-01-01

Objective The effect of mechanical preconditioning on skeletal myoblasts in engineered tissue constructs was investigated to resolve issues associated with conduction block between skeletal myoblast cells and cardiomyocytes. Methods Murine skeletal myoblasts were used to generate engineered tissue constructs with or without application of mechanical strain. After in vitro myotube formation, engineered tissue constructs were co-cultured for 6 days with viable embryonic heart slices. With the use of sharp electrodes, electrical coupling between engineered tissue constructs and embryonic heart slices was assessed in the presence or absence of pharmacologic agents. Results The isolation and expansion procedure for skeletal myoblasts resulted in high yields of homogeneously desmin-positive (97.1% ± 0.1%) cells. Mechanical strain was exerted on myotubes within engineered tissue constructs during gelation of the matrix, generating preconditioned engineered tissue constructs. Electrical coupling between preconditioned engineered tissue constructs and embryonic heart slices was observed; however, no coupling was apparent when engineered tissue constructs were not subjected to mechanical strain. Coupling of cells from engineered tissue constructs to cells in embryonic heart slices showed slower conduction velocities than myocardial cells with the embryonic heart slices (preconditioned engineered tissue constructs vs embryonic heart slices: 0.04 ± 0.02 ms vs 0.10 ± 0.05 ms, P = .011), lower stimulation frequencies (preconditioned engineered tissue constructs vs maximum embryonic heart slices: 4.82 ± 1.42 Hz vs 10.58 ± 1.56 Hz; P = .0009), and higher sensitivities to the gap junction inhibitor (preconditioned engineered tissue constructs vs embryonic heart slices: 0.22 ± 0.07 mmol/L vs 0.93 ± 0.15 mmol/L; P = .0004). Conclusions We have generated skeletal myoblast–based transplantable grafts that electrically couple to myocardium. PMID:22980065

Fetal asphyctic preconditioning modulates the acute cytokine response thereby protecting against perinatal asphyxia in neonatal rats.

PubMed

Vlassaks, Evi; Strackx, Eveline; Vles, Johan Sh; Nikiforou, Maria; Martinez-Martinez, Pilar; Kramer, Boris W; Gavilanes, Antonio Wd

2013-01-26

Perinatal asphyxia (PA) is a major cause of brain damage and neurodevelopmental impairment in infants. Recent investigations have shown that experimental sublethal fetal asphyxia (FA preconditioning) protects against a subsequent more severe asphyctic insult at birth. The molecular mechanisms of this protection have, however, not been elucidated. Evidence implicates that inflammatory cytokines play a protective role in the induction of ischemic tolerance in the adult brain. Accordingly, we hypothesize that FA preconditioning leads to changes in the fetal cytokine response, thereby protecting the newborn against a subsequent asphyctic insult. In rats, FA preconditioning was induced at embryonic day 17 by clamping the uterine vasculature for 30 min. At term birth, global PA was induced by placing the uterine horns, containing the pups, in a saline bath for 19 min. We assessed, at different time points after FA and PA, mRNA and protein expression of several cytokines and related receptor mRNA levels in total hemispheres of fetal and neonatal brains. Additionally, we measured pSTAT3/STAT3 levels to investigate cellular responses to these cytokines. Prenatally, FA induced acute downregulation in IL-1β, TNF-α and IL-10 mRNA levels. At 96 h post FA, IL-6 mRNA and IL-10 protein expression were increased in FA brains compared with controls. Two hours after birth, all proinflammatory cytokines and pSTAT3/STAT3 levels decreased in pups that experienced FA and/or PA. Interestingly, IL-10 and IL-6 mRNA levels increased after PA. When pups were FA preconditioned, however, IL-10 and IL-6 mRNA levels were comparable to those in controls. FA leads to prenatal changes in the neuroinflammatory response. This modulation of the cytokine response probably results in the protective inflammatory phenotype seen when combining FA and PA and may have significant implications for preventing post-asphyctic perinatal encephalopathy.

A third-order implicit discontinuous Galerkin method based on a Hermite WENO reconstruction for time-accurate solution of the compressible Navier-Stokes equations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xia, Yidong; Liu, Xiaodong; Luo, Hong

2015-06-01

Here, a space and time third-order discontinuous Galerkin method based on a Hermite weighted essentially non-oscillatory reconstruction is presented for the unsteady compressible Euler and Navier–Stokes equations. At each time step, a lower-upper symmetric Gauss–Seidel preconditioned generalized minimal residual solver is used to solve the systems of linear equations arising from an explicit first stage, single diagonal coefficient, diagonally implicit Runge–Kutta time integration scheme. The performance of the developed method is assessed through a variety of unsteady flow problems. Numerical results indicate that this method is able to deliver the designed third-order accuracy of convergence in both space and time,more » while requiring remarkably less storage than the standard third-order discontinous Galerkin methods, and less computing time than the lower-order discontinous Galerkin methods to achieve the same level of temporal accuracy for computing unsteady flow problems.« less

Ischemic preconditioning of the muscle improves maximal exercise performance but not maximal oxygen uptake in humans.

PubMed

Crisafulli, Antonio; Tangianu, Flavio; Tocco, Filippo; Concu, Alberto; Mameli, Ombretta; Mulliri, Gabriele; Caria, Marcello A

2011-08-01

Brief episodes of nonlethal ischemia, commonly known as "ischemic preconditioning" (IP), are protective against cell injury induced by infarction. Moreover, muscle IP has been found capable of improving exercise performance. The aim of the study was the comparison of standard exercise performances carried out in normal conditions with those carried out following IP, achieved by brief muscle ischemia at rest (RIP) and after exercise (EIP). Seventeen physically active, healthy male subjects performed three incremental, randomly assigned maximal exercise tests on a cycle ergometer up to exhaustion. One was the reference (REF) test, whereas the others were performed after the RIP and EIP sessions. Total exercise time (TET), total work (TW), and maximal power output (W(max)), oxygen uptake (VO(2max)), and pulmonary ventilation (VE(max)) were assessed. Furthermore, impedance cardiography was used to measure maximal heart rate (HR(max)), stroke volume (SV(max)), and cardiac output (CO(max)). A subgroup of volunteers (n = 10) performed all-out tests to assess their anaerobic capacity. We found that both RIP and EIP protocols increased in a similar fashion TET, TW, W(max), VE(max), and HR(max) with respect to the REF test. In particular, W(max) increased by ∼ 4% in both preconditioning procedures. However, preconditioning sessions failed to increase traditionally measured variables such as VO(2max), SV(max,) CO(max), and anaerobic capacity(.) It was concluded that muscle IP improves performance without any difference between RIP and EIP procedures. The mechanism of this effect could be related to changes in fatigue perception.

Preconditioned conjugate gradient technique for the analysis of symmetric anisotropic structures

NASA Technical Reports Server (NTRS)

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 multilevel preconditioner for domain decomposition boundary systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bramble, J.H.; Pasciak, J.E.; Xu, Jinchao.

1991-12-11

In this note, we consider multilevel preconditioning of the reduced boundary systems which arise in non-overlapping domain decomposition methods. It will be shown that the resulting preconditioned systems have condition numbers which be bounded in the case of multilevel spaces on the whole domain and grow at most proportional to the number of levels in the case of multilevel boundary spaces without multilevel extensions into the interior.

A framework for directional and higher-order reconstruction in photoacoustic tomography

NASA Astrophysics Data System (ADS)

Boink, Yoeri E.; Lagerwerf, Marinus J.; Steenbergen, Wiendelt; van Gils, Stephan A.; Manohar, Srirang; Brune, Christoph

2018-02-01

Photoacoustic tomography is a hybrid imaging technique that combines high optical tissue contrast with high ultrasound resolution. Direct reconstruction methods such as filtered back-projection, time reversal and least squares suffer from curved line artefacts and blurring, especially in the case of limited angles or strong noise. In recent years, there has been great interest in regularised iterative methods. These methods employ prior knowledge of the image to provide higher quality reconstructions. However, easy comparisons between regularisers and their properties are limited, since many tomography implementations heavily rely on the specific regulariser chosen. To overcome this bottleneck, we present a modular reconstruction framework for photoacoustic tomography, which enables easy comparisons between regularisers with different properties, e.g. nonlinear, higher-order or directional. We solve the underlying minimisation problem with an efficient first-order primal-dual algorithm. Convergence rates are optimised by choosing an operator-dependent preconditioning strategy. A variety of reconstruction methods are tested on challenging 2D synthetic and experimental data sets. They outperform direct reconstruction approaches for strong noise levels and limited angle measurements, offering immediate benefits in terms of acquisition time and quality. This work provides a basic platform for the investigation of future advanced regularisation methods in photoacoustic tomography.

Low-energy shock wave preconditioning reduces renal ischemic reperfusion injury caused by renal artery occlusion.

PubMed

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.

Major role of the PI3K/Akt pathway in ischemic tolerance induced by sublethal oxygen-glucose deprivation in cortical neurons in vitro.

PubMed

Bhuiyan, Mohammad Iqbal Hossain; Jung, Seo Yun; Kim, Hyoung Ja; Lee, Yong Sup; Jin, Changbae

2011-06-01

Ischemic preconditioning can provide protection to neurons from subsequent lethal ischemia. The molecular mechanisms of neuronal ischemic tolerance, however, are still not well-known. The present study, therefore, examined the role of MAPK and PI3K/Akt pathways in ischemic tolerance induced by preconditioning with sublethal oxygen-glucose deprivation (OGD) in cultured rat cortical neurons. Ischemic tolerance was simulated by preconditioning of the neurons with sublethal 1-h OGD imposed 12 h before lethal 3-h OGD. The time-course studies of relative phosphorylation and expression levels of ERK1/2, JNK and p38 MAPK showed lack of their involvement in ischemic tolerance. However, there were significant increases in Akt phosphorylation levels during the reperfusion period following preconditioned lethal OGD. In addition, Bcl-2 associated death promoter (Bad) and GSK-3β were also found to be inactivated during that reperfusion period. Finally, treatment with an inhibitor of PI3K, wortmannin, applied from 15 min before and during lethal OGD abolished not only the preconditioning-induced neuroprotection but also the Akt activation. Concomitant with blockade of the Akt activation, PI3K inhibition also resulted in activation of Bad and GSK-3β. The results suggest that ischemic tolerance induced by sublethal OGD preconditioning is primarily mediated through activation of the PI3K/Akt pathway, but not the MAPK pathway, in rat cortical neurons.

Transverse Uniaxial Composite Thermal Properties Data Base of Thermally Conductive Graphite Fibers with and without Contiguous Grown Graphite Fins

DTIC Science & Technology

2013-07-01

Vacuum Heat Capacity: Test Method: Conventional MCDS Heating Rate 2 oC/min Temperature(oC): -75 -50 -25 0 25 50 75 100 Average (J/goC): 0.5555...PreConditioning Time-Duration: 24hrs at 125oC and -29inch Vacuum Heat Capacity: Test Method: Conventional MCDS Heating Rate 2 oC/min Temperature(oC...29inch Vacuum Heat Capacity: Test Method: Conventional MCDS Heating Rate 2 oC/min Temperature(oC): -75 -50 -25 0 - - - - Average (J/goC

Conjugate gradient coupled with multigrid for an indefinite problem

NASA Technical Reports Server (NTRS)

Gozani, J.; Nachshon, A.; Turkel, E.

1984-01-01

An iterative algorithm for the Helmholtz equation is presented. This scheme was based on the preconditioned conjugate gradient method for the normal equations. The preconditioning is one cycle of a multigrid method for the discrete Laplacian. The smoothing algorithm is red-black Gauss-Seidel and is constructed so it is a symmetric operator. The total number of iterations needed by the algorithm is independent of h. By varying the number of grids, the number of iterations depends only weakly on k when k(3)h(2) is constant. Comparisons with a SSOR preconditioner are presented.

Multigrid preconditioned conjugate-gradient method for large-scale wave-front reconstruction.

PubMed

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.

Multirate Particle-in-Cell Time Integration Techniques of Vlasov-Maxwell Equations for Collisionless Kinetic Plasma Simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Guangye; Chacon, Luis; Knoll, Dana Alan

2015-07-31

A multi-rate PIC formulation was developed that employs large timesteps for slow field evolution, and small (adaptive) timesteps for particle orbit integrations. Implementation is based on a JFNK solver with nonlinear elimination and moment preconditioning. The approach is free of numerical instabilities (ω peΔt >>1, and Δx >> λ D), and requires many fewer dofs (vs. explicit PIC) for comparable accuracy in challenging problems. Significant gains (vs. conventional explicit PIC) may be possible for large scale simulations. The paper is organized as follows: Vlasov-Maxwell Particle-in-cell (PIC) methods for plasmas; Explicit, semi-implicit, and implicit time integrations; Implicit PIC formulation (Jacobian-Free Newton-Krylovmore » (JFNK) with nonlinear elimination allows different treatments of disparate scales, discrete conservation properties (energy, charge, canonical momentum, etc.)); Some numerical examples; and Summary.« less

2-D weighted least-squares phase unwrapping

DOEpatents

Ghiglia, Dennis C.; Romero, Louis A.

1995-01-01

Weighted values of interferometric signals are unwrapped by determining the least squares solution of phase unwrapping for unweighted values of the interferometric signals; and then determining the least squares solution of phase unwrapping for weighted values of the interferometric signals by preconditioned conjugate gradient methods using the unweighted solutions as preconditioning values. An output is provided that is representative of the least squares solution of phase unwrapping for weighted values of the interferometric signals.

2-D weighted least-squares phase unwrapping

DOEpatents

Ghiglia, D.C.; Romero, L.A.

1995-06-13

Weighted values of interferometric signals are unwrapped by determining the least squares solution of phase unwrapping for unweighted values of the interferometric signals; and then determining the least squares solution of phase unwrapping for weighted values of the interferometric signals by preconditioned conjugate gradient methods using the unweighted solutions as preconditioning values. An output is provided that is representative of the least squares solution of phase unwrapping for weighted values of the interferometric signals. 6 figs.

Repeated Red-Black ordering

NASA Astrophysics Data System (ADS)

Ciarlet, P.

1994-09-01

Hereafter, we describe and analyze, from both a theoretical and a numerical point of view, an iterative method for efficiently solving symmetric elliptic problems with possibly discontinuous coefficients. In the following, we use the Preconditioned Conjugate Gradient method to solve the symmetric positive definite linear systems which arise from the finite element discretization of the problems. We focus our interest on sparse and efficient preconditioners. In order to define the preconditioners, we perform two steps: first we reorder the unknowns and then we carry out a (modified) incomplete factorization of the original matrix. We study numerically and theoretically two preconditioners, the second preconditioner corresponding to the one investigated by Brand and Heinemann [2]. We prove convergence results about the Poisson equation with either Dirichlet or periodic boundary conditions. For a meshsizeh, Brand proved that the condition number of the preconditioned system is bounded byO(h-1/2) for Dirichlet boundary conditions. By slightly modifying the preconditioning process, we prove that the condition number is bounded byO(h-1/3).

Direct reconstruction of cardiac PET kinetic parametric images using a preconditioned conjugate gradient approach

PubMed Central

Rakvongthai, Yothin; Ouyang, Jinsong; Guerin, Bastien; Li, Quanzheng; Alpert, Nathaniel M.; El Fakhri, Georges

2013-01-01

Purpose: Our research goal is to develop an algorithm to reconstruct cardiac positron emission tomography (PET) kinetic parametric images directly from sinograms and compare its performance with the conventional indirect approach. Methods: Time activity curves of a NCAT phantom were computed according to a one-tissue compartmental kinetic model with realistic kinetic parameters. The sinograms at each time frame were simulated using the activity distribution for the time frame. The authors reconstructed the parametric images directly from the sinograms by optimizing a cost function, which included the Poisson log-likelihood and a spatial regularization terms, using the preconditioned conjugate gradient (PCG) algorithm with the proposed preconditioner. The proposed preconditioner is a diagonal matrix whose diagonal entries are the ratio of the parameter and the sensitivity of the radioactivity associated with parameter. The authors compared the reconstructed parametric images using the direct approach with those reconstructed using the conventional indirect approach. Results: At the same bias, the direct approach yielded significant relative reduction in standard deviation by 12%–29% and 32%–70% for 50 × 106 and 10 × 106 detected coincidences counts, respectively. Also, the PCG method effectively reached a constant value after only 10 iterations (with numerical convergence achieved after 40–50 iterations), while more than 500 iterations were needed for CG. Conclusions: The authors have developed a novel approach based on the PCG algorithm to directly reconstruct cardiac PET parametric images from sinograms, and yield better estimation of kinetic parameters than the conventional indirect approach, i.e., curve fitting of reconstructed images. The PCG method increases the convergence rate of reconstruction significantly as compared to the conventional CG method. PMID:24089922

Remote Ischemic Preconditioning and Outcomes of Cardiac Surgery.

PubMed

Hausenloy, Derek J; Candilio, Luciano; Evans, Richard; Ariti, Cono; Jenkins, David P; Kolvekar, Shyam; Knight, Rosemary; Kunst, Gudrun; Laing, Christopher; Nicholas, Jennifer; Pepper, John; Robertson, Steven; Xenou, Maria; Clayton, Tim; Yellon, Derek M

2015-10-08

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, patients were randomly assigned to remote ischemic preconditioning (four 5-minute inflations and deflations of a standard blood-pressure cuff on the upper arm) or sham conditioning (control group). Anesthetic management and perioperative care were not standardized. The combined primary end point was death from cardiovascular causes, nonfatal myocardial infarction, coronary revascularization, or stroke, assessed 12 months after randomization. We enrolled a total of 1612 patients (811 in the control group and 801 in the ischemic-preconditioning group) at 30 cardiac surgery centers in the United Kingdom. There was no significant difference in the cumulative incidence of the primary end point at 12 months between the patients in the remote ischemic preconditioning group and those in the control group (212 patients [26.5%] and 225 patients [27.7%], respectively; hazard ratio with ischemic preconditioning, 0.95; 95% confidence interval, 0.79 to 1.15; P=0.58). Furthermore, there were no significant between-group differences in either adverse events or the secondary end points of perioperative myocardial injury (assessed on the basis of the area under the curve for the high-sensitivity assay of serum troponin T at 72 hours), inotrope score (calculated from the maximum dose of the individual inotropic agents administered in the first 3 days after surgery), acute kidney injury, duration of stay in the intensive care unit and hospital, distance on the 6-minute walk test, and quality of life. Remote ischemic preconditioning did not improve clinical outcomes in patients undergoing elective on-pump CABG with or without valve surgery. (Funded by the Efficacy and Mechanism Evaluation Program [a Medical Research Council and National Institute of Health Research partnership] and the British Heart Foundation; ERICCA ClinicalTrials.gov number, NCT01247545.).

Ultraviolet B preconditioning enhances the hair growth-promoting effects of adipose-derived stem cells via generation of reactive oxygen species.

PubMed

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.

A Molecular Approach to Epilepsy Management: from Current Therapeutic Methods to Preconditioning Efforts.

PubMed

Amini, Elham; Rezaei, Mohsen; Mohamed Ibrahim, Norlinah; Golpich, Mojtaba; Ghasemi, Rasoul; Mohamed, Zahurin; Raymond, Azman Ali; Dargahi, Leila; Ahmadiani, Abolhassan

2015-08-01

Epilepsy is the most common and chronic neurological disorder characterized by recurrent unprovoked seizures. The key aim in treating patients with epilepsy is the suppression of seizures. An understanding of focal changes that are involved in epileptogenesis may therefore provide novel approaches for optimal treatment of the seizure. Although the actual pathogenesis of epilepsy is still uncertain, recently growing lines of evidence declare that microglia and astrocyte activation, oxidative stress and reactive oxygen species (ROS) production, mitochondria dysfunction, and damage of blood-brain barrier (BBB) are involved in its pathogenesis. Impaired GABAergic function in the brain is probably the most accepted hypothesis regarding the pathogenesis of epilepsy. Clinical neuroimaging of patients and experimental modeling have demonstrated that seizures may induce neuronal apoptosis. Apoptosis signaling pathways are involved in the pathogenesis of several types of epilepsy such as temporal lobe epilepsy (TLE). The quality of life of patients is seriously affected by treatment-related problems and also by unpredictability of epileptic seizures. Moreover, the available antiepileptic drugs (AED) are not significantly effective to prevent epileptogenesis. Thus, novel therapies that are proficient to control seizure in people who are suffering from epilepsy are needed. The preconditioning method promises to serve as an alternative therapeutic approach because this strategy has demonstrated the capability to curtail epileptogenesis. For this reason, understanding of molecular mechanisms underlying brain tolerance induced by preconditioning is crucial to delineate new neuroprotective ways against seizure damage and epileptogenesis. In this review, we summarize the work to date on the pathogenesis of epilepsy and discuss recent therapeutic strategies in the treatment of epilepsy. We will highlight that novel therapy targeting such as preconditioning process holds great promise. In addition, we will also highlight the role of gene reprogramming and mitochondrial biogenesis in the preconditioning-mediated neuroprotective events.

Voltage Preconditioning Allows Modulated Gene Expression in Neurons Using PEI-complexed siRNA

PubMed Central

Sridharan, Arati; Patel, Chetan; Muthuswamy, Jit

2013-01-01

We present here a high efficiency, high viability siRNA-delivery method using a voltage-controlled chemical transfection strategy to achieve modulated delivery of polyethylenimine (PEI) complexed with siRNA in an in vitro culture of neuro2A cells and neurons. Low voltage pulses were applied to adherent cells before the administration of PEI-siRNA complexes. Live assays of neuro2a cells transfected with fluorescently tagged siRNA showed an increase in transfection efficiency from 62 ± 14% to 98 ± 3.8% (after −1 V). In primary hippocampal neurons, transfection efficiencies were increased from 30 ± 18% to 76 ± 18% (after −1 V). Negligible or low-level transfection was observed after preconditioning at higher voltages, suggesting an inverse relationship with applied voltage. Experiments with propidium iodide ruled out the role of electroporation in the transfection of siRNAs suggesting an alternate electro-endocytotic mechanism. In addition, image analysis of preconditioned and transfected cells demonstrates siRNA uptake and loading that is tuned to preconditioning voltage levels. There is approximately a fourfold increase in siRNA loading after preconditioning at −1 V compared with the same at ±2–3 V. Modulated gene expression is demonstrated in a functional knockdown of glyceraldehyde 3-phosphate dehydrogenase (GAPDH) in neuro2A cells using siRNA. Cell density and dendritic morphological changes are also demonstrated in modulated knockdown of brain derived neurotrophic factor (BDNF) in primary hippocampal neurons. The method reported here has potential applications in the development of high-throughput screening systems for large libraries of siRNA molecules involving difficult-to-transfect cells like neurons. PMID:23531602

Voltage Preconditioning Allows Modulated Gene Expression in Neurons Using PEI-complexed siRNA.

PubMed

Sridharan, Arati; Patel, Chetan; Muthuswamy, Jit

2013-03-26

We present here a high efficiency, high viability siRNA-delivery method using a voltage-controlled chemical transfection strategy to achieve modulated delivery of polyethylenimine (PEI) complexed with siRNA in an in vitro culture of neuro2A cells and neurons. Low voltage pulses were applied to adherent cells before the administration of PEI-siRNA complexes. Live assays of neuro2a cells transfected with fluorescently tagged siRNA showed an increase in transfection efficiency from 62 ± 14% to 98 ± 3.8% (after -1 V). In primary hippocampal neurons, transfection efficiencies were increased from 30 ± 18% to 76 ± 18% (after -1 V). Negligible or low-level transfection was observed after preconditioning at higher voltages, suggesting an inverse relationship with applied voltage. Experiments with propidium iodide ruled out the role of electroporation in the transfection of siRNAs suggesting an alternate electro-endocytotic mechanism. In addition, image analysis of preconditioned and transfected cells demonstrates siRNA uptake and loading that is tuned to preconditioning voltage levels. There is approximately a fourfold increase in siRNA loading after preconditioning at -1 V compared with the same at ±2-3 V. Modulated gene expression is demonstrated in a functional knockdown of glyceraldehyde 3-phosphate dehydrogenase (GAPDH) in neuro2A cells using siRNA. Cell density and dendritic morphological changes are also demonstrated in modulated knockdown of brain derived neurotrophic factor (BDNF) in primary hippocampal neurons. The method reported here has potential applications in the development of high-throughput screening systems for large libraries of siRNA molecules involving difficult-to-transfect cells like neurons.Molecular Therapy-Nucleic Acids (2013) 2, e82; doi:10.1038/mtna.2013.10; published online 26 March 2013.

Validation of Magnetospheric Magnetohydrodynamic Models

NASA Astrophysics Data System (ADS)

Curtis, Brian

Magnetospheric magnetohydrodynamic (MHD) models are commonly used for both prediction and modeling of Earth's magnetosphere. To date, very little validation has been performed to determine their limits, uncertainties, and differences. In this work, we performed a comprehensive analysis using several commonly used validation techniques in the atmospheric sciences to MHD-based models of Earth's magnetosphere for the first time. The validation techniques of parameter variability/sensitivity analysis and comparison to other models were used on the OpenGGCM, BATS-R-US, and SWMF magnetospheric MHD models to answer several questions about how these models compare. The questions include: (1) the difference between the model's predictions prior to and following to a reversal of Bz in the upstream interplanetary field (IMF) from positive to negative, (2) the influence of the preconditioning duration, and (3) the differences between models under extreme solar wind conditions. A differencing visualization tool was developed and used to address these three questions. We find: (1) For a reversal in IMF Bz from positive to negative, the OpenGGCM magnetopause is closest to Earth as it has the weakest magnetic pressure near-Earth. The differences in magnetopause positions between BATS-R-US and SWMF are explained by the influence of the ring current, which is included in SWMF. Densities are highest for SWMF and lowest for OpenGGCM. The OpenGGCM tail currents differ significantly from BATS-R-US and SWMF; (2) A longer preconditioning time allowed the magnetosphere to relax more, giving different positions for the magnetopause with all three models before the IMF Bz reversal. There were differences greater than 100% for all three models before the IMF Bz reversal. The differences in the current sheet region for the OpenGGCM were small after the IMF Bz reversal. The BATS-R-US and SWMF differences decreased after the IMF Bz reversal to near zero; (3) For extreme conditions in the solar wind, the OpenGGCM has a large region of Earthward flow velocity (Ux) in the current sheet region that grows as time progresses in a compressed environment. BATS-R-US Bz , rho and Ux stabilize to a near constant value approximately one hour into the run under high compression conditions. Under high compression, the SWMF parameters begin to oscillate approximately 100 minutes into the run. All three models have similar magnetopause positions under low pressure conditions. The OpenGGCM current sheet velocities along the Sun-Earth line are largest under low pressure conditions. The results of this analysis indicate the need for accounting for model uncertainties and differences when comparing model predictions with data, provide error bars on model prediction in various magnetospheric regions, and show that the magnetotail is sensitive to the preconditioning time.

Multiple Time-Step Dual-Hamiltonian Hybrid Molecular Dynamics — Monte Carlo Canonical Propagation Algorithm

PubMed Central

Weare, Jonathan; Dinner, Aaron R.; Roux, Benoît

2016-01-01

A multiple time-step integrator based on a dual Hamiltonian and a hybrid method combining molecular dynamics (MD) and Monte Carlo (MC) is proposed to sample systems in the canonical ensemble. The Dual Hamiltonian Multiple Time-Step (DHMTS) algorithm is based on two similar Hamiltonians: a computationally expensive one that serves as a reference and a computationally inexpensive one to which the workload is shifted. The central assumption is that the difference between the two Hamiltonians is slowly varying. Earlier work has shown that such dual Hamiltonian multiple time-step schemes effectively precondition nonlinear differential equations for dynamics by reformulating them into a recursive root finding problem that can be solved by propagating a correction term through an internal loop, analogous to RESPA. Of special interest in the present context, a hybrid MD-MC version of the DHMTS algorithm is introduced to enforce detailed balance via a Metropolis acceptance criterion and ensure consistency with the Boltzmann distribution. The Metropolis criterion suppresses the discretization errors normally associated with the propagation according to the computationally inexpensive Hamiltonian, treating the discretization error as an external work. Illustrative tests are carried out to demonstrate the effectiveness of the method. PMID:26918826

Non-preconditioned conjugate gradient on cell and FPGA based hybrid supercomputer nodes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dubois, David H; Dubois, Andrew J; Boorman, Thomas M

2009-01-01

This work presents a detailed implementation of a double precision, non-preconditioned, Conjugate Gradient algorithm on a Roadrunner heterogeneous supercomputer node. These nodes utilize the Cell Broadband Engine Architecture{sup TM} in conjunction with x86 Opteron{sup TM} processors from AMD. We implement a common Conjugate Gradient algorithm, on a variety of systems, to compare and contrast performance. Implementation results are presented for the Roadrunner hybrid supercomputer, SRC Computers, Inc. MAPStation SRC-6 FPGA enhanced hybrid supercomputer, and AMD Opteron only. In all hybrid implementations wall clock time is measured, including all transfer overhead and compute timings.

Non-preconditioned conjugate gradient on cell and FPCA-based hybrid supercomputer nodes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dubois, David H; Dubois, Andrew J; Boorman, Thomas M

2009-03-10

This work presents a detailed implementation of a double precision, Non-Preconditioned, Conjugate Gradient algorithm on a Roadrunner heterogeneous supercomputer node. These nodes utilize the Cell Broadband Engine Architecture{trademark} in conjunction with x86 Opteron{trademark} processors from AMD. We implement a common Conjugate Gradient algorithm, on a variety of systems, to compare and contrast performance. Implementation results are presented for the Roadrunner hybrid supercomputer, SRC Computers, Inc. MAPStation SRC-6 FPGA enhanced hybrid supercomputer, and AMD Opteron only. In all hybrid implementations wall clock time is measured, including all transfer overhead and compute timings.

Simultaneous optical flow and source estimation: Space–time discretization and preconditioning

PubMed Central

Andreev, R.; Scherzer, O.; Zulehner, W.

2015-01-01

We consider the simultaneous estimation of an optical flow field and an illumination source term in a movie sequence. The particular optical flow equation is obtained by assuming that the image intensity is a conserved quantity up to possible sources and sinks which represent varying illumination. We formulate this problem as an energy minimization problem and propose a space–time simultaneous discretization for the optimality system in saddle-point form. We investigate a preconditioning strategy that renders the discrete system well-conditioned uniformly in the discretization resolution. Numerical experiments complement the theory. PMID:26435561

Weighted SGD for ℓ p Regression with Randomized Preconditioning.

PubMed

Yang, Jiyan; Chow, Yin-Lam; Ré, Christopher; Mahoney, Michael W

2016-01-01

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., ℓ 2 and ℓ 1 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 ℓ p regression problem as a stochastic optimization problem, we connect pwSGD to several existing ℓ p 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 ℓ 1 regression with size n by d , pwSGD returns an approximate solution with ε relative error in the objective value in (log n ·nnz( A )+poly( d )/ ε 2 ) 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 ℓ 2 regression, pwSGD returns an approximate solution with ε relative error in the objective value and the solution vector measured in prediction norm in (log n ·nnz( A )+poly( d ) log(1/ ε )/ ε ) time. We show that for unconstrained ℓ 2 regression, this complexity is comparable to that of RLA and is asymptotically better over several state-of-the-art solvers in the regime where the desired accuracy ε , high dimension n and low dimension d satisfy d ≥ 1/ ε and n ≥ d 2 / ε . We also provide lower bounds on the coreset complexity for more general regression problems, indicating that still new ideas will be needed to extend similar RLA preconditioning ideas to weighted SGD algorithms for more general regression problems. Finally, the effectiveness of such algorithms is illustrated numerically on both synthetic and real datasets, and the results are consistent with our theoretical findings and demonstrate that pwSGD converges to a medium-precision solution, e.g., ε = 10 -3 , more quickly.

Weighted SGD for ℓp Regression with Randomized Preconditioning*

PubMed Central

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 prediction norm in 𝒪(log n·nnz(A)+poly(d) log(1/ε)/ε) time. We show that for unconstrained ℓ2 regression, this complexity is comparable to that of RLA and is asymptotically better over several state-of-the-art solvers in the regime where the desired accuracy ε, high dimension n and low dimension d satisfy d ≥ 1/ε and n ≥ d2/ε. We also provide lower bounds on the coreset complexity for more general regression problems, indicating that still new ideas will be needed to extend similar RLA preconditioning ideas to weighted SGD algorithms for more general regression problems. Finally, the effectiveness of such algorithms is illustrated numerically on both synthetic and real datasets, and the results are consistent with our theoretical findings and demonstrate that pwSGD converges to a medium-precision solution, e.g., ε = 10−3, more quickly. PMID:29782626

Organisational readiness: exploring the preconditions for success in organisation-wide patient safety improvement programmes.

PubMed

Burnett, Susan; Benn, Jonathan; Pinto, Anna; Parand, Anam; Iskander, Sandra; Vincent, Charles

2010-08-01

Patient safety has been high on the agenda for more than a decade. Despite many national initiatives aimed at improving patient safety, the challenge remains to find coherent and sustainable organisation-wide safety-improvement programmes. In the UK, the Safer Patients' Initiative (SPI) was established to address this challenge. Important in the success of such an endeavour is understanding 'readiness' at the organisational level, identifying the preconditions for success in this type of programme. This article reports on a case study of the four NHS organisations participating in the first phase of SPI, examining the perceptions of organisational readiness and the relationship of these factors with impact by those actively involved in the initiative. A mixed-methods design was used, involving a survey and semistructured interviews with senior executive leads, the principal SPI programme coordinator and the four operational leads in each of the SPI clinical work areas in all four organisations taking part in the first phase of SPI. This preliminary work would suggest that prior to the start of organisation-wide quality- and safety-improvement programmes, organisations would benefit from an assessment of readiness with time spent in the preparation of the organisational infrastructure, processes and culture. Furthermore, a better understanding of the preconditions that mark an organisation as ready for improvement work would allow policymakers to set realistic expectations about the outcomes of safety campaigns.

Relaxation and Preconditioning for High Order Discontinuous Galerkin Methods with Applications to Aeroacoustics and High Speed Flows

NASA Technical Reports Server (NTRS)

Shu, Chi-Wang

2004-01-01

This project is about the investigation of the development of the discontinuous Galerkin finite element methods, for general geometry and triangulations, for solving convection dominated problems, with applications to aeroacoustics. Other related issues in high order WENO finite difference and finite volume methods have also been investigated. methods are two classes of high order, high resolution methods suitable for convection dominated simulations with possible discontinuous or sharp gradient solutions. In [18], we first review these two classes of methods, pointing out their similarities and differences in algorithm formulation, theoretical properties, implementation issues, applicability, and relative advantages. We then present some quantitative comparisons of the third order finite volume WENO methods and discontinuous Galerkin methods for a series of test problems to assess their relative merits in accuracy and CPU timing. In [3], we review the development of the Runge-Kutta discontinuous Galerkin (RKDG) methods for non-linear convection-dominated problems. These robust and accurate methods have made their way into the main stream of computational fluid dynamics and are quickly finding use in a wide variety of applications. They combine a special class of Runge-Kutta time discretizations, that allows the method to be non-linearly stable regardless of its accuracy, with a finite element space discretization by discontinuous approximations, that incorporates the ideas of numerical fluxes and slope limiters coined during the remarkable development of the high-resolution finite difference and finite volume schemes. The resulting RKDG methods are stable, high-order accurate, and highly parallelizable schemes that can easily handle complicated geometries and boundary conditions. We review the theoretical and algorithmic aspects of these methods and show several applications including nonlinear conservation laws, the compressible and incompressible Navier-Stokes equations, and Hamilton-Jacobi-like equations.

Mechanisms of acetylcholine- and bradykinin-induced preconditioning.

PubMed

Critz, Stuart D; Cohen, Michael V; Downey, James M

2005-01-01

Acetylcholine (ACh) and bradykinin (BK) are potent pharmacological agents which mimic ischemic preconditioning (IPC) enabling hearts to resist infarction during a subsequent period of ischemia. The cardioprotective pathways activated by BK but not ACh may also protect when activated at reperfusion. ACh and BK stimulate Gi/o-linked receptors and ultimately mediate protection by opening mitochondrial ATP-sensitive potassium channels with the generation of reactive oxygen species that act as second messengers to activate protein kinase C (PKC). There appear to be key differences, however, in the pathways prior to potassium channel opening for these two receptors. This review aims to summarize what is currently known about pharmacological preconditioning by ACh and BK with an emphasis on differences that are seen in the signal transduction cascades. Understanding the cellular basis of protection by ACh and BK is a critical step towards developing pharmacological agents that will prevent infarction during ischemia resulting from coronary occlusion or heart attack.

Krylov Deferred Correction Accelerated Method of Lines Transpose for Parabolic Problems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jia, Jun; Jingfang, Huang

2008-01-01

In this paper, a new class of numerical methods for the accurate and efficient solutions of parabolic partial differential equations is presented. Unlike traditional method of lines (MoL), the new {\\bf \\it Krylov deferred correction (KDC) accelerated method of lines transpose (MoL^T)} first discretizes the temporal direction using Gaussian type nodes and spectral integration, and symbolically applies low-order time marching schemes to form a preconditioned elliptic system, which is then solved iteratively using Newton-Krylov techniques such as Newton-GMRES or Newton-BiCGStab method. Each function evaluation in the Newton-Krylov method is simply one low-order time-stepping approximation of the error by solving amore » decoupled system using available fast elliptic equation solvers. Preliminary numerical experiments show that the KDC accelerated MoL^T technique is unconditionally stable, can be spectrally accurate in both temporal and spatial directions, and allows optimal time-step sizes in long-time simulations.« less

Myocardial protection using diadenosine tetraphosphate with pharmacological preconditioning.

PubMed

Ahmet, I; Sawa, Y; Nishimura, M; Yamaguchi, T; Kitakaze, M; Matsuda, H

2000-09-01

We have reported a similar cardioprotective effect and mechanism of diadenosine tetraphosphate (AP4A) and ischemic preconditioning in rat hearts. In this study, the applicability of AP4A administration to cardiac surgery was tested by using a canine cardiopulmonary bypass model. Hearts underwent 60 minutes of cardioplegic arrest (34 degrees C) by a single dose of cardioplegia. Cardioplegia contained either AP4A (40 micromol/L; n = 6) or saline (n = 6). Beagles were weaned from cardiopulmonary bypass 30 minutes after reperfusion, and left ventricular function was evaluated after another 30 minutes by using the cardiac loop analysis system. Administration of AP4A significantly improved the postischemic recovery of cardiac function and reduced the leakage of serum creatine kinase compared with saline. Systemic vascular resistance, mean aortic blood pressure, and the electrocardiographic indices were not significantly altered by AP4A administration. Administration of AP4A was cardioprotective without apparent adverse effects. Because the cardioprotective mechanism may be similar to that of ischemic preconditioning, the addition of AP4A into cardioplegia may be a novel safe method for clinical application of preconditioning cardioprotection.

Electrochemical evidences and consequences of significant differences in ions diffusion rate in polyacrylate-based ion-selective membranes.

PubMed

Woźnica, Emilia; Mieczkowski, Józef; Michalska, Agata

2011-11-21

The origin and effect of surface accumulation of primary ions within the ion-selective poly(n-butyl acrylate)-based membrane, obtained by thermal polymerization, is discussed. Using a new method, based on the relation between the shape of a potentiometric plot and preconditioning time, the diffusion of copper ions in the membrane was found to be slow (the diffusion coefficient estimated to be close to 10(-11) cm(2) s(-1)), especially when compared to ion-exchanger counter ions--sodium cations diffusion (a diffusion coefficient above 10(-9) cm(2) s(-1)). The higher mobility of sodium ions than those of the copper-ionophore complex results in exposed ion-exchanger role leading to undesirably exposed sensitivity to sodium or potassium ions.

Using Argumentation Theory to Identify the Challenges of Shared Decision-Making when the Doctor and the Patient have a Difference of Opinion

PubMed Central

Zanini, Claudia A.; Rubinelli, Sara

2012-01-01

This paper aims to identify the challenges in the implementation of shared decision-making (SDM) when the doctor and the patient have a difference of opinion. It analyses the preconditions of the resolution of this difference of opinion by using an analytical and normative framework known in the field of argumentation theory as the ideal model of critical discussion. This analysis highlights the communication skills and attitudes that both doctors and patients must apply in a dispute resolution-oriented communication. Questions arise over the methods of empowerment of doctors and patients in these skills and attitudes as the preconditions of SDM. Overall, the paper highlights aspects in which research is needed to design appropriate programmes of training, education and support in order to equip doctors and patients with the means to successfully engage in shared decision-making. Acknowledgements the authors would like to thank the Swiss National Science Foundation for funding this project (project number: PDFMP1_132523. Enhancing doctor-patient argumentation through the International Classification of Functioning, Disability and Health (ICF). Insights from a study in the field of chronic pain). PMID:25170461

Preconditioned conjugate residual methods for the solution of spectral equations

NASA Technical Reports Server (NTRS)

Wong, Y. S.; Zang, T. A.; Hussaini, M. Y.

1986-01-01

Conjugate residual methods for the solution of spectral equations are described. An inexact finite-difference operator is introduced as a preconditioner in the iterative procedures. Application of these techniques is limited to problems for which the symmetric part of the coefficient matrix is positive definite. Although the spectral equation is a very ill-conditioned and full matrix problem, the computational effort of the present iterative methods for solving such a system is comparable to that for the sparse matrix equations obtained from the application of either finite-difference or finite-element methods to the same problems. Numerical experiments are shown for a self-adjoint elliptic partial differential equation with Dirichlet boundary conditions, and comparison with other solution procedures for spectral equations is presented.

Xenon Preconditioning Protects against Renal Ischemic-Reperfusion Injury via HIF-1α Activation

PubMed Central

Ma, Daqing; Lim, Ta; Xu, Jing; Tang, Haidy; Wan, Yanjie; Zhao, Hailin; Hossain, Mahmuda; Maxwell, Patrick H.; Maze, Mervyn

2009-01-01

The mortality rate from acute kidney injury after major cardiovascular operations can be as high as 60%, and no therapies have been proved to prevent acute kidney injury in this setting. Here, we show that preconditioning with the anesthetic gas xenon activates hypoxia-inducible factor 1α (HIF-1α) and its downstream effectors erythropoietin and vascular endothelial growth factor in a time-dependent manner in the kidneys of adult mice. Xenon increased the efficiency of HIF-1α translation via modulation of the mammalian target of rapamycin pathway. In a model of renal ischemia-reperfusion injury, xenon provided morphologic and functional renoprotection; hydrodynamic injection of HIF-1α small interfering RNA demonstrated that this protection is HIF-1α dependent. These results suggest that xenon preconditioning is a natural inducer of HIF-1α and that administration of xenon before renal ischemia can prevent acute renal failure. If these data are confirmed in the clinical setting, then preconditioning with xenon may be beneficial before procedures that temporarily interrupt renal perfusion. PMID:19144758

A Well-Tempered Hybrid Method for Solving Challenging Time-Dependent Density Functional Theory (TDDFT) Systems.

PubMed

Kasper, Joseph M; Williams-Young, David B; Vecharynski, Eugene; Yang, Chao; Li, Xiaosong

2018-04-10

The time-dependent Hartree-Fock (TDHF) and time-dependent density functional theory (TDDFT) equations allow one to probe electronic resonances of a system quickly and inexpensively. However, the iterative solution of the eigenvalue problem can be challenging or impossible to converge, using standard methods such as the Davidson algorithm for spectrally dense regions in the interior of the spectrum, as are common in X-ray absorption spectroscopy (XAS). More robust solvers, such as the generalized preconditioned locally harmonic residual (GPLHR) method, can alleviate this problem, but at the expense of higher average computational cost. A hybrid method is proposed which adapts to the problem in order to maximize computational performance while providing the superior convergence of GPLHR. In addition, a modification to the GPLHR algorithm is proposed to adaptively choose the shift parameter to enforce a convergence of states above a predefined energy threshold.

An accelerated lambda iteration method for multilevel radiative transfer. I - Non-overlapping lines with background continuum

NASA Technical Reports Server (NTRS)

Rybicki, G. B.; Hummer, D. G.

1991-01-01

A method is presented for solving multilevel transfer problems when nonoverlapping lines and background continuum are present and active continuum transfer is absent. An approximate lambda operator is employed to derive linear, 'preconditioned', statistical-equilibrium equations. A method is described for finding the diagonal elements of the 'true' numerical lambda operator, and therefore for obtaining the coefficients of the equations. Iterations of the preconditioned equations, in conjunction with the transfer equation's formal solution, are used to solve linear equations. Some multilevel problems are considered, including an eleven-level neutral helium atom. Diagonal and tridiagonal approximate lambda operators are utilized in the problems to examine the convergence properties of the method, and it is found to be effective for the line transfer problems.

Efficient block preconditioned eigensolvers for linear response time-dependent density functional theory

NASA Astrophysics Data System (ADS)

Vecharynski, Eugene; Brabec, Jiri; Shao, Meiyue; Govind, Niranjan; Yang, Chao

2017-12-01

We present two efficient iterative algorithms for solving the linear response eigenvalue problem arising from the time dependent density functional theory. Although the matrix to be diagonalized is nonsymmetric, it has a special structure that can be exploited to save both memory and floating point operations. In particular, the nonsymmetric eigenvalue problem can be transformed into an eigenvalue problem that involves the product of two matrices M and K. We show that, because MK is self-adjoint with respect to the inner product induced by the matrix K, this product eigenvalue problem can be solved efficiently by a modified Davidson algorithm and a modified locally optimal block preconditioned conjugate gradient (LOBPCG) algorithm that make use of the K-inner product. The solution of the product eigenvalue problem yields one component of the eigenvector associated with the original eigenvalue problem. We show that the other component of the eigenvector can be easily recovered in an inexpensive postprocessing procedure. As a result, the algorithms we present here become more efficient than existing methods that try to approximate both components of the eigenvectors simultaneously. In particular, our numerical experiments demonstrate that the new algorithms presented here consistently outperform the existing state-of-the-art Davidson type solvers by a factor of two in both solution time and storage.

[Effects of xenon preconditioning against ischemia/reperfusion injury and oxidative stress in immature heart].

PubMed

Li, Qian; Lian, Chun-Wei; Fang, Li-Qun; Liu, Bin; Yang, Bo

2014-09-01

To investigate whether xenon preconditioning (PC) could protect immature myocardium against ischemia-reperfusion (I/R) injury in a dose-dependent manner and clarify the role of xenon PC on oxidative stress. Forty-eight isolated perfused immature rabbit hearts were randomly divided into four groups (n = 12): The sham group had the hearts perfused continuously for 300 min. In I/R group, the hearts were subjected to 60 min perfusion followed by 60 min ischemia and 180 min reperfusion. In 1 minimum alveolar concentration (MAC) and 0.5 MAC xenon PC groups, the hearts were preconditioned with 1 MAC or 0.5 MAC xenon respectively, following 60 min ischemia and 180 min reperfusion. The cardiac function, myocardial infarct size, mitochondrial structure, superoxide dismutase (SOD) activity and malondialdehyde (MDA) level in each group were determined after reperfusion. Compared with I/R group, both 1 MAC and 0. 5 MAC xenon preconditioning significantly improved cardiac function (P < 0.01), reduced myocardial infarct size (P < 0.01) and mitochondrial damage, increased SOD activity and decreased MDA level (P < 0.01). There were no differences between 1 MAC group and 0.5 MAC xenon group (P > 0.05). Xenon preconditioning at 0. 5 and 1 MAC produce similar cardioprotective effects against I/R injury in isolated perfused immature heart.

Loss of glycogen during preconditioning is not a prerequisite for protection of the rabbit heart.

PubMed

Weinbrenner, C; Wang, P; Downey, J M

1996-01-01

Depletion of glycogen has been proposed as the mechanism of protection from ischemic preconditioning. The hypothesis was tested by seeing whether pharmacological manipulation of preconditioning causes parallel changes in cardiac glycogen content. Five groups of isolated rabbit hearts were studied. Group 1 experienced 30 min of ischemia only. Group 2 (PC) was preconditioned with 5 min of global ischemia followed by 10 min of reperfusion. Group 3 was preconditioned with 5 min exposure to 400 nM bradykinin followed by a 10 min washout period. Group 4 experienced exposure to 10 microM adenosine followed by a 10 min washout period, and the fifth group was also preconditioned with 5 min ischemia and 10 min reperfusion but 100 microM 8-(p-sulfophenyl)theophylline (SPT), which blocks adenosine receptors, was included in the buffer to block preconditioning's protection. Transmural biopsies were taken before treatment, just prior to the 30 min period of global ischemia, and after 30 min of global ischemia. Glycogen in the samples was digested with amyloglucosidase and the resulting glucose was assayed. Baseline glycogen averaged 17.3 +/- 0.6 mumol glucose/g wet weight. After preconditioning glycogen decreased to 13.3 +/- 1.3 mumol glucose/g wet weight (p < 0.005 vs. baseline). Glycogen was similarly depleted after pharmacological preconditioning with adenosine (14.0 +/- 1.0 mumol glucose/g wet weight, p < 0.05 vs. baseline) suggesting a correlation. However, when preconditioning was performed in the presence of SPT, which blocks protection, glycogen was also depleted by the same amount (13.3 +/- 0.7 mumol glucose/g wet weight, p = ns vs. PC). Bradykinin, which also mimics preconditioning, caused no depletion of glycogen (16.3 +/- 0.8 mumol glucose/g wet weight, p = ns vs. baseline). Because preconditioning with bradykinin did not deplete glycogen and because glycogen continued to be low when protection from preconditioning was blocked with SPT, we conclude that loss of glycogen per se does not cause the protection of preconditioning.

Weighted graph based ordering techniques for preconditioned conjugate gradient methods

NASA Technical Reports Server (NTRS)

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.

Physics-Based Preconditioning of a Compressible Flow Solver for Large-Scale Simulations of Additive Manufacturing Processes

NASA Astrophysics Data System (ADS)

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.

P1 Nonconforming Finite Element Method for the Solution of Radiation Transport Problems

NASA Technical Reports Server (NTRS)

Kang, Kab S.

2002-01-01

The simulation of radiation transport in the optically thick flux-limited diffusion regime has been identified as one of the most time-consuming tasks within large simulation codes. Due to multimaterial complex geometry, the radiation transport system must often be solved on unstructured grids. In this paper, we investigate the behavior and the benefits of the unstructured P(sub 1) nonconforming finite element method, which has proven to be flexible and effective on related transport problems, in solving unsteady implicit nonlinear radiation diffusion problems using Newton and Picard linearization methods. Key words. nonconforrning finite elements, radiation transport, inexact Newton linearization, multigrid preconditioning

Isoflurane preconditioning protects neurons from male and female mice against oxygen and glucose deprivation and is modulated by estradiol only in neurons from female mice.

PubMed

Johnsen, D; Murphy, S J

2011-12-29

The volatile anesthetic, isoflurane, can protect the brain if administered before an insult such as an ischemic stroke. However, this protective "preconditioning" response to isoflurane is specific to males, with females showing an increase in brain damage following isoflurane preconditioning and subsequent focal cerebral ischemia. Innate cell sex is emerging as an important player in neuronal cell death, but its role in the sexually dimorphic response to isoflurane preconditioning has not been investigated. We used an in vitro model of isoflurane preconditioning and ischemia (oxygen and glucose deprivation, OGD) to test the hypotheses that innate cell sex dictates the response to isoflurane preconditioning and that 17β-estradiol attenuates any protective effect from isoflurane preconditioning in neurons via nuclear estrogen receptors. Sex-segregated neuron cultures derived from postnatal day 0-1 mice were exposed to either 0% or 3% isoflurane preconditioning for 1 h. In separate experiments, 17β-estradiol and the non-selective estrogen receptor antagonist ICI 182,780 were added 24 h before preconditioning and then removed at the end of the preconditioning period. Twenty-three hours after preconditioning, all cultures underwent 2 h of OGD. Twenty-four hours following OGD, cell viability was quantified using calcein-AM fluorescence. We observed that isoflurane preconditioning increased cell survival following subsequent OGD regardless of innate cell sex, but that the presence of 17β-estradiol before and during isoflurane preconditioning attenuated this protection only in female neurons independent of nuclear estrogen receptors. We also found that independent of preconditioning treatment, female neurons were less sensitive to OGD compared with male neurons and that transient treatment with 17β-estradiol protected both male and female neurons from subsequent OGD. More studies are needed to determine how cell type, cell sex, and sex steroids like 17β-estradiol may impact on anesthetic preconditioning and subsequent ischemic outcomes in the brain. Copyright © 2011 IBRO. Published by Elsevier Ltd. All rights reserved.

The role of remote ischemic preconditioning in organ protection after cardiac surgery: a meta-analysis.

PubMed

Haji Mohd Yasin, Nur A B; Herbison, Peter; Saxena, Pankaj; Praporski, Slavica; Konstantinov, Igor E

2014-01-01

Remote ischemic preconditioning (RIPC) appears to protect distant organs from ischemia-reperfusion injury. We undertook meta-analysis of clinical studies to evaluate the effects of RIPC on organ protection and clinical outcomes in patients undergoing cardiac surgery. A review of evidence for cardiac, renal, and pulmonary protection after RIPC was performed. We also did meta-regressions on RIPC variables, such as duration of ischemia, cuff pressure, and timing of application of preconditioning. Secondary outcomes included length of hospital and intensive care unit stay, duration of mechanical ventilation, and mortality at 30 days. Randomized control trials (n = 25) were included in the study for quantitative analysis of cardiac (n = 16), renal (n = 6), and pulmonary (n = 3) protection. RIPC provided statistically significant cardiac protection (standardized mean difference [SMD], -0.77; 95% confidence interval [CI], -1.15, -0.39; Z = 3.98; P < 0.0001) and on subgroup analysis, the protective effect remained consistent for all types of cardiac surgical procedures. However, there was no evidence of renal protection (SMD, 0.74; 95% CI, 0.53, 1.02; Z = 1.81; P = 0.07) or pulmonary protection (SMD, -0.03; 95% CI, -0.56, 0.50; Z = 0.12; P = 0.91). There was no statistical difference in the short-term clinical outcomes between the RIPC and control groups. RIPC provides cardiac protection, but there is no evidence of renal or pulmonary protection in patients undergoing cardiac surgery using cardiopulmonary bypass. Larger multicenter trials are required to define the role of RIPC in surgical practice. Crown Copyright © 2014. Published by Elsevier Inc. All rights reserved.

System Design for Ocean Sensor Data Transmission Based on Inductive Coupling

NASA Astrophysics Data System (ADS)

Xu, Ming; Liu, Fei; Zong, Yuan; Hong, Feng

Ocean observation is the precondition to explore and utilize ocean. How to acquire ocean data in a precise, efficient and real-time way is the key question of ocean surveillance. Traditionally, there are three types of methods for ocean data transmission: underwater acoustic, GPRS via mobile network and satellite communication. However, none of them can meet the requirements of efficiency, accuracy, real-time and low cost at the same time. In this paper, we propose a new wireless transmission system for underwater sensors, which established on FGR wireless modules, combined with inductive coupling lab and offshore experiments confirmed the feasibility and effectiveness of the proposed wireless transmission system.

Two new modified Gauss-Seidel methods for linear system with M-matrices

NASA Astrophysics Data System (ADS)

Zheng, Bing; Miao, Shu-Xin

2009-12-01

In 2002, H. Kotakemori et al. proposed the modified Gauss-Seidel (MGS) method for solving the linear system with the preconditioner [H. Kotakemori, K. Harada, M. Morimoto, H. Niki, A comparison theorem for the iterative method with the preconditioner () J. Comput. Appl. Math. 145 (2002) 373-378]. Since this preconditioner is constructed by only the largest element on each row of the upper triangular part of the coefficient matrix, the preconditioning effect is not observed on the nth row. In the present paper, to deal with this drawback, we propose two new preconditioners. The convergence and comparison theorems of the modified Gauss-Seidel methods with these two preconditioners for solving the linear system are established. The convergence rates of the new proposed preconditioned methods are compared. In addition, numerical experiments are used to show the effectiveness of the new MGS methods.

Direct reconstruction of cardiac PET kinetic parametric images using a preconditioned conjugate gradient approach.

PubMed

Rakvongthai, Yothin; Ouyang, Jinsong; Guerin, Bastien; Li, Quanzheng; Alpert, Nathaniel M; El Fakhri, Georges

2013-10-01

Our research goal is to develop an algorithm to reconstruct cardiac positron emission tomography (PET) kinetic parametric images directly from sinograms and compare its performance with the conventional indirect approach. Time activity curves of a NCAT phantom were computed according to a one-tissue compartmental kinetic model with realistic kinetic parameters. The sinograms at each time frame were simulated using the activity distribution for the time frame. The authors reconstructed the parametric images directly from the sinograms by optimizing a cost function, which included the Poisson log-likelihood and a spatial regularization terms, using the preconditioned conjugate gradient (PCG) algorithm with the proposed preconditioner. The proposed preconditioner is a diagonal matrix whose diagonal entries are the ratio of the parameter and the sensitivity of the radioactivity associated with parameter. The authors compared the reconstructed parametric images using the direct approach with those reconstructed using the conventional indirect approach. At the same bias, the direct approach yielded significant relative reduction in standard deviation by 12%-29% and 32%-70% for 50 × 10(6) and 10 × 10(6) detected coincidences counts, respectively. Also, the PCG method effectively reached a constant value after only 10 iterations (with numerical convergence achieved after 40-50 iterations), while more than 500 iterations were needed for CG. The authors have developed a novel approach based on the PCG algorithm to directly reconstruct cardiac PET parametric images from sinograms, and yield better estimation of kinetic parameters than the conventional indirect approach, i.e., curve fitting of reconstructed images. The PCG method increases the convergence rate of reconstruction significantly as compared to the conventional CG method.

Acceleration of Linear Finite-Difference Poisson-Boltzmann Methods on Graphics Processing Units.

PubMed

Qi, Ruxi; Botello-Smith, Wesley M; Luo, Ray

2017-07-11

Electrostatic interactions play crucial roles in biophysical processes such as protein folding and molecular recognition. Poisson-Boltzmann equation (PBE)-based models have emerged as widely used in modeling these important processes. Though great efforts have been put into developing efficient PBE numerical models, challenges still remain due to the high dimensionality of typical biomolecular systems. In this study, we implemented and analyzed commonly used linear PBE solvers for the ever-improving graphics processing units (GPU) for biomolecular simulations, including both standard and preconditioned conjugate gradient (CG) solvers with several alternative preconditioners. Our implementation utilizes the standard Nvidia CUDA libraries cuSPARSE, cuBLAS, and CUSP. Extensive tests show that good numerical accuracy can be achieved given that the single precision is often used for numerical applications on GPU platforms. The optimal GPU performance was observed with the Jacobi-preconditioned CG solver, with a significant speedup over standard CG solver on CPU in our diversified test cases. Our analysis further shows that different matrix storage formats also considerably affect the efficiency of different linear PBE solvers on GPU, with the diagonal format best suited for our standard finite-difference linear systems. Further efficiency may be possible with matrix-free operations and integrated grid stencil setup specifically tailored for the banded matrices in PBE-specific linear systems.

Factors influencing poststocking dispersal of razorback sucker

USGS Publications Warehouse

Mueller, G.A.; Marsh, P.C.; Foster, D.; Ulibarri, M.; Burke, T.

2003-01-01

Efforts to reintroduce razorback suckers Xyrauchen texanus to specific river reaches have been plagued by downstream drift and poor survival, which have been attributed to stress, disorientation, predation, and poor conditioning. Poststocking dispersal of eight test groups (15 fish each) of razorback suckers was examined for 28 d with telemetry equipment. Fish were released in three different locations in the Colorado River basin of Utah, Arizona, and Nevada: (1) a 65,000-ha reservoir, (2) a small (<1-ha) backwater, and (3) a large (30-ha) backwater on the mainstem river. At each location, subgroups were released immediately (reference) or held to acclimate them to the site (3–7 d) before release. Two of four subgroups for the large-backwater test were preconditioned to flow. Dispersal from the stocking sites was rapid and declined with time for all tests, as fish appeared to seek and find cover. Downstream drift was most pronounced (x = 69.5 km) from the small backwater and significantly (Kruskal–Wallis test, P < 0.01) greater than either the reservoir (x = 3.7 km) or large-backwater sites (x = 7.7 km). Site-acclimation tests were inconclusive, but downstream movement was significantly (Wilcoxon two-sample test, Z = −2.298, P < 0.01) less for fish preconditioned to flow (x = 1.9 km) compared with pond-reared fish (x = 7.7 km). We concluded that poststocking dispersal may decrease if razorback suckers are preconditioned to flow.

Large scale Brownian dynamics of confined suspensions of rigid particles

NASA Astrophysics Data System (ADS)

Sprinkle, Brennan; Balboa Usabiaga, Florencio; Patankar, Neelesh A.; Donev, Aleksandar

2017-12-01

We introduce methods for large-scale Brownian Dynamics (BD) simulation of many rigid particles of arbitrary shape suspended in a fluctuating fluid. Our method adds Brownian motion to the rigid multiblob method [F. Balboa Usabiaga et al., Commun. Appl. Math. Comput. Sci. 11(2), 217-296 (2016)] at a cost comparable to the cost of deterministic simulations. We demonstrate that we can efficiently generate deterministic and random displacements for many particles using preconditioned Krylov iterative methods, if kernel methods to efficiently compute the action of the Rotne-Prager-Yamakawa (RPY) mobility matrix and its "square" root are available for the given boundary conditions. These kernel operations can be computed with near linear scaling for periodic domains using the positively split Ewald method. Here we study particles partially confined by gravity above a no-slip bottom wall using a graphical processing unit implementation of the mobility matrix-vector product, combined with a preconditioned Lanczos iteration for generating Brownian displacements. We address a major challenge in large-scale BD simulations, capturing the stochastic drift term that arises because of the configuration-dependent mobility. Unlike the widely used Fixman midpoint scheme, our methods utilize random finite differences and do not require the solution of resistance problems or the computation of the action of the inverse square root of the RPY mobility matrix. We construct two temporal schemes which are viable for large-scale simulations, an Euler-Maruyama traction scheme and a trapezoidal slip scheme, which minimize the number of mobility problems to be solved per time step while capturing the required stochastic drift terms. We validate and compare these schemes numerically by modeling suspensions of boomerang-shaped particles sedimented near a bottom wall. Using the trapezoidal scheme, we investigate the steady-state active motion in dense suspensions of confined microrollers, whose height above the wall is set by a combination of thermal noise and active flows. We find the existence of two populations of active particles, slower ones closer to the bottom and faster ones above them, and demonstrate that our method provides quantitative accuracy even with relatively coarse resolutions of the particle geometry.

Realization of preconditioned Lanczos and conjugate gradient algorithms on optical linear algebra processors.

PubMed

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.

Pre-conditioning procedure suitable for internal-RF-antenna of J-PARC RF-driven H{sup −} ion source

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ueno, A., E-mail: akira.ueno@j-parc.jp; Ohkoshi, K.; Ikegami, K.

The Japan Proton Accelerator Research Complex (J-PARC) cesiated RF-driven H{sup −} ion source has been successfully operated for about 1 yr. By the world brightest level beam, the J-PARC design beam power of 1 MW was successfully demonstrated. Although no internal-RF-antenna failure, except for the once caused by an excess cesium due to a misoperation, occurred in the operation, many antennas failed in pre-conditionings for the first hundred days. The antenna failure rate was drastically decreased by using an antenna with coating thicker than a standard value and the pre-conditioning procedure repeating 15 min 25 kW RF-power operation and impurity-gasmore » evacuation a few times, before the full power (50 kW) operation.« less

A capillary zone electrophoresis method for detection of Apolipoprotein C-III glycoforms and other related artifactually modified species.

PubMed

Ruel, Coralie; Morani, Marco; Bruneel, Arnaud; Junot, Christophe; Taverna, Myriam; Fenaille, François; Tran, Nguyet Thuy

2018-01-12

ApolipoproteinC-III (ApoC-III) is a human plasma glycoprotein whose O-glycosylation can be altered as a result of congenital disorders of glycosylation (CDG). ApoC-III exhibits three major glycoforms whose relative quantification is of utmost importance for the diagnosis of CDG patients. Considering the very close structures of these glycoforms and their tendency to adsorb on the capillary, a thorough optimization of capillary electrophoresis (CE) parameters including preconditioning and in-between rinsing procedures was required to efficiently separate all the ApoC-III glycoforms. Permanent coatings did not contribute to high resolution separations. A fast and reliable method based on a bare-silica capillary combining the effect of urea and diamine additives allowed to separate up to six different ApoC-III forms. We demonstrated by a combination of MALDI-TOF mass spectrometry (MS) analyses and CE of intact and neuraminidase-treated samples that this method well resolved glycoforms differing not only by their sialylation degree but also by carbamylation state, an undesired chemical modification of primary amines. This method allowed to demonstrate the carbamylation of ApoC-III glycoforms for the first time. Our CZE method proved robust and accurate with excellent intermediate precision regarding migration times (RSDs < 0.7%) while RSDs for peak areas were less than 5%. Finally, the quality of three distinct batches of commercial ApoC-III obtained from different suppliers was assessed and compared. Quite similar but highly structurally heterogeneous ApoC-III profiles were observed for these samples. Copyright © 2017 Elsevier B.V. All rights reserved.

Generalized conjugate-gradient methods for the Navier-Stokes equations

NASA Technical Reports Server (NTRS)

Ajmani, Kumud; Ng, Wing-Fai; Liou, Meng-Sing

1991-01-01

A generalized conjugate-gradient method is used to solve the two-dimensional, compressible Navier-Stokes equations of fluid flow. The equations are discretized with an implicit, upwind finite-volume formulation. Preconditioning techniques are incorporated into the new solver to accelerate convergence of the overall iterative method. The superiority of the new solver is demonstrated by comparisons with a conventional line Gauss-Siedel Relaxation solver. Computational test results for transonic flow (trailing edge flow in a transonic turbine cascade) and hypersonic flow (M = 6.0 shock-on-shock phenoena on a cylindrical leading edge) are presented. When applied to the transonic cascade case, the new solver is 4.4 times faster in terms of number of iterations and 3.1 times faster in terms of CPU time than the Relaxation solver. For the hypersonic shock case, the new solver is 3.0 times faster in terms of number of iterations and 2.2 times faster in terms of CPU time than the Relaxation solver.

Iterative methods for elliptic finite element equations on general meshes

NASA Technical Reports Server (NTRS)

Nicolaides, R. A.; Choudhury, Shenaz

1986-01-01

Iterative methods for arbitrary mesh discretizations of elliptic partial differential equations are surveyed. The methods discussed are preconditioned conjugate gradients, algebraic multigrid, deflated conjugate gradients, an element-by-element techniques, and domain decomposition. Computational results are included.

Substitution of Hospital Care with Primary Care: Defining the Conditions of Primary Care Plus

PubMed Central

Kroese, Mariëlle Elisabeth Aafje Lydia; Spreeuwenberg, Marieke Dingena; Elissen, Arianne Mathilda Josephus; Meerlo, Ronald Johan; Hanraets, Monique Margaretha Henriëtte; Ruwaard, Dirk

2016-01-01

Objective: To analyse barriers and facilitators in substituting hospital care with primary care to define preconditions for successful implementation. Methods: A descriptive feasibility study was performed to collect information on the feasibility of substituting hospital care with primary care. General practitioners were able to refer patients, about whom they had doubts regarding diagnosis, treatment and/or the need to refer to hospital care, to medical specialists who performed low-complex consultations at general practitioner practices. Qualitative data were collected through interviews with general practitioners and medical specialists, focus groups and notes from meetings in the Netherlands between April 2013 and January 2014. Data were analysed using a conventional content analysis which resulted in categorised barriers, facilitators and policy adjustments, after which preconditions were formulated. Results: The most important preconditions were make arrangements on governmental level, arrange a collective integrated IT-system, determine the appropriate profile for medical specialists, design a referral protocol for eligible patients, arrange deliberation possibilities for general practitioners and medical specialists and formulate a diagnostic protocol. Conclusions: The barriers, facilitators and formulated preconditions provided relevant input to change the design of substituting hospital care with primary care. PMID:27616956

Hypoxic-Preconditioned Bone Marrow Stem Cell Medium Significantly Improves Outcome After Retinal Ischemia in Rats

PubMed Central

Roth, Steven; Dreixler, John C.; Mathew, Biji; Balyasnikova, Irina; Mann, Jacob R.; Boddapati, Venkat; Xue, Lai; Lesniak, Maciej S.

2016-01-01

Purpose We have previously demonstrated the protective effect of bone marrow stem cell (BMSC)-conditioned medium in retinal ischemic injury. We hypothesized here that hypoxic preconditioning of stem cells significantly enhances the neuroprotective effect of the conditioned medium and thereby augments the protective effect in ischemic retina. Methods Rats were subjected to retinal ischemia by increasing intraocular pressure to 130 to 135 mm Hg for 55 minutes. Hypoxic-preconditioned, hypoxic unconditioned, or normoxic medium was injected into the vitreous 24 hours after ischemia ended. Recovery was assessed 7 days after injections by comparing electroretinography measurements, histologic examination, and apoptosis (TUNEL, terminal deoxynucleotidyl transferase–mediated dUTP nick end labeling assay). To compare proteins secreted into the medium in the groups and the effect of hypoxic exposure, we used rat cytokine arrays. Results Eyes injected with hypoxic BMSC–conditioned medium 24 hours after ischemia demonstrated significantly enhanced return of retinal function, decreased retinal ganglion cell layer loss, and attenuated apoptosis compared to those administered normoxic or hypoxic unconditioned medium. Hypoxic-preconditioned medium had 21 significantly increased protein levels compared to normoxic medium. Conclusions The medium from hypoxic-preconditioned BMSCs robustly restored retinal function and prevented cell loss after ischemia when injected 24 hours after ischemia. The protective effect was even more pronounced than in our previous studies of normoxic conditioned medium. Prosurvival signals triggered by the secretome may play a role in this neuroprotective effect. PMID:27367588

Experiments with conjugate gradient algorithms for homotopy curve tracking

NASA Technical Reports Server (NTRS)

Irani, Kashmira M.; Ribbens, Calvin J.; Watson, Layne T.; Kamat, Manohar P.; Walker, Homer F.

1991-01-01

There are algorithms for finding zeros or fixed points of nonlinear systems of equations that are globally convergent for almost all starting points, i.e., with probability one. The essence of all such algorithms is the construction of an appropriate homotopy map and then tracking some smooth curve in the zero set of this homotopy map. HOMPACK is a mathematical software package implementing globally convergent homotopy algorithms with three different techniques for tracking a homotopy zero curve, and has separate routines for dense and sparse Jacobian matrices. The HOMPACK algorithms for sparse Jacobian matrices use a preconditioned conjugate gradient algorithm for the computation of the kernel of the homotopy Jacobian matrix, a required linear algebra step for homotopy curve tracking. Here, variants of the conjugate gradient algorithm are implemented in the context of homotopy curve tracking and compared with Craig's preconditioned conjugate gradient method used in HOMPACK. The test problems used include actual large scale, sparse structural mechanics problems.

Preconditioning for traumatic brain injury

PubMed Central

Yokobori, Shoji; Mazzeo, Anna T; Hosein, Khadil; Gajavelli, Shyam; Dietrich, W. Dalton; Bullock, M. Ross

2016-01-01

Traumatic brain injury (TBI) treatment is now focused on the prevention of primary injury and reduction of secondary injury. However, no single effective treatment is available as yet for the mitigation of traumatic brain damage in humans. Both chemical and environmental stresses applied before injury, have been shown to induce consequent protection against post-TBI neuronal death. This concept termed “preconditioning” is achieved by exposure to different pre-injury stressors, to achieve the induction of “tolerance” to the effect of the TBI. However, the precise mechanisms underlying this “tolerance” phenomenon are not fully understood in TBI, and therefore even less information is available about possible indications in clinical TBI patients. In this review we will summarize TBI pathophysiology, and discuss existing animal studies demonstrating the efficacy of preconditioning in diffuse and focal type of TBI. We will also review other non-TBI preconditionng studies, including ischemic, environmental, and chemical preconditioning, which maybe relevant to TBI. To date, no clinical studies exist in this field, and we speculate on possible futureclinical situation, in which pre-TBI preconditioning could be considered. PMID:24323189

Solving Graph Laplacian Systems Through Recursive Bisections and Two-Grid Preconditioning

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ponce, Colin; Vassilevski, Panayot S.

2016-02-18

We present a parallelizable direct method for computing the solution to graph Laplacian-based linear systems derived from graphs that can be hierarchically bipartitioned with small edge cuts. For a graph of size n with constant-size edge cuts, our method decomposes a graph Laplacian in time O(n log n), and then uses that decomposition to perform a linear solve in time O(n log n). We then use the developed technique to design a preconditioner for graph Laplacians that do not have this property. Finally, we augment this preconditioner with a two-grid method that accounts for much of the preconditioner's weaknesses. Wemore » present an analysis of this method, as well as a general theorem for the condition number of a general class of two-grid support graph-based preconditioners. Numerical experiments illustrate the performance of the studied methods.« less

Research on the Changes to the Lipid/Polymer Membrane Used in the Acidic Bitterness Sensor Caused by Preconditioning

PubMed Central

Harada, Yuhei; Noda, Junpei; Yatabe, Rui; Ikezaki, Hidekazu; Toko, Kiyoshi

2016-01-01

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. PMID:26891299

Fourier domain preconditioned conjugate gradient algorithm for atmospheric tomography.

PubMed

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.

A Three Year Comparison of Acute Respiratory Disease, Shrink and Weight Gain in Preconditioned and Non-preconditioned Illinois Beef Calves Sold at the Same Auction and Mixed in a Feedlot

PubMed Central

Woods, G. T.; Mansfield, M. E.; Webb, R. J.

1973-01-01

During 1969 to 1971, 78 preconditioned (PC) and 79 non-preconditioned (NPC) beef calves were purchased at the same auction and mixed in a feedlot. Preconditioned calves were weaned 30 days before the sale, used to drinking from a tank, and vaccinated against blackleg, malignant edema, infectious bovine rhinotracheitis (IBR), parainfluenza-3 (PI3) and bovine virus diarrhea (BVD) in 1970 and 1971, and Pasteurella hemolytica and multocida in 1971. All vaccinations were completed two to three weeks before the sale. PC calves were given thiabenzadole. PC calves had significantly less shrink after shipment and in 1971 significantly more rapid daily gain during the first weeks of the feeding period. In 1969 more PC calves were treated for acute respiratory disease than NPC calves during an outbreak of PI3 and BVD infection. In 1970 and 1971 fewer PC than NPC calves were treated for acute respiratory tract disease during outbreaks of PI3 infection. The differences in clinical respiratory disease were significant in 1971. Inclusion of two doses of P. hemolytica and P. multocida bacterin before the sale in 1971 and use of an intranasal PI3 vaccine was considered to improve the PC program. Fecal egg counts for gastrointestinal nematodes were much lower in PC calves treated with thiabenzadole than untreated NPC calves. PMID:4355470

Parallelization of the preconditioned IDR solver for modern multicore computer systems

NASA Astrophysics Data System (ADS)

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).

ILUBCG2-11: Solution of 11-banded nonsymmetric linear equation systems by a preconditioned biconjugate gradient routine

NASA Astrophysics Data System (ADS)

Chen, Y.-M.; Koniges, A. E.; Anderson, D. V.

1989-10-01

The biconjugate gradient method (BCG) provides an attractive alternative to the usual conjugate gradient algorithms for the solution of sparse systems of linear equations with nonsymmetric and indefinite matrix operators. A preconditioned algorithm is given, whose form resembles the incomplete L-U conjugate gradient scheme (ILUCG2) previously presented. Although the BCG scheme requires the storage of two additional vectors, it converges in a significantly lesser number of iterations (often half), while the number of calculations per iteration remains essentially the same.

Nonuniform update for sparse target recovery in fluorescence molecular tomography accelerated by ordered subsets.

PubMed

Zhu, Dianwen; Li, Changqing

2014-12-01

Fluorescence molecular tomography (FMT) is a promising imaging modality and has been actively studied in the past two decades since it can locate the specific tumor position three-dimensionally in small animals. However, it remains a challenging task to obtain fast, robust and accurate reconstruction of fluorescent probe distribution in small animals due to the large computational burden, the noisy measurement and the ill-posed nature of the inverse problem. In this paper we propose a nonuniform preconditioning method in combination with L (1) regularization and ordered subsets technique (NUMOS) to take care of the different updating needs at different pixels, to enhance sparsity and suppress noise, and to further boost convergence of approximate solutions for fluorescence molecular tomography. Using both simulated data and phantom experiment, we found that the proposed nonuniform updating method outperforms its popular uniform counterpart by obtaining a more localized, less noisy, more accurate image. The computational cost was greatly reduced as well. The ordered subset (OS) technique provided additional 5 times and 3 times speed enhancements for simulation and phantom experiments, respectively, without degrading image qualities. When compared with the popular L (1) algorithms such as iterative soft-thresholding algorithm (ISTA) and Fast iterative soft-thresholding algorithm (FISTA) algorithms, NUMOS also outperforms them by obtaining a better image in much shorter period of time.

Arctic atmospheric preconditioning: do not rule out shortwave radiation just yet

NASA Astrophysics Data System (ADS)

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.

The role of adenosine in preconditioning by brief pressure overload in rats.

PubMed

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 < 0.001). Pretreatment with 8-(p-sulfophenyl)-theophylline (SPT), an inhibitor of adenosine receptors, did not significantly limit the protection by pressure overload and ischemic preconditioning (18.3 ± 1.5% and 18.2 ± 2.0%, respectively, p < 0.001). SPT itself did not affect the extent of infarct (25.4 ± 2.0%). The hemodynamics, area at risk and mortality were not significantly different among all groups of animals. Brief pressure 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.

Use of upscaled elevation and surface roughness data in two-dimensional surface water models

USGS Publications Warehouse

Hughes, J.D.; Decker, J.D.; Langevin, C.D.

2011-01-01

In this paper, we present an approach that uses a combination of cell-block- and cell-face-averaging of high-resolution cell elevation and roughness data to upscale hydraulic parameters and accurately simulate surface water flow in relatively low-resolution numerical models. The method developed allows channelized features that preferentially connect large-scale grid cells at cell interfaces to be represented in models where these features are significantly smaller than the selected grid size. The developed upscaling approach has been implemented in a two-dimensional finite difference model that solves a diffusive wave approximation of the depth-integrated shallow surface water equations using preconditioned Newton–Krylov methods. Computational results are presented to show the effectiveness of the mixed cell-block and cell-face averaging upscaling approach in maintaining model accuracy, reducing model run-times, and how decreased grid resolution affects errors. Application examples demonstrate that sub-grid roughness coefficient variations have a larger effect on simulated error than sub-grid elevation variations.

Implicit solvers for unstructured meshes

NASA Technical Reports Server (NTRS)

Venkatakrishnan, V.; Mavriplis, Dimitri J.

1991-01-01

Implicit methods for unstructured mesh computations are developed and tested. The approximate system which arises from the Newton-linearization of the nonlinear evolution operator is solved by using the preconditioned generalized minimum residual technique. These different preconditioners are investigated: the incomplete LU factorization (ILU), block diagonal factorization, and the symmetric successive over-relaxation (SSOR). The preconditioners have been optimized to have good vectorization properties. The various methods are compared over a wide range of problems. Ordering of the unknowns, which affects the convergence of these sparse matrix iterative methods, is also investigated. Results are presented for inviscid and turbulent viscous calculations on single and multielement airfoil configurations using globally and adaptively generated meshes.

Acoustic 3D modeling by the method of integral equations

NASA Astrophysics Data System (ADS)

Malovichko, M.; Khokhlov, N.; Yavich, N.; Zhdanov, M.

2018-02-01

This paper presents a parallel algorithm for frequency-domain acoustic modeling by the method of integral equations (IE). The algorithm is applied to seismic simulation. The IE method reduces the size of the problem but leads to a dense system matrix. A tolerable memory consumption and numerical complexity were achieved by applying an iterative solver, accompanied by an effective matrix-vector multiplication operation, based on the fast Fourier transform (FFT). We demonstrate that, the IE system matrix is better conditioned than that of the finite-difference (FD) method, and discuss its relation to a specially preconditioned FD matrix. We considered several methods of matrix-vector multiplication for the free-space and layered host models. The developed algorithm and computer code were benchmarked against the FD time-domain solution. It was demonstrated that, the method could accurately calculate the seismic field for the models with sharp material boundaries and a point source and receiver located close to the free surface. We used OpenMP to speed up the matrix-vector multiplication, while MPI was used to speed up the solution of the system equations, and also for parallelizing across multiple sources. The practical examples and efficiency tests are presented as well.

An overview of NSPCG: A nonsymmetric preconditioned conjugate gradient package

NASA Astrophysics Data System (ADS)

Oppe, Thomas C.; Joubert, Wayne D.; Kincaid, David R.

1989-05-01

The most recent research-oriented software package developed as part of the ITPACK Project is called "NSPCG" since it contains many nonsymmetric preconditioned conjugate gradient procedures. It is designed to solve large sparse systems of linear algebraic equations by a variety of different iterative methods. One of the main purposes for the development of the package is to provide a common modular structure for research on iterative methods for nonsymmetric matrices. Another purpose for the development of the package is to investigate the suitability of several iterative methods for vector computers. Since the vectorizability of an iterative method depends greatly on the matrix structure, NSPCG allows great flexibility in the operator representation. The coefficient matrix can be passed in one of several different matrix data storage schemes. These sparse data formats allow matrices with a wide range of structures from highly structured ones such as those with all nonzeros along a relatively small number of diagonals to completely unstructured sparse matrices. Alternatively, the package allows the user to call the accelerators directly with user-supplied routines for performing certain matrix operations. In this case, one can use the data format from an application program and not be required to copy the matrix into one of the package formats. This is particularly advantageous when memory space is limited. Some of the basic preconditioners that are available are point methods such as Jacobi, Incomplete LU Decomposition and Symmetric Successive Overrelaxation as well as block and multicolor preconditioners. The user can select from a large collection of accelerators such as Conjugate Gradient (CG), Chebyshev (SI, for semi-iterative), Generalized Minimal Residual (GMRES), Biconjugate Gradient Squared (BCGS) and many others. The package is modular so that almost any accelerator can be used with almost any preconditioner.

Roles of thioredoxin in nitric oxide-dependent preconditioning-induced tolerance against MPTP neurotoxin

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chiueh, C.C.; Andoh, Tsugunobu; Chock, P. Boon

2005-09-01

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 {center_dot}NO-cGMP-PKG (protein kinase G) may mediate preconditioning phenomenon. We developed a human SH-SY5Y cell model for investigating {sup {center_dot}}NO-mediated signaling pathway, gene regulation, and protein expression following a sublethal preconditioning stress caused by a brief 2-h serum deprivation.more » 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{sup +}). Both sublethal and lethal oxidative stress caused by serum withdrawal increased neuronal nitric oxide synthase (nNOS/NOS1) expression and {sup {center_dot}}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{sup +}, which was blocked by Trx mRNA antisense oligonucleotide and Trx reductase inhibitor. It is concluded that Trx plays a pivotal role in {sup {center_dot}}NO-dependent preconditioning hormesis against MPTP/MPP{sup +}.« less

Preconditioning mesenchymal stem cells with the mood stabilizers lithium and valproic acid enhances therapeutic efficacy in a mouse model of Huntington's disease.

PubMed

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. Our results suggest that preconditioning stem cells with the mood stabilizers lithium and VPA before transplantation may serve as an effective strategy for enhancing the therapeutic efficacy of stem cell-based therapies. Copyright © 2016. Published by Elsevier Inc.

Remote Ischemic Preconditioning Enhances the Expression of Genes Encoding Antioxidant Enzymes and Endoplasmic Reticulum Stress-Related Proteins in Rat Skeletal Muscle.

PubMed

Park, Ui Jun; Kim, Hyoung Tae; Cho, Won Hyun; Park, Jae Hyoung; Jung, Hye Ra; Kim, Min Young

2016-12-01

Ischemic preconditioning (IPC), including remote IPC (rIPC) and direct IPC (dIPC), is a promising method to decrease ischemia-reperfusion (IR) injury. This study tested the effect of both rIPC and dIPC on the genes for antioxidant enzymes and endoplasmic reticulum (ER) stress-related proteins. Twenty rats were randomly divided into the control and study groups. In the control group (n=10), the right hind limb was sham-operated. The left hind limb (IscR) of the control group underwent IR injury without IPC. In the study group (n=10), the right hind limb received IR injury after 3 cycles of rIPC. The IscR received IR injury after 3 cycles of dIPC. Gene expression was analyzed by Quantitative real-time polymerase chain reaction from the anterior tibialis muscle. The expression of the antioxidant enzyme genes including glutathione peroxidase (GPx), superoxide dismutase (SOD) 1 and catalase (CAT) were significantly reduced in IscR compared with sham treatment. In comparison with IscR, rIPC enhanced the expression of GPx, SOD2, and CAT genes. dIPC enhanced the expression of SOD2 and CAT genes. The expression of SOD2 genes was consistently higher in rIPC than in dIPC, but the difference was only significant for SOD2. The expression of genes for ER stress-related proteins tended to be reduced in IscR in comparison with sham treatment. However, the difference was only significant for C/EBP homologous protein (CHOP). In comparison with IscR, rIPC significantly up-regulated activating transcription factor 4 and CHOP, whereas dIPC up-regulated CHOP. Both rIPC and dIPC enhanced expression of genes for antioxidant enzymes and ER stress-related proteins.

A Weakest Precondition Approach to Robustness

NASA Astrophysics Data System (ADS)

Balliu, Musard; Mastroeni, Isabella

With the increasing complexity of information management computer systems, security becomes a real concern. E-government, web-based financial transactions or military and health care information systems are only a few examples where large amount of information can reside on different hosts distributed worldwide. It is clear that any disclosure or corruption of confidential information in these contexts can result fatal. Information flow controls constitute an appealing and promising technology to protect both data confidentiality and data integrity. The certification of the security degree of a program that runs in untrusted environments still remains an open problem in the area of language-based security. Robustness asserts that an active attacker, who can modify program code in some fixed points (holes), is unable to disclose more private information than a passive attacker, who merely observes unclassified data. In this paper, we extend a method recently proposed for checking declassified non-interference in presence of passive attackers only, in order to check robustness by means of weakest precondition semantics. In particular, this semantics simulates the kind of analysis that can be performed by an attacker, i.e., from public output towards private input. The choice of semantics allows us to distinguish between different attacks models and to characterize the security of applications in different scenarios.

Implementation of density-based solver for all speeds in the framework of OpenFOAM

NASA Astrophysics Data System (ADS)

Shen, Chun; Sun, Fengxian; Xia, Xinlin

2014-10-01

In the framework of open source CFD code OpenFOAM, a density-based solver for all speeds flow field is developed. In this solver the preconditioned all speeds AUSM+(P) scheme is adopted and the dual time scheme is implemented to complete the unsteady process. Parallel computation could be implemented to accelerate the solving process. Different interface reconstruction algorithms are implemented, and their accuracy with respect to convection is compared. Three benchmark tests of lid-driven cavity flow, flow crossing over a bump, and flow over a forward-facing step are presented to show the accuracy of the AUSM+(P) solver for low-speed incompressible flow, transonic flow, and supersonic/hypersonic flow. Firstly, for the lid driven cavity flow, the computational results obtained by different interface reconstruction algorithms are compared. It is indicated that the one dimensional reconstruction scheme adopted in this solver possesses high accuracy and the solver developed in this paper can effectively catch the features of low incompressible flow. Then via the test cases regarding the flow crossing over bump and over forward step, the ability to capture characteristics of the transonic and supersonic/hypersonic flows are confirmed. The forward-facing step proves to be the most challenging for the preconditioned solvers with and without the dual time scheme. Nonetheless, the solvers described in this paper reproduce the main features of this flow, including the evolution of the initial transient.

Minimally invasive hip arthroplasty: what role does patient preconditioning play?

PubMed

Pour, Aidin Eslam; Parvizi, Javad; Sharkey, Peter F; Hozack, William J; Rothman, Richard H

2007-09-01

The benefits of minimally invasive total hip arthroplasty continue to be debated. The objective of this study was to investigate the role of patient education, accelerated rehabilitation, and improved pain control on the outcome of total hip arthroplasty performed through a small incision. One hundred patients undergoing total hip arthroplasty at our institution were randomized into one of four groups on the basis of the size of the incision, preoperative counseling, the type of preoperative and postoperative rehabilitation, and the analgesia protocol. The operative parameters, complications, time to discharge to home, functional improvement, and patient satisfaction were assessed. The demographic distribution among the four groups was similar. The extent of functional improvement at the time of discharge to home, patient satisfaction, and walking ability at the time of discharge were better in patients who had received an accelerated preoperative and postoperative rehabilitation regimen regardless of the size of the incision. There was no difference in estimated blood loss, mean operative time, transfusion needs, or complications among the groups. This study highlights the importance of factors such as family education, patient preconditioning, preemptive analgesia, and accelerated preoperative and postoperative rehabilitation in influencing the outcome of total hip arthroplasty. The aforementioned factors, and not the surgical technique per se, may play a major role in imparting the better outcome after minimally invasive total hip arthroplasty that has been reported by various investigators.

Efficient block preconditioned eigensolvers for linear response time-dependent density functional theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vecharynski, Eugene; Brabec, Jiri; Shao, Meiyue

Within this paper, we present two efficient iterative algorithms for solving the linear response eigenvalue problem arising from the time dependent density functional theory. Although the matrix to be diagonalized is nonsymmetric, it has a special structure that can be exploited to save both memory and floating point operations. In particular, the nonsymmetric eigenvalue problem can be transformed into an eigenvalue problem that involves the product of two matrices M and K. We show that, because MK is self-adjoint with respect to the inner product induced by the matrix K, this product eigenvalue problem can be solved efficiently by amore » modified Davidson algorithm and a modified locally optimal block preconditioned conjugate gradient (LOBPCG) algorithm that make use of the K-inner product. Additionally, the solution of the product eigenvalue problem yields one component of the eigenvector associated with the original eigenvalue problem. We show that the other component of the eigenvector can be easily recovered in an inexpensive postprocessing procedure. As a result, the algorithms we present here become more efficient than existing methods that try to approximate both components of the eigenvectors simultaneously. In particular, our numerical experiments demonstrate that the new algorithms presented here consistently outperform the existing state-of-the-art Davidson type solvers by a factor of two in both solution time and storage.« less

Efficient block preconditioned eigensolvers for linear response time-dependent density functional theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vecharynski, Eugene; Brabec, Jiri; Shao, Meiyue

In this article, we present two efficient iterative algorithms for solving the linear response eigenvalue problem arising from the time dependent density functional theory. Although the matrix to be diagonalized is nonsymmetric, it has a special structure that can be exploited to save both memory and floating point operations. In particular, the nonsymmetric eigenvalue problem can be transformed into an eigenvalue problem that involves the product of two matrices M and K. We show that, because MK is self-adjoint with respect to the inner product induced by the matrix K, this product eigenvalue problem can be solved efficiently by amore » modified Davidson algorithm and a modified locally optimal block preconditioned conjugate gradient (LOBPCG) algorithm that make use of the K-inner product. The solution of the product eigenvalue problem yields one component of the eigenvector associated with the original eigenvalue problem. We show that the other component of the eigenvector can be easily recovered in an inexpensive postprocessing procedure. As a result, the algorithms we present here become more efficient than existing methods that try to approximate both components of the eigenvectors simultaneously. In particular, our numerical experiments demonstrate that the new algorithms presented here consistently outperform the existing state-of-the-art Davidson type solvers by a factor of two in both solution time and storage.« less

Efficient block preconditioned eigensolvers for linear response time-dependent density functional theory

DOE PAGES

Vecharynski, Eugene; Brabec, Jiri; Shao, Meiyue; ...

2017-12-01

In this article, we present two efficient iterative algorithms for solving the linear response eigenvalue problem arising from the time dependent density functional theory. Although the matrix to be diagonalized is nonsymmetric, it has a special structure that can be exploited to save both memory and floating point operations. In particular, the nonsymmetric eigenvalue problem can be transformed into an eigenvalue problem that involves the product of two matrices M and K. We show that, because MK is self-adjoint with respect to the inner product induced by the matrix K, this product eigenvalue problem can be solved efficiently by amore » modified Davidson algorithm and a modified locally optimal block preconditioned conjugate gradient (LOBPCG) algorithm that make use of the K-inner product. The solution of the product eigenvalue problem yields one component of the eigenvector associated with the original eigenvalue problem. We show that the other component of the eigenvector can be easily recovered in an inexpensive postprocessing procedure. As a result, the algorithms we present here become more efficient than existing methods that try to approximate both components of the eigenvectors simultaneously. In particular, our numerical experiments demonstrate that the new algorithms presented here consistently outperform the existing state-of-the-art Davidson type solvers by a factor of two in both solution time and storage.« less

Efficient block preconditioned eigensolvers for linear response time-dependent density functional theory

DOE PAGES

Vecharynski, Eugene; Brabec, Jiri; Shao, Meiyue; ...

2017-08-24

Within this paper, we present two efficient iterative algorithms for solving the linear response eigenvalue problem arising from the time dependent density functional theory. Although the matrix to be diagonalized is nonsymmetric, it has a special structure that can be exploited to save both memory and floating point operations. In particular, the nonsymmetric eigenvalue problem can be transformed into an eigenvalue problem that involves the product of two matrices M and K. We show that, because MK is self-adjoint with respect to the inner product induced by the matrix K, this product eigenvalue problem can be solved efficiently by amore » modified Davidson algorithm and a modified locally optimal block preconditioned conjugate gradient (LOBPCG) algorithm that make use of the K-inner product. Additionally, the solution of the product eigenvalue problem yields one component of the eigenvector associated with the original eigenvalue problem. We show that the other component of the eigenvector can be easily recovered in an inexpensive postprocessing procedure. As a result, the algorithms we present here become more efficient than existing methods that try to approximate both components of the eigenvectors simultaneously. In particular, our numerical experiments demonstrate that the new algorithms presented here consistently outperform the existing state-of-the-art Davidson type solvers by a factor of two in both solution time and storage.« less

A nonrecursive 'Order N' preconditioned conjugate gradient/range space formulation of MDOF dynamics

NASA Technical Reports Server (NTRS)

Kurdila, A. J.; Menon, R.; Sunkel, John

1991-01-01

This paper addresses the requirements of present-day mechanical system simulations of algorithms that induce parallelism on a fine scale and of transient simulation methods which must be automatically load balancing for a wide collection of system topologies and hardware configurations. To this end, a combination range space/preconditioned conjugage gradient formulation of multidegree-of-freedon dynamics is developed, which, by employing regular ordering of the system connectivity graph, makes it possible to derive an extremely efficient preconditioner from the range space metric (as opposed to the system coefficient matrix). Because of the effectiveness of the preconditioner, the method can achieve performance rates that depend linearly on the number of substructures. The method, termed 'Order N' does not require the assembly of system mass or stiffness matrices, and is therefore amenable to implementation on work stations. Using this method, a 13-substructure model of the Space Station was constructed.

Efficient Power Network Analysis with Modeling of Inductive Effects

NASA Astrophysics Data System (ADS)

Zeng, Shan; Yu, Wenjian; Hong, Xianlong; Cheng, Chung-Kuan

In this paper, an efficient method is proposed to accurately analyze large-scale power/ground (P/G) networks, where inductive parasitics are modeled with the partial reluctance. The method is based on frequency-domain circuit analysis and the technique of vector fitting [14], and obtains the time-domain voltage response at given P/G nodes. The frequency-domain circuit equation including partial reluctances is derived, and then solved with the GMRES algorithm with rescaling, preconditioning and recycling techniques. With the merit of sparsified reluctance matrix and iterative solving techniques for the frequency-domain circuit equations, the proposed method is able to handle large-scale P/G networks with complete inductive modeling. Numerical results show that the proposed method is orders of magnitude faster than HSPICE, several times faster than INDUCTWISE [4], and capable of handling the inductive P/G structures with more than 100, 000 wire segments.

A conjugate gradient method for solving the non-LTE line radiation transfer problem

NASA Astrophysics Data System (ADS)

Paletou, F.; Anterrieu, E.

2009-12-01

This study concerns the fast and accurate solution of the line radiation transfer problem, under non-LTE conditions. We propose and evaluate an alternative iterative scheme to the classical ALI-Jacobi method, and to the more recently proposed Gauss-Seidel and successive over-relaxation (GS/SOR) schemes. Our study is indeed based on applying a preconditioned bi-conjugate gradient method (BiCG-P). Standard tests, in 1D plane parallel geometry and in the frame of the two-level atom model with monochromatic scattering are discussed. Rates of convergence between the previously mentioned iterative schemes are compared, as are their respective timing properties. The smoothing capability of the BiCG-P method is also demonstrated.

Fast optimal wavefront reconstruction for multi-conjugate adaptive optics using the Fourier domain preconditioned conjugate gradient algorithm.

PubMed

Vogel, Curtis R; Yang, Qiang

2006-08-21

We present two different implementations of the Fourier domain preconditioned conjugate gradient algorithm (FD-PCG) to efficiently solve the large structured linear systems that arise in optimal volume turbulence estimation, or tomography, for multi-conjugate adaptive optics (MCAO). We describe how to deal with several critical technical issues, including the cone coordinate transformation problem and sensor subaperture grid spacing. We also extend the FD-PCG approach to handle the deformable mirror fitting problem for MCAO.

One- and three-time mild hypobaric hypoxia modifies expression of mitochondrial thioredoxin-2 in hippocampus of rat.

PubMed

Stroev, Sergey Alexandrovich; Tjulkova, Ekaterina Iosifovna; Samoilov, Michail Olegovich; Pelto-Huikko, Markku Tapio

2011-01-01

Our previous study demonstrated that preconditioning by 3-times repetitive mild hypoxia significantly augmented expression of mitochondrial thioredoxin-2 (Trx-2) at 3 h after subsequent acute severe hypoxia in rat hippocampus. However, it was unclear whether this augmentation was due to build up of Trx-2 by mild hypoxia before severe hypoxia or by modification of reaction to severe hypoxia itself. To answer on this question we study the expression level during and after preconditioning without subsequent severe hypoxia. Trx-2 expression was studied by immunocytochemistry 3 h and 24 h after first session and 3 h and 24 h after last session of 3-times (spaced at 24 h) mild hypobaric hypoxia (360 Torr, 2h). At 3 h after 1-time hypoxia (first session of 3-time hypoxia) the total number of Trx-2-immunoreactive cells (Nt) was significantly decreased in contrast with control in CA2, CA3 and DG. The number of cells with intensive expression of Trx-2 (Ni) was reduced in CA1 and CA3. At 24 h after the same 1-time hypoxia Nt was lower than in control and at 3 h time-point in all hippocampal areas studied (CA1, CA2, CA3 and DG); Ni was decreased only compared to control in CA1 and CA3. At 3 h after last session of 3-times hypoxia Nt and Ni were significantly down regulated in comparison with control only in CA1. At 24 h after it Nt was significantly decreased compared to control in CA1, CA2 and CA3 (in DG the decrease was not statistically significant) but in all areas was higher than at 24 h after 1-time hypoxia. Dynamics of Nt changes from 3-hours after single to 24-hours after triple moderate hypoxia had the wave phase character. These findings indicate that Trx-2 expression in most areas of hippocampus was decreased to 24 h after 3-time mild hypoxia. Thus the augmentation of Trx-2 expression in hippocampal neurons of preconditioned animals in response to subsequent severe hypoxia is caused obviously not by Trx-2 accumulation during preconditioning sessions but by modification of reaction to severe impact.

Sirtinol abrogates late phase of cardiac ischemia preconditioning in rats.

PubMed

Safari, Fereshteh; Shekarforoosh, Shahnaz; Hashemi, Tahmineh; Namvar Aghdash, Simin; Fekri, Asefeh; Safari, Fatemeh

2017-07-01

The aim of this study was to investigate the effect of sirtinol, as an inhibitor of sirtuin NAD-dependent histone deacetylases, on myocardial ischemia reperfusion injury following early and late ischemia preconditioning (IPC). Rats underwent sustained ischemia and reperfusion (IR) alone or proceeded by early or late IPC. Sirtinol (S) was administered before IPC. Arrhythmias were evaluated based on the Lambeth model. Infarct size (IS) was measured using triphenyltetrazolium chloride staining. The transcription level of antioxidant-coding genes was assessed by real-time PCR. In early and late IPC groups, IS and the number of arrhythmia were significantly decreased (P < 0.05 and P < 0.01 vs IR, respectively). In S + early IPC, incidences of arrhythmia and IS were not different compared with the early IPC group. However, in S + late IPC the IS was different from the late IPC group (P < 0.05). In late IPC but not early IPC, transcription levels of catalase (P < 0.01) and Mn-SOD (P < 0.05) increased, although this upregulation was not significant in the S + late IPC group. Our results are consistent with the notion that different mechanisms are responsible for early and late IPC. In addition, sirtuin NAD-dependent histone deacetylases may be implicated in late IPC-induced cardioprotection.

Fast Multilevel Solvers for a Class of Discrete Fourth Order Parabolic Problems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zheng, Bin; Chen, Luoping; Hu, Xiaozhe

2016-03-05

In this paper, we study fast iterative solvers for the solution of fourth order parabolic equations discretized by mixed finite element methods. We propose to use consistent mass matrix in the discretization and use lumped mass matrix to construct efficient preconditioners. We provide eigenvalue analysis for the preconditioned system and estimate the convergence rate of the preconditioned GMRes method. Furthermore, we show that these preconditioners only need to be solved inexactly by optimal multigrid algorithms. Our numerical examples indicate that the proposed preconditioners are very efficient and robust with respect to both discretization parameters and diffusion coefficients. We also investigatemore » the performance of multigrid algorithms with either collective smoothers or distributive smoothers when solving the preconditioner systems.« less

True logarithmic amplification of frequency clock in SS-OCT for calibration

PubMed Central

Liu, Bin; Azimi, Ehsan; Brezinski, Mark E.

2011-01-01

With swept source optical coherence tomography (SS-OCT), imprecise signal calibration prevents optimal imaging of biological tissues such as coronary artery. This work demonstrates an approach using a true logarithmic amplifier to precondition the clock signal, with the effort to minimize the noises and phase errors for optimal calibration. This method was validated and tested with a high-speed SS-OCT. The experimental results manifest its superior ability on optimization of the calibration and improvement of the imaging performance. Particularly, this hardware-based approach is suitable for real-time calibration in a high-speed system where computation time is constrained. PMID:21698036

The in vitro preconditioning of myoblasts to enhance subsequent survival in an in vivo tissue engineering chamber model.

PubMed

Tilkorn, Daniel J; Davies, E Michele; Keramidaris, Effie; Dingle, Aaron M; Gerrand, Yi-Wen; Taylor, Caroline J; Han, Xiao Lian; Palmer, Jason A; Penington, Anthony J; Mitchell, Christina A; Morrison, Wayne A; Dusting, Gregory J; Mitchell, Geraldine M

2012-05-01

The effects of in vitro preconditioning protocols on the ultimate survival of myoblasts implanted in an in vivo tissue engineering chamber were examined. In vitro testing: L6 myoblasts were preconditioned by heat (42 °C; 1.5 h); hypoxia (<8% O(2); 1.5 h); or nitric oxide donors: S-nitroso-N-acetylpenicillamine (SNAP, 200 μM, 1.5 h) or 1-[N-(2-aminoethyl)-N-(2-aminoethyl)amino]-diazen-1-ium-1,2-diolate (DETA-NONOate, 500 μM, 7 h). Following a rest phase preconditioned cells were exposed to 24 h hypoxia, and demonstrated minimal overall cell loss, whilst controls (not preconditioned, but exposed to 24 h hypoxia) demonstrated a 44% cell loss. Phosphoimmunoblot analysis of pro-survival signaling pathways revealed significant activation of serine threonine kinase Akt with DETA-NONOate (p < 0.01) and heat preconditioning (p < 0.05). DETA-NONOate also activated ERK 1/2 signaling (p < 0.05). In vivo implantation: 100,000 preconditioned (heat, hypoxia, or DETA-NONOate) myoblasts were implanted in SCID mouse tissue engineering chambers. 100,000 (not preconditioned) myoblasts were implanted in control chambers. At 3 weeks, morphometric assessment of surviving myoblasts indicated myoblast percent volume (p = 0.012) and myoblasts/mm(2) (p = 0.0005) overall significantly increased in preconditioned myoblast chambers compared to control, with DETA-NONOate-preconditioned myoblasts demonstrating the greatest increase in survival (p = 0.007 and p = 0.001 respectively). DETA-NONOate therefore has potential therapeutic benefits to significantly improve survival of transplanted cells. Copyright © 2012 Elsevier Ltd. All rights reserved.

Exploring the Role of TRPV and CGRP in Adenosine Preconditioning and Remote Hind Limb Preconditioning-Induced Cardioprotection in Rats.

PubMed

Singh, Amritpal; Randhawa, Puneet Kaur; Bali, Anjana; Singh, Nirmal; Jaggi, Amteshwar Singh

2017-04-01

The cardioprotective effects of remote hind limb preconditioning (RIPC) are well known, but mechanisms by which protection occurs still remain to be explored. Therefore, the present study was designed to investigate the role of TRPV and CGRP in adenosine and remote preconditioning-induced cardioprotection, using sumatriptan, a CGRP release inhibitor and ruthenium red, a TRPV inhibitor, in rats. For remote preconditioning, a pressure cuff was tied around the hind limb of the rat and was inflated with air up to 150 mmHg to produce ischemia in the hind limb and during reperfusion pressure was released. Four cycles of ischemia and reperfusion, each consisting of 5 min of inflation and 5 min of deflation of pressure cuff were used to produce remote limb preconditioning. An ex vivo Langendorff's isolated rat heart model was used to induce ischemia reperfusion injury by 30 min of global ischemia followed by 120 min of reperfusion. RIPC demonstrated a significant decrease in ischemia reperfusion-induced significant myocardial injury in terms of increase in LDH, CK, infarct size and decrease in LVDP, +dp/dt max and -dp/dt min . Moreover, pharmacological preconditioning with adenosine produced cardioprotective effects in a similar manner to RIPC. Pretreatment with sumatriptan, a CGRP release blocker, abolished RIPC and adenosine preconditioning-induced cardioprotective effects. Administration of ruthenium red, a TRPV inhibitor, also abolished adenosine preconditioning-induced cardioprotection. It may be proposed that the cardioprotective effects of adenosine and remote preconditioning are possibly mediated through activation of a TRPV channels and consequent, release of CGRP.

Three-dimensional wideband electromagnetic modeling on massively parallel computers

NASA Astrophysics Data System (ADS)

Alumbaugh, David L.; Newman, Gregory A.; Prevost, Lydie; Shadid, John N.

1996-01-01

A method is presented for modeling the wideband, frequency domain electromagnetic (EM) response of a three-dimensional (3-D) earth to dipole sources operating at frequencies where EM diffusion dominates the response (less than 100 kHz) up into the range where propagation dominates (greater than 10 MHz). The scheme employs the modified form of the vector Helmholtz equation for the scattered electric fields to model variations in electrical conductivity, dielectric permitivity and magnetic permeability. The use of the modified form of the Helmholtz equation allows for perfectly matched layer ( PML) absorbing boundary conditions to be employed through the use of complex grid stretching. Applying the finite difference operator to the modified Helmholtz equation produces a linear system of equations for which the matrix is sparse and complex symmetrical. The solution is obtained using either the biconjugate gradient (BICG) or quasi-minimum residual (QMR) methods with preconditioning; in general we employ the QMR method with Jacobi scaling preconditioning due to stability. In order to simulate larger, more realistic models than has been previously possible, the scheme has been modified to run on massively parallel (MP) computer architectures. Execution on the 1840-processor Intel Paragon has indicated a maximum model size of 280 × 260 × 200 cells with a maximum flop rate of 14.7 Gflops. Three different geologic models are simulated to demonstrate the use of the code for frequencies ranging from 100 Hz to 30 MHz and for different source types and polarizations. The simulations show that the scheme is correctly able to model the air-earth interface and the jump in the electric and magnetic fields normal to discontinuities. For frequencies greater than 10 MHz, complex grid stretching must be employed to incorporate absorbing boundaries while below this normal (real) grid stretching can be employed.

Effect of preconditioning on silver leaching and bromide removal properties of silver-impregnated activated carbon (SIAC).

PubMed

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.

Possible role of thromboxane A2 in remote hind limb preconditioning-induced cardioprotection.

PubMed

Sharma, Roohani; Randhawa, Puneet Kaur; Singh, Nirmal; Jaggi, Amteshwar Singh

2016-01-01

Remote hind limb preconditioning (RIPC) is a protective strategy in which short episodes of ischemia and reperfusion in a remote organ (hind limb) protects the target organ (heart) against sustained ischemic reperfusion injury. The present study was designed to investigate the possible role of thromboxane A2 in RIPC-induced cardioprotection in rats. Remote hind limb preconditioning was performed by four episodes of 5 min of inflation and 5 min of deflation of pressure cuff. Occlusion of the hind limb with blood pressure cuff is most feasible, non-invasive, clinically relevant, and safe method for inducing RIPC. Isolated rat hearts were perfused on Langendorff apparatus and were subjected to global ischemia for 30 min followed by 120-min reperfusion. The levels of lactate dehydrogenase (LDH) and creatine kinase (CK) were measured in coronary effluent to assess the degree of myocardial injury. The extent of myocardial infarct size along with the functional parameters including left ventricular developed pressure (LVDP), dp/dtmax, and dp/dtmin were also measured. Ozagrel (thromboxane synthase inhibitor) and seratrodast (thromboxane A2 receptor antagonist) were employed as pharmacological modulators of thromboxane A2. Remote hind limb preconditioning significantly attenuated ischemia/reperfusion-induced myocardial injury and produced cardioprotective effects. However, administration of ozagrel and seratrodast completely abolished the cardioprotective effects of RIPC suggesting the key role of thromboxane A2 in RIPC-induced cardioprotection. It may be concluded that brief episodes of preconditioning ischemia and reperfusion activates the thromboxane synthase enzyme that produces thromboxane A2, which may elicit cardioprotection either involving humoral or neurogenic pathway.

Enhanced shock wave generation via pre-breakdown acceleration using water electrolysis in negative streamer pulsed spark discharges

NASA Astrophysics Data System (ADS)

Lee, Kern; Chung, Kyoung-Jae; Hwang, Y. S.

2018-03-01

This paper presents a method for enhancement of shock waves generated from underwater pulsed spark discharges with negative (anode-directed) subsonic streamers, for which the pre-breakdown process is accelerated by preconditioning a gap with water electrolysis. Hydrogen microbubbles are produced at the cathode by the electrolysis and move towards the anode during the preconditioning phase. The numbers and spatial distributions of the microbubbles vary with the amplitude and duration of each preconditioning pulse. Under our experimental conditions, the optimum pulse duration is determined to be ˜250 ms at a pulse voltage of 400 V, where the buoyancy force overwhelms the electric force and causes the microbubbles to be swept out from the water gap. When a high-voltage pulse is applied to the gap just after the preconditioning pulse, the pre-breakdown process is significantly accelerated in the presence of the microbubbles. At the optimum preconditioning pulse duration, the average breakdown delay is reduced by 87% and, more importantly, the energy consumed during the pre-breakdown period decreases by 83%. This reduced energy consumption during the pre-breakdown period, when combined with the morphological advantages of negative streamers, such as thicker and longer stalks, leads to a significant improvement in the measured peak pressure (˜40%) generated by the underwater pulsed spark discharge. This acceleration of pre-breakdown using electrolysis overcomes the biggest drawback of negative subsonic discharges, which is slow vapor bubble formation due to screening effects, and thus enhances the efficiency of the shock wave generation process using pulsed spark discharges in water.

Nonlinearly preconditioned semismooth Newton methods for variational inequality solution of two-phase flow in porous media

NASA Astrophysics Data System (ADS)

Yang, Haijian; Sun, Shuyu; Yang, Chao

2017-03-01

Most existing methods for solving two-phase flow problems in porous media do not take the physically feasible saturation fractions between 0 and 1 into account, which often destroys the numerical accuracy and physical interpretability of the simulation. To calculate the solution without the loss of this basic requirement, we introduce a variational inequality formulation of the saturation equilibrium with a box inequality constraint, and use a conservative finite element method for the spatial discretization and a backward differentiation formula with adaptive time stepping for the temporal integration. The resulting variational inequality system at each time step is solved by using a semismooth Newton algorithm. To accelerate the Newton convergence and improve the robustness, we employ a family of adaptive nonlinear elimination methods as a nonlinear preconditioner. Some numerical results are presented to demonstrate the robustness and efficiency of the proposed algorithm. A comparison is also included to show the superiority of the proposed fully implicit approach over the classical IMplicit Pressure-Explicit Saturation (IMPES) method in terms of the time step size and the total execution time measured on a parallel computer.

Too Good to be True? Ideomotor Theory from a Computational Perspective

PubMed Central

Herbort, Oliver; Butz, Martin V.

2012-01-01

In recent years, Ideomotor Theory has regained widespread attention and sparked the development of a number of theories on goal-directed behavior and learning. However, there are two issues with previous studies’ use of Ideomotor Theory. Although Ideomotor Theory is seen as very general, it is often studied in settings that are considerably more simplistic than most natural situations. Moreover, Ideomotor Theory’s claim that effect anticipations directly trigger actions and that action-effect learning is based on the formation of direct action-effect associations is hard to address empirically. We address these points from a computational perspective. A simple computational model of Ideomotor Theory was tested in tasks with different degrees of complexity. The model evaluation showed that Ideomotor Theory is a computationally feasible approach for understanding efficient action-effect learning for goal-directed behavior if the following preconditions are met: (1) The range of potential actions and effects has to be restricted. (2) Effects have to follow actions within a short time window. (3) Actions have to be simple and may not require sequencing. The first two preconditions also limit human performance and thus support Ideomotor Theory. The last precondition can be circumvented by extending the model with more complex, indirect action generation processes. In conclusion, we suggest that Ideomotor Theory offers a comprehensive framework to understand action-effect learning. However, we also suggest that additional processes may mediate the conversion of effect anticipations into actions in many situations. PMID:23162524

Effects of Whey Protein Supplementation Associated With Resistance Training on Muscular Strength, Hypertrophy, and Muscle Quality in Preconditioned Older Women.

PubMed

Sugihara Junior, Paulo; Ribeiro, Alex S; Nabuco, Hellen C G; Fernandes, Rodrigo R; Tomeleri, Crisieli M; Cunha, Paolo M; Venturini, Danielle; Barbosa, Décio S; Schoenfeld, Brad J; Cyrino, Edilson S

2018-06-22

The purpose of this study was to investigate the effect of whey protein (WP) supplementation on muscular strength, hypertrophy, and muscular quality in older women preconditioned to resistance training (RT). In a randomized, double-blind, and placebo (PLA)-controlled design, 31 older women (67.4 ± 4.0 years, 62.0 ± 6.9 kg, 155.9 ± 5.7 cm, and 25.5 ± 2.4 kg/m 2 ) received either 35 g of WP (n = 15) or 35 g of PLA (n = 16) over a 12-week study period while performing an RT program three times a week. Dietary intake, one-repetition maximum test, and skeletal muscle mass by dual-energy X-ray absorptiometry were assessed before and after the intervention period. Both groups showed significant (p < .05) improvements in skeletal muscle mass and total strength, and the WP group realized greater increases (p < .05) in these measures compared with PLA (skeletal muscle mass: WP = +4.8% vs. PLA = +2.3%; strength: WP = +8.7% vs. PLA = +4.9%). Muscular quality increased (p < .05) in both groups (WP = +2.9% vs. PLA = +1.5%) without statistical differences (p > .05) noted between conditions. We conclude that WP supplementation in combination with RT induces higher increases in both strength and hypertrophy in older women preconditioned to RT.

LONG-TERM PRECONDITIONING OF PLANTLETS: A PRACTICAL METHOD FOR ENHANCING SURVIVAL OF PINEAPPLE (Ananas comosus Merr.) SHOOT TIPS CRYOPRESERVED USING VITRIFICATION.

PubMed

Hu, W H; Liu, S F; Liaw, S I

2015-01-01

The purpose of this study was to develop an efficient cryopreservation protocol for pineapple (Ananas comosus Merr.) shoot tips. The optimal state of pineapple plantlets was investigated by using sucrose preconditioning to enhance survival after cryostorage. To achieve a suitable state of plantlets before cryopreservation, 0.2 M to 0.4 M sucrose concentrations combined with short- (0-7 days), medium- (15-30 days), and long-term (75-150 days) preconditioning periods were compared. The highest survival (100 %) was achieved using the following procedure: intact plantlets underwent long-term preconditioning with 0.2 M sucrose for 135 days, dissected shoot tips were treated with a loading solution containing 2.0 M glycerol + 0.4 M sucrose for 60 min at 25 degree and the shoot tips were dehydrated in PVS2 for 2h at 0 degree C before being plunged in liquid nitrogen. Rewarming was conducted in a water-bath for 30 s at 40 degree C and PVS2 was replaced with a 1.2 M sucrose solution for 30 min at 25 degree C. The shoot tips were transferred on semisolid medium and left in the dark for 1 week, then in dim light for 3 weeks.

Ischemic preconditioning protects against gap junctional uncoupling in cardiac myofibroblasts.

PubMed

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.

Silencing heat shock factor 1 by small interfering RNA abrogates heat shock-induced cardioprotection against ischemia-reperfusion injury in mice.

PubMed

Yin, Chang; Xi, Lei; Wang, Xiaoyin; Eapen, Mareen; Kukreja, Rakesh C

2005-10-01

Induction of heat shock factor 1 (HSF1) is known to associate with cellular response to divergent pathophysiological stresses including whole body hyperthermia (WBH) and ischemia-reperfusion. However, a direct cause-effect relationship between HSF1 activation and cytoprotection induced by myocardial preconditioning has not been conclusively established, mainly due to the limitations of available experiment tools. In the present studies, we used a novel approach to block HSF1 with small interfering RNA (siRNA) technique in vivo. Male adult ICR mice were treated intraperitoneally with amine (vehicle) or siRNA specific to HSF1 (siRNA-HSF1). Three days later, WBH preconditioning protocol (rectal temperature 42 degrees C for 15 min) was applied to these mice under light anesthesia. WBH preconditioning resulted in 2.7-fold and 3.4-fold increase in cardiac HSF1 mRNA and protein expression respectively 2 hours after WBH, which was inhibited in the siRNA-treated mice. The silencing effect of siRNA on HSF1 was associated with complete loss of the infarct- limiting protection by WBH preconditioning after 48 hours. Pretreatment with siRNA-HSF1 had no effect on infarct size in the sham control animals as compared with the amine-treated group. DNA micro-array analysis revealed that siRNA-HSF1 caused a general inhibition on multiple members of HSP family, except Hsp32, Hsp47 and Hsp60. In addition, the silencing effect of siRNA on HSF1 and HSPs gene expression was transient and its inhibitory effect disappeared by 10 days after treatment. siRNA-HSF1 also impaired the thermotolerance of the heat shocked mice as indicated by higher mortality following WBH. For the first time, we have applied siRNA technique in the field of myocardial preconditioning to demonstrate HSF1 activation as an essential step in WBH preconditioning against cardiac ischemia-reperfusion injury.

miR-21 contributes to xenon-conferred amelioration of renal ischemia-reperfusion injury in mice.

PubMed

Jia, Ping; Teng, Jie; Zou, Jianzhou; Fang, Yi; Zhang, Xiaoyan; Bosnjak, Zeljko J; Liang, Mingyu; Ding, Xiaoqiang

2013-09-01

MicroRNAs participate in the regulation of numerous physiological and disease processes. The in vivo role of microRNAs in anesthetics-conferred organoprotection is unknown. Mice were exposed for 2 h to either 70% xenon, or 70% nitrogen, 24 h before the induction of renal ischemia-reperfusion injury. The role of microRNA, miR-21, in renal protection conferred by the delayed xenon preconditioning was examined using in vivo knockdown of miR-21 and analysis of miR-21 target pathways. Xenon preconditioning provided morphologic and functional protection against renal ischemia-reperfusion injury (n = 6), characterized by attenuation of renal tubular damage, apoptosis, and oxidative stress. Xenon preconditioning significantly increased the expression of miR-21 in the mouse kidney. A locked nucleic acid-modified anti-miR-21, given before xenon preconditioning, knocked down miR-21 effectively, and exacerbated subsequent renal ischemia-reperfusion injury. Mice treated with anti-miR-21 and ischemia-reperfusion injury showed significantly higher serum creatinine than antiscrambled oligonucleotides-treated mice, 24 h after ischemia-reperfusion (1.37 ± 0.28 vs. 0.81 ± 0.14 mg/dl; n = 5; P < 0.05). Knockdown of miR-21 induced significant up-regulation of programmed cell death protein 4 and phosphatase and tensin homolog deleted on chromosome 10, two proapoptotic target effectors of miR-21, and resulted in significant down-regulation of phosphorylated protein kinase B and increased tubular cell apoptosis. In addition, xenon preconditioning up-regulated hypoxia-inducible factor-1α and its downstream effector vascular endothelial growth factor in a time-dependent manner. Knockdown of miR-21 resulted in a significant decrease of hypoxia-inducible factor-1α. These results indicate that miR-21 contributes to the renoprotective effect of xenon preconditioning.

Effect of Ischemia Duration and Protective Interventions on the Temporal Dynamics of Tissue Composition After Myocardial Infarction

PubMed Central

Fernández-Jiménez, Rodrigo; Galán-Arriola, Carlos; Sánchez-González, Javier; Agüero, Jaume; López-Martín, Gonzalo J.; Gomez-Talavera, Sandra; Garcia-Prieto, Jaime; Benn, Austin; Molina-Iracheta, Antonio; Barreiro-Pérez, Manuel; Martin-García, Ana; García-Lunar, Inés; Pizarro, Gonzalo; Sanz, Javier; Sánchez, Pedro L.; Fuster, Valentin

2017-01-01

Rationale: The impact of cardioprotective strategies and ischemia duration on postischemia/reperfusion (I/R) myocardial tissue composition (edema, myocardium at risk, infarct size, salvage, intramyocardial hemorrhage, and microvascular obstruction) is not well understood. Objective: To study the effect of ischemia duration and protective interventions on the temporal dynamics of myocardial tissue composition in a translational animal model of I/R by the use of state-of-the-art imaging technology. Methods and Results: Four 5-pig groups underwent different I/R protocols: 40-minute I/R (prolonged ischemia, controls), 20-minute I/R (short-duration ischemia), prolonged ischemia preceded by preconditioning, or prolonged ischemia followed by postconditioning. Serial cardiac magnetic resonance (CMR)-based tissue characterization was done in all pigs at baseline and at 120 minutes, day 1, day 4, and day 7 after I/R. Reference myocardium at risk was assessed by multidetector computed tomography during the index coronary occlusion. After the final CMR, hearts were excised and processed for water content quantification and histology. Five additional healthy pigs were euthanized after baseline CMR as reference. Edema formation followed a bimodal pattern in all 40-minute I/R pigs, regardless of cardioprotective strategy and the degree of intramyocardial hemorrhage or microvascular obstruction. The hyperacute edematous wave was ameliorated only in pigs showing cardioprotection (ie, those undergoing short-duration ischemia or preconditioning). In all groups, CMR-measured edema was barely detectable at 24 hours postreperfusion. The deferred healing-related edematous wave was blunted or absent in pigs undergoing preconditioning or short-duration ischemia, respectively. CMR-measured infarct size declined progressively after reperfusion in all groups. CMR-measured myocardial salvage, and the extent of intramyocardial hemorrhage and microvascular obstruction varied dramatically according to CMR timing, ischemia duration, and cardioprotective strategy. Conclusions: Cardioprotective therapies, duration of index ischemia, and the interplay between these greatly influence temporal dynamics and extent of tissue composition changes after I/R. Consequently, imaging techniques and protocols for assessing edema, myocardium at risk, infarct size, salvage, intramyocardial hemorrhage, and microvascular obstruction should be standardized accordingly. PMID:28596216

A Top Pilot Tunnel Preconditioning Method for the Prevention of Extremely Intense Rockbursts in Deep Tunnels Excavated by TBMs

NASA Astrophysics Data System (ADS)

Zhang, Chuanqing; Feng, Xiating; Zhou, Hui; Qiu, Shili; Wu, Wenping

2012-05-01

The headrace tunnels at the Jinping II Hydropower Station cross the Jinping Mountain with a maximum overburden depth of 2,525 m, where 80% of the strata along the tunnels consist of marble. A number of extremely intense rockbursts occurred during the excavation of the auxiliary tunnels and the drainage tunnel. In particular, a tunnel boring machine (TBM) was destroyed by an extremely intense rockburst in a 7.2-m-diameter drainage tunnel. Two of the four subsequent 12.4-m-diameter headrace tunnels will be excavated with larger size TBMs, where a high risk of extremely intense rockbursts exists. Herein, a top pilot tunnel preconditioning method is proposed to minimize this risk, in which a drilling and blasting method is first recommended for the top pilot tunnel excavation and support, and then the TBM excavation of the main tunnel is conducted. In order to evaluate the mechanical effectiveness of this method, numerical simulation analyses using the failure approaching index, energy release rate, and excess shear stress indices are carried out. Its construction feasibility is discussed as well. Moreover, a microseismic monitoring technique is used in the experimental tunnel section for the real-time monitoring of the microseismic activities of the rock mass in TBM excavation and for assessing the effect of the top pilot tunnel excavation in reducing the risk of rockbursts. This method is applied to two tunnel sections prone to extremely intense rockbursts and leads to a reduction in the risk of rockbursts in TBM excavation.

Pneumoperitoneum induced ischemia-reperfusion injury of the peritoneum-Preconditioning may reduce the negative side-effects caused by carbon-dioxide pneumoperitoneum-Pilot study.

PubMed

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.

The effectiveness of a preconditioning programme on preventing running-related injuries in novice runners: a randomised controlled trial.

PubMed

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.

Fast preconditioned multigrid solution of the Euler and Navier-Stokes equations for steady, compressible flows

NASA Astrophysics Data System (ADS)

Caughey, David A.; Jameson, Antony

2003-10-01

New versions of implicit algorithms are developed for the efficient solution of the Euler and Navier-Stokes equations of compressible flow. The methods are based on a preconditioned, lower-upper (LU) implementation of a non-linear, symmetric Gauss-Seidel (SGS) algorithm for use as a smoothing algorithm in a multigrid method. Previously, this method had been implemented for flows in quasi-one-dimensional ducts and for two-dimensional flows past airfoils on boundary-conforming O-type grids for a variety of symmetric limited positive (SLIP) spatial approximations, including the scalar dissipation and convective upwind split pressure (CUSP) schemes. Here results are presented for both inviscid and viscous (laminar) flows past airfoils on boundary-conforming C-type grids. The method is significantly faster than earlier explicit or implicit methods for inviscid problems, allowing solution of these problems to the level of truncation error in three to five multigrid cycles. Viscous solutions still require as many as twenty multigrid cycles.

Matrix preconditioning: a robust operation for optical linear algebra processors.

PubMed

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.

Spectral analysis and multigrid preconditioners for two-dimensional space-fractional diffusion equations

NASA Astrophysics Data System (ADS)

Moghaderi, Hamid; Dehghan, Mehdi; Donatelli, Marco; Mazza, Mariarosa

2017-12-01

Fractional diffusion equations (FDEs) are a mathematical tool used for describing some special diffusion phenomena arising in many different applications like porous media and computational finance. In this paper, we focus on a two-dimensional space-FDE problem discretized by means of a second order finite difference scheme obtained as combination of the Crank-Nicolson scheme and the so-called weighted and shifted Grünwald formula. By fully exploiting the Toeplitz-like structure of the resulting linear system, we provide a detailed spectral analysis of the coefficient matrix at each time step, both in the case of constant and variable diffusion coefficients. Such a spectral analysis has a very crucial role, since it can be used for designing fast and robust iterative solvers. In particular, we employ the obtained spectral information to define a Galerkin multigrid method based on the classical linear interpolation as grid transfer operator and damped-Jacobi as smoother, and to prove the linear convergence rate of the corresponding two-grid method. The theoretical analysis suggests that the proposed grid transfer operator is strong enough for working also with the V-cycle method and the geometric multigrid. On this basis, we introduce two computationally favourable variants of the proposed multigrid method and we use them as preconditioners for Krylov methods. Several numerical results confirm that the resulting preconditioning strategies still keep a linear convergence rate.

Analysis of Monte Carlo accelerated iterative methods for sparse linear systems: Analysis of Monte Carlo accelerated iterative methods for sparse linear systems

DOE PAGES

Benzi, Michele; Evans, Thomas M.; Hamilton, Steven P.; ...

2017-03-05

Here, we consider hybrid deterministic-stochastic iterative algorithms for the solution of large, sparse linear systems. Starting from a convergent splitting of the coefficient matrix, we analyze various types of Monte Carlo acceleration schemes applied to the original preconditioned Richardson (stationary) iteration. We expect that these methods will have considerable potential for resiliency to faults when implemented on massively parallel machines. We also establish sufficient conditions for the convergence of the hybrid schemes, and we investigate different types of preconditioners including sparse approximate inverses. Numerical experiments on linear systems arising from the discretization of partial differential equations are presented.

A frequency dependent preconditioned wavelet method for atmospheric tomography

NASA Astrophysics Data System (ADS)

Yudytskiy, Mykhaylo; Helin, Tapio; Ramlau, Ronny

2013-12-01

Atmospheric tomography, i.e. the reconstruction of the turbulence in the atmosphere, is a main task for the adaptive optics systems of the next generation telescopes. For extremely large telescopes, such as the European Extremely Large Telescope, this problem becomes overly complex and an efficient algorithm is needed to reduce numerical costs. Recently, a conjugate gradient method based on wavelet parametrization of turbulence layers was introduced [5]. An iterative algorithm can only be numerically efficient when the number of iterations required for a sufficient reconstruction is low. A way to achieve this is to design an efficient preconditioner. In this paper we propose a new frequency-dependent preconditioner for the wavelet method. In the context of a multi conjugate adaptive optics (MCAO) system simulated on the official end-to-end simulation tool OCTOPUS of the European Southern Observatory we demonstrate robustness and speed of the preconditioned algorithm. We show that three iterations are sufficient for a good reconstruction.

Simultaneous stochastic inversion for geomagnetic main field and secular variation. I - A large-scale inverse problem

NASA Technical Reports Server (NTRS)

Bloxham, Jeremy

1987-01-01

The method of stochastic inversion is extended to the simultaneous inversion of both main field and secular variation. In the present method, the time dependency is represented by an expansion in Legendre polynomials, resulting in a simple diagonal form for the a priori covariance matrix. The efficient preconditioned Broyden-Fletcher-Goldfarb-Shanno algorithm is used to solve the large system of equations resulting from expansion of the field spatially to spherical harmonic degree 14 and temporally to degree 8. Application of the method to observatory data spanning the 1900-1980 period results in a data fit of better than 30 nT, while providing temporally and spatially smoothly varying models of the magnetic field at the core-mantle boundary.

Effective matrix-free preconditioning for the augmented immersed interface method

NASA Astrophysics Data System (ADS)

Xia, Jianlin; Li, Zhilin; Ye, Xin

2015-12-01

We present effective and efficient matrix-free preconditioning techniques for the augmented immersed interface method (AIIM). AIIM has been developed recently and is shown to be very effective for interface problems and problems on irregular domains. GMRES is often used to solve for the augmented variable(s) associated with a Schur complement A in AIIM that is defined along the interface or the irregular boundary. The efficiency of AIIM relies on how quickly the system for A can be solved. For some applications, there are substantial difficulties involved, such as the slow convergence of GMRES (particularly for free boundary and moving interface problems), and the inconvenience in finding a preconditioner (due to the situation that only the products of A and vectors are available). Here, we propose matrix-free structured preconditioning techniques for AIIM via adaptive randomized sampling, using only the products of A and vectors to construct a hierarchically semiseparable matrix approximation to A. Several improvements over existing schemes are shown so as to enhance the efficiency and also avoid potential instability. The significance of the preconditioners includes: (1) they do not require the entries of A or the multiplication of AT with vectors; (2) constructing the preconditioners needs only O (log ⁡ N) matrix-vector products and O (N) storage, where N is the size of A; (3) applying the preconditioners needs only O (N) flops; (4) they are very flexible and do not require any a priori knowledge of the structure of A. The preconditioners are observed to significantly accelerate the convergence of GMRES, with heuristical justifications of the effectiveness. Comprehensive tests on several important applications are provided, such as Navier-Stokes equations on irregular domains with traction boundary conditions, interface problems in incompressible flows, mixed boundary problems, and free boundary problems. The preconditioning techniques are also useful for several other problems and methods.

On an adaptive preconditioned Crank-Nicolson MCMC algorithm for infinite dimensional Bayesian inference

NASA Astrophysics Data System (ADS)

Hu, Zixi; Yao, Zhewei; Li, Jinglai

2017-03-01

Many scientific and engineering problems require to perform Bayesian inference for unknowns of infinite dimension. In such problems, many standard Markov Chain Monte Carlo (MCMC) algorithms become arbitrary slow under the mesh refinement, which is referred to as being dimension dependent. To this end, a family of dimensional independent MCMC algorithms, known as the preconditioned Crank-Nicolson (pCN) methods, were proposed to sample the infinite dimensional parameters. In this work we develop an adaptive version of the pCN algorithm, where the covariance operator of the proposal distribution is adjusted based on sampling history to improve the simulation efficiency. We show that the proposed algorithm satisfies an important ergodicity condition under some mild assumptions. Finally we provide numerical examples to demonstrate the performance of the proposed method.

Run Clever – No difference in risk of injury when comparing progression in running volume and running intensity in recreational runners: A randomised trial

PubMed Central

Rasmussen, Sten; Sørensen, Henrik; Parner, Erik Thorlund; Lind, Martin; Nielsen, Rasmus Oestergaard

2018-01-01

Background/aim The Run Clever trial investigated if there was a difference in injury occurrence across two running schedules, focusing on progression in volume of running intensity (Sch-I) or in total running volume (Sch-V). It was hypothesised that 15% more runners with a focus on progression in volume of running intensity would sustain an injury compared with runners with a focus on progression in total running volume. Methods Healthy recreational runners were included and randomly allocated to Sch-I or Sch-V. In the first eight weeks of the 24-week follow-up, all participants (n=839) followed the same running schedule (preconditioning). Participants (n=447) not censored during the first eight weeks entered the 16-week training period with a focus on either progression in intensity (Sch-I) or volume (Sch-V). A global positioning system collected all data on running. During running, all participants received real-time, individualised feedback on running intensity and running volume. The primary outcome was running-related injury (RRI). Results After preconditioning a total of 80 runners sustained an RRI (Sch-I n=36/Sch-V n=44). The cumulative incidence proportion (CIP) in Sch-V (reference group) were CIP2 weeks 4.6%; CIP4 weeks 8.2%; CIP8 weeks 13.2%; CIP16 weeks 28.0%. The risk differences (RD) and 95% CI between the two schedules were RD2 weeks=2.9%(−5.7% to 11.6%); RD4 weeks=1.8%(−9.1% to 12.8%); RD8 weeks=−4.7%(−17.5% to 8.1%); RD16 weeks=−14.0% (−36.9% to 8.9%). Conclusion A similar proportion of runners sustained injuries in the two running schedules. PMID:29527322

Reliability enhancement of Navier-Stokes codes through convergence acceleration

NASA Technical Reports Server (NTRS)

Merkle, Charles L.; Dulikravich, George S.

1995-01-01

Methods for enhancing the reliability of Navier-Stokes computer codes through improving convergence characteristics are presented. The improving of these characteristics decreases the likelihood of code unreliability and user interventions in a design environment. The problem referred to as a 'stiffness' in the governing equations for propulsion-related flowfields is investigated, particularly in regard to common sources of equation stiffness that lead to convergence degradation of CFD algorithms. Von Neumann stability theory is employed as a tool to study the convergence difficulties involved. Based on the stability results, improved algorithms are devised to ensure efficient convergence in different situations. A number of test cases are considered to confirm a correlation between stability theory and numerical convergence. The examples of turbulent and reacting flow are presented, and a generalized form of the preconditioning matrix is derived to handle these problems, i.e., the problems involving additional differential equations for describing the transport of turbulent kinetic energy, dissipation rate and chemical species. Algorithms for unsteady computations are considered. The extension of the preconditioning techniques and algorithms derived for Navier-Stokes computations to three-dimensional flow problems is discussed. New methods to accelerate the convergence of iterative schemes for the numerical integration of systems of partial differential equtions are developed, with a special emphasis on the acceleration of convergence on highly clustered grids.

Platelet rich plasma clot releasate preconditioning induced PI3K/AKT/NFκB signaling enhances survival and regenerative function of rat bone marrow mesenchymal stem cells in hostile microenvironments.

PubMed

Peng, Yan; Huang, Sha; Wu, Yan; Cheng, Biao; Nie, Xiaohu; Liu, Hongwei; Ma, Kui; Zhou, Jiping; Gao, Dongyun; Feng, Changjiang; Yang, Siming; Fu, Xiaobing

2013-12-15

Mesenchymal stem cells (MSCs) have been optimal targets in the development of cell based therapies, but their limited availability and high death rate after transplantation remains a concern in clinical applications. This study describes novel effects of platelet rich clot releasate (PRCR) on rat bone marrow-derived MSCs (BM-MSCs), with the former driving a gene program, which can reduce apoptosis and promote the regenerative function of the latter in hostile microenvironments through enhancement of paracrine/autocrine factors. By using reverse transcription-polymerase chain reaction, immunofluorescence and western blot analyses, we showed that PRCR preconditioning could alleviate the apoptosis of BM-MSCs under stress conditions induced by hydrogen peroxide (H2O2) and serum deprivation by enhancing expression of vascular endothelial growth factor and platelet-derived growth factor (PDGF) via stimulation of the platelet-derived growth factor receptor (PDGFR)/PI3K/AKT/NF-κB signaling pathways. Furthermore, the effects of PRCR preconditioned GFP-BM-MSCs subcutaneously transplanted into rats 6 h after wound surgery were examined by histological and other tests from days 0-22 after transplantation. Engraftment of the PRCR preconditioned BM-MSCs not only significantly attenuated apoptosis and wound size but also improved epithelization and blood vessel regeneration of skin via regulation of the wound microenvironment. Thus, preconditioning with PRCR, which reprograms BM-MSCs to tolerate hostile microenvironments and enhance regenerative function by increasing levels of paracrine factors through PDGFR-α/PI3K/AKT/NF-κB signaling pathways would be a safe method for boosting the effectiveness of transplantation therapy in the clinic.

Smooth muscle cell seeding of decellularized scaffolds: the importance of bioreactor preconditioning to development of a more native architecture for tissue-engineered blood vessels.

PubMed

Yazdani, Saami K; Watts, Benjamin; Machingal, Masood; Jarajapu, Yagna P R; Van Dyke, Mark E; Christ, George J

2009-04-01

Vascular smooth muscle cells (VSMCs) impart important functional characteristics in the native artery and, therefore, should logically be incorporated in the development of tissue-engineered blood vessels. However, the native architecture and low porosity of naturally derived biomaterials (i.e., decellularized vessels) have impeded efforts to seed and incorporate a VSMC layer in tissue-engineered blood vessels. To this end, the goal of this study was to develop improved methods for seeding, proliferation, and maturation of VSMCs on decellularized porcine carotid arteries. Decellularized vessels were prepared in the absence and presence of the adventitial layer, and statically seeded with a pipette containing a suspension of rat aortic VSMCs. After cell seeding, recellularized engineered vessels were placed in a custom bioreactor system for 1-2 weeks to enhance cellular proliferation, alignment, and maturation. Initial attachment of VSMCs was dramatically enhanced by removing the adventitial layer of the decellularized porcine artery. Moreover, cyclic bioreactor conditioning (i.e., flow and pressure) resulted in increased VSMC proliferation and accelerated formation of a muscularized medial layer in the absence of the adventitial layer during the first week of preconditioning. Fura-2-based digital imaging microscopy revealed marked and reproducible depolarization-induced calcium mobilization after bioreactor preconditioning in the absence, but not in the presence, of the adventitia. The major finding of this investigation is that bioreactor preconditioning accelerates the formation of a significant muscular layer on decellularized scaffolds, in particular on adventitia-denuded scaffolds. Further, the VSMC layer of bioreactor-preconditioned vessels was capable of mobilizing calcium in response to cellular depolarization. These findings represent an important first step toward the development of tissue-engineered vascular grafts that more closely mimic native vasculature.

Acetylation of histones in neocortex and hippocampus of rats exposed to different modes of hypobaric hypoxia: Implications for brain hypoxic injury and tolerance.

PubMed

Samoilov, Mikhail; Churilova, Anna; Gluschenko, Tatjana; Vetrovoy, Oleg; Dyuzhikova, Natalia; Rybnikova, Elena

2016-03-01

Acetylation of nucleosome histones results in relaxation of DNA and its availability for the transcriptional regulators, and is generally associated with the enhancement of gene expression. Although it is well known that activation of a variety of pro-adaptive genes represents a key event in the development of brain hypoxic/ischemic tolerance, the role of epigenetic mechanisms, in particular histone acetylation, in this process is still unexplored. The aim of the present study was to investigate changes in acetylation of histones in vulnerable brain neurons using original well-standardized model of hypobaric hypoxia and preconditioning-induced tolerance of the brain. Using quantitative immunohistochemistry and Western blot, effects of severe injurious hypobaric hypoxia (SH, 180mm Hg, 3h) and neuroprotective preconditioning mode (three episodes of 360mm Hg for 2h spaced at 24h) on the levels of the acetylated proteins and acetylated H3 Lys24 (H3K24ac) in the neocortex and hippocampus of rats were studied. SH caused global repression of the acetylation processes in the neocortex (layers II-III, V) and hippocampus (CA1, CA3) by 3-24h, and this effect was prevented by the preconditioning. Moreover, hypoxic preconditioning remarkably increased the acetylation of H3K24 in response to SH in the brain areas examined. The preconditioning hypoxia without subsequent SH also stimulated acetylation processes in the neocortex and hippocampus. The moderately enhanced expression of the acetylated proteins in the preconditioned rats was maintained for 24h, whereas acetylation of H3K24 was intense but transient, peaked at 3h. The novel data obtained in the present study indicate that large activation of the acetylation processes, in particular acetylation of histones might be essential for the development of brain hypoxic tolerance. Copyright © 2015 Elsevier GmbH. All rights reserved.

Determinants of the Efficacy of Cardiac Ischemic Preconditioning: A Systematic Review and Meta-Analysis of Animal Studies

PubMed Central

Wever, Kimberley E.; Hooijmans, Carlijn R.; Riksen, Niels P.; Sterenborg, Thomas B.; Sena, Emily S.; Ritskes-Hoitinga, Merel; Warlé, Michiel C.

2015-01-01

Background Ischemic preconditioning (IPC) of the heart is a protective strategy in which a brief ischemic stimulus immediately before a lethal ischemic episode potently limits infarct size. Although very promising in animal models of myocardial infarction, IPC has not yet been successfully translated to benefit for patients. Objective To appraise all preclinical evidence on IPC for myocardial infarction and identify factors hampering translation. Methods and results Using systematic review and meta-analysis, we identified 503 animal studies reporting infarct size data from 785 comparisons between IPC-treated and control animals. Overall, IPC reduced myocardial infarction by 24.6% [95%CI 23.5, 25.6]. Subgroup analysis showed that IPC efficacy was reduced in comorbid animals and non-rodents. Efficacy was highest in studies using 2–3 IPC cycles applied <45 minutes before myocardial infarction. Local and remote IPC were equally effective. Reporting of study quality indicators was low: randomization, blinding and a sample size calculation were reported in 49%, 11% and 2% of publications, respectively. Conclusions Translation of IPC to the clinical setting may be hampered by the observed differences between the animals used in preclinical IPC studies and the patient population, regarding comorbidity, sex and age. Furthermore, the IPC protocols currently used in clinical trials could be optimized in terms of timing and the number of ischemic cycles applied. In order to inform future clinical trials successfully, future preclinical studies on IPC should aim to maximize both internal and external validity, since poor methodological quality may limit the value of the preclinical evidence. PMID:26580958

Detailed qualitative dynamic knowledge representation using a BioNetGen model of TLR-4 signaling and preconditioning.

PubMed

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 preconditioning behavior with increasing LPS at 10, 100, 1000 and 10,000 and a secondary dose of LPS at 10,000 administered at approximately 27h of simulated time. Simulations of 'knockout' versions of the model allowed further examination of the interactions within the signaling cascade. The model demonstrated a dose-dependent TNF response curve to increasing stimulus by LPS. Preconditioning simulations demonstrated a similar dose-dependency of preconditioning doses leading to attenuation of response to subsequent LPS challenge - a 'tolerance' dynamic. These responses match dynamics reported in the literature. Furthermore, the simulated 'knockout' results suggested the existence and need for dual negative feedback control mechanisms, represented by the zinc ring-finger protein A20 and inhibitor kappa B proteins (IkappaB), in order for both effective attenuation of the initial stimulus signal and subsequent preconditioned 'tolerant' behavior. We present an example of detailed, qualitative dynamic knowledge representation using the TLR-4 signaling pathway, its control mechanisms and overall behavior with respect to preconditioning. The intent of this approach is to demonstrate a method of translating the extensive mechanistic knowledge being generated at the basic science level into an executable framework that can provide a means of 'conceptual model verification.' This allows for both the 'checking' of the dynamic consequences of a mechanistic hypothesis and the creation of a modular component of an overall model directed at the engineering goal of biomedical research. It is hoped that this paper will increase the use of knowledge representation and communication in this fashion, and facilitate the concatenation and integration of community-wide knowledge.

The New LMK Primary Standard for Dew-Point Sensor Calibration: Evaluation of the High-Range Saturator Efficiency

NASA Astrophysics Data System (ADS)

Hudoklin, Domen; Drnovšek, Janko

2008-10-01

In the field of hygrometry, a primary dew-point standard can be realized according to several proven principles, such as single-pressure (1-P), two-pressure (2-P), or divided flow. Different realizations have been introduced by various national laboratories, each resulting in a stand-alone complex generation system. Recent trends in generator design favor the single-pressure principle without recirculation because it promises theoretically lower uncertainty and because it avoids problems regarding the leak tightness of the recirculation. Instead of recirculation, the efficiency of saturation, the key factor, is increased by preconditioning the inlet gas entering the saturator. For preconditioning, a presaturator or purifier is used to bring the dew point of the inlet stream close to the saturator temperature. The purpose of the paper is to identify the minimum requirements for the preconditioning system and the main saturator to assure efficient saturation for the LMK generator. Moreover, the aim is also to find out if the preconditioning system can be avoided despite the rather simple construction of the main saturator. If this proves to be the case, the generator design can be simplified while maintaining an accurate value of the generated dew point. Experiments were carried out within the scope of improving our existing primary generator in the above-ambient dew-point range up to +70°C. These results show the generated dew point is within the measurement uncertainty for any dew-point value of the inlet gas. Thus, the preconditioning subsystem can be avoided, which leads to a simplified generator design.

Finite Element Methods for real-time Haptic Feedback of Soft-Tissue Models in Virtual Reality Simulators

NASA Technical Reports Server (NTRS)

Frank, Andreas O.; Twombly, I. Alexander; Barth, Timothy J.; Smith, Jeffrey D.; Dalton, Bonnie P. (Technical Monitor)

2001-01-01

We have applied the linear elastic finite element method to compute haptic force feedback and domain deformations of soft tissue models for use in virtual reality simulators. Our results show that, for virtual object models of high-resolution 3D data (>10,000 nodes), haptic real time computations (>500 Hz) are not currently possible using traditional methods. Current research efforts are focused in the following areas: 1) efficient implementation of fully adaptive multi-resolution methods and 2) multi-resolution methods with specialized basis functions to capture the singularity at the haptic interface (point loading). To achieve real time computations, we propose parallel processing of a Jacobi preconditioned conjugate gradient method applied to a reduced system of equations resulting from surface domain decomposition. This can effectively be achieved using reconfigurable computing systems such as field programmable gate arrays (FPGA), thereby providing a flexible solution that allows for new FPGA implementations as improved algorithms become available. The resulting soft tissue simulation system would meet NASA Virtual Glovebox requirements and, at the same time, provide a generalized simulation engine for any immersive environment application, such as biomedical/surgical procedures or interactive scientific applications.

ACL graft constructs: In-vitro fatigue testing highlights the occurrence of irrecoverable lengthening and the need for adequate (pre)conditioning to avert the recurrence of knee instability.

PubMed

Blythe, A; Tasker, T; Zioupos, P

2006-01-01

The performance of ACL grafts in both the short and long term is only as good as the condition of the graft at the time of surgery. If the graft lengthens under load at the two fixation ends incorporation will take longer to occur. Previous studies have shown that the various grafts currently used are strong enough. However, data on strength came primarily from quasistatic single pull to failure tests with, in some cases, modest cycling to precondition the grafts. The present study examined the in-vitro biomechanical behaviour of model ACL grafts, which have been fatigue cycled to failure over a wide range of loads in physiological ambient conditions. Load/deformation curves and the stretch of the grafts was continuously recorded until final rupture. The grafts demonstrated typical creep-rupture like behaviour with elongation (non-recoverable stretch) and loss of stiffness leading to gradual failure. Some of the graft designs were consistently shown to elongate up to 20 mm in length within the first 2000 cycles at moderate physiological loads and a further 10 mm of elongation occurred between the initial preconditioned state and just prior to complete rupture. Not enough attention has been paid previously to the likely long term elongation patterns of ACL grafts post-surgery and even after the usual empirical preconditioning has been performed by the surgeon. Increased graft dimensions may result in recurrent knee instability and may also lead to failure of the graft to incorporate. Preconditioning in-vitro may still be a way to remove some slack and prepare the graft for its operational environment by stiffening in particular the tissue/fixation interface for those grafts that use soft polymer fixation ends.

The effect of Emdogain and 24% EDTA root conditioning on periodontal healing of replanted dog's teeth.

PubMed

Guzmán-Martínez, Nayelli; Silva-Herzog, Flores Daniel; Méndez, González Verónica; Martín-Pérez, Silvia; Cerda-Cristerna, Bernardino Isaac; Cohenca, Nestor

2009-02-01

Controversies still exist as for the regenerative role of enamel matrix derivatives and the need for removal of the periodontal ligament in replanted teeth. The purpose of this study was to evaluate the effect of Emdogain and 24% ethylenediamine tetraacetic acid (EDTA) root conditioning on periodontal healing of replanted dog's teeth. Teeth were extracted, endodontically treated and preconditioned as follows: group 1, Emdogain; group 2, Emdogain + EDTA and group 3, EDTA. Teeth were replanted after 30 min extraoral time, splinted for 15 days and animals sacrificed after 8 weeks of observation. Histological evaluation was performed using hematoxylin/eosin and Masson trichrome and results scored based on previously reported criteria for histological evaluation. Replacement root resorption was histologically diagnosed in all groups except in the negative control. A parametric analysis showed no statistically significant differences between experimental groups. Root preconditioning with Emdogain alone or in combination with 24% EDTA showed no evidence of regeneration of collagen fibers and consequently did not prevent the development of replacement root resorption on replanted dog's teeth.

Fast algorithms for chiral fermions in 2 dimensions

NASA Astrophysics Data System (ADS)

Hyka (Xhako), Dafina; Osmanaj (Zeqirllari), Rudina

2018-03-01

In lattice QCD simulations the formulation of the theory in lattice should be chiral in order that symmetry breaking happens dynamically from interactions. In order to guarantee this symmetry on the lattice one uses overlap and domain wall fermions. On the other hand high computational cost of lattice QCD simulations with overlap or domain wall fermions remains a major obstacle of research in the field of elementary particles. We have developed the preconditioned GMRESR algorithm as fast inverting algorithm for chiral fermions in U(1) lattice gauge theory. In this algorithm we used the geometric multigrid idea along the extra dimension.The main result of this work is that the preconditioned GMRESR is capable to accelerate the convergence 2 to 12 times faster than the other optimal algorithms (SHUMR) for different coupling constant and lattice 32x32. Also, in this paper we tested it for larger lattice size 64x64. From the results of simulations we can see that our algorithm is faster than SHUMR. This is a very promising result that this algorithm can be adapted also in 4 dimension.

Thigmomorphogenesis: the role of ethylene in the response of Pinus taeda and Abies fraseri to mechanical perturbation

NASA Technical Reports Server (NTRS)

Telewski, F. W.; Jaffe, M. J.

1986-01-01

Ethylene production was monitored for 48 h in two half-sibs of Pinus taeda L. grown in the greenhouse and given mechanical perturbation (MP) by flexing; and for 22 h in Abies fraseri (Pursh) Poir. grown in the field and exposed to wind-mediated MP. Both species produced a peak of ethylene 18 h after MP. Seedlings of P. taeda exposed to MP for the duration of the growing season (preconditioned) produced less ethylene compared to non-MP controls, with a peak production at 8 h. One half-sib which responded to MP by an increase in radial growth produced 16 times more ethylene than another half-sib which had no significant change in radial growth. Preconditioned A. fraseri produced no significant quantities of ethylene after MP. The production of wound ethylene appears to be different from MP-induced ethylene. When an ethylene-generating solution was applied to P. taeda seedlings, it mimicked many of the morphological and mechanical characteristics of MP seedlings. The putative role of ethylene in the thigmomorphogenetic response is addressed.

Positivity-preserving dual time stepping schemes for gas dynamics

NASA Astrophysics Data System (ADS)

Parent, Bernard

2018-05-01

A new approach at discretizing the temporal derivative of the Euler equations is here presented which can be used with dual time stepping. The temporal discretization stencil is derived along the lines of the Cauchy-Kowalevski procedure resulting in cross differences in spacetime but with some novel modifications which ensure the positivity of the discretization coefficients. It is then shown that the so-obtained spacetime cross differences result in changes to the wave speeds and can thus be incorporated within Roe or Steger-Warming schemes (with and without reconstruction-evolution) simply by altering the eigenvalues. The proposed approach is advantaged over alternatives in that it is positivity-preserving for the Euler equations. Further, it yields monotone solutions near discontinuities while exhibiting a truncation error in smooth regions less than the one of the second- or third-order accurate backward-difference-formula (BDF) for either small or large time steps. The high resolution and positivity preservation of the proposed discretization stencils are independent of the convergence acceleration technique which can be set to multigrid, preconditioning, Jacobian-free Newton-Krylov, block-implicit, etc. Thus, the current paper also offers the first implicit integration of the time-accurate Euler equations that is positivity-preserving in the strict sense (that is, the density and temperature are guaranteed to remain positive). This is in contrast to all previous positivity-preserving implicit methods which only guaranteed the positivity of the density, not of the temperature or pressure. Several stringent reacting and inert test cases confirm the positivity-preserving property of the proposed method as well as its higher resolution and higher computational efficiency over other second-order and third-order implicit temporal discretization strategies.

Acetylcholine but not adenosine triggers preconditioning through PI3-kinase and a tyrosine kinase.

PubMed

Qin, Qining; Downey, James M; Cohen, Michael V

2003-02-01

Adenosine and acetylcholine (ACh) trigger preconditioning by different signaling pathways. The involvement of phosphatidylinositol 3-kinase (PI3-kinase), a protein tyrosine kinase, and Src family tyrosine kinase in preconditioning was evaluated in isolated rabbit hearts. Either wortmannin (PI3-kinase blocker), genistein (tyrosine kinase blocker), lavendustin A (tyrosine kinase blocker), or 4-amino-5-(4-chlorophenyl)-7-(t-butyl)pyrazolol[3,4-d]pyrimidine (PP2; Src family tyrosine kinase blocker) was given for 15 min to bracket a 5-min infusion of either adenosine or ACh (trigger phase). The hearts then underwent 30 min of regional ischemia. Infarct size for ACh alone was 9.3 +/- 3.5% of the risk zone versus 34.3 +/- 4.1% in controls. All four inhibitors blocked ACh-induced protection. When wortmannin or PP2 was infused only during the 30-min ischemic period (mediator phase), ACh-induced protection was not affected (7.4 +/- 2.1% and 9.7 +/- 1.7% infarction, respectively). Adenosine-triggered protection was not blocked by any of the inhibitors. Therefore, PI3-kinase and at least one protein tyrosine kinase, probably Src kinase, are involved in the trigger phase of ACh-induced, but not adenosine-induced, preconditioning. Neither PI3-kinase nor Src kinase is a mediator of the protection of ACh.

Research report: the effects of hyperbaric oxygen preconditioning on myocardial biomarkers of cardioprotection in patients having coronary artery bypass graft surgery.

PubMed

Jeysen, Zivan Yogaratnam; Gerard, Laden; Levant, Guvendik; Cowen, Mike; Cale, Alex; Griffin, Steve

2011-01-01

We have previously conducted and reported on the primary endpoint of a clinical study which demonstrated that hyperbaric oxygen (HBO2) preconditioning consisting of two 30-minute intervals of 100% oxygen at 2.4 atmospheres absolute (ATA) prior to coronary artery bypass graft (CABG) surgery leads to an improvement in left ventricular stroke work (LVSW) 24 hours following CABG. In that study, 81 patients were randomized to treatment with HBO2 (HBO2; n = 41) or routine treatment (Control Group; n = 40) prior to surgery. The objective of this manuscript is to further report on the result of the exploratory secondary endpoints from that study, specifically the effects of HBO2 preconditioning on biomarkers of myocardial protection. Intraoperative right atrial biopsies were assessed, via an Enzyme Linked ImmunoSorbent Assay (ELISA), for the expression of eNOS and HSP72. In this study, no significant differences were observed between the groups with respect to the quantity of myocardial eNOS and HSP72. However, in the HBO2 Group, following ischemia and reperfusion, the quantities of myocardial eNOS and HSP72 were increased. This suggests that HBO2 preconditioning in this group of patients may be capable of inducing endogenous cardioprotection following ischemic reperfusion injury (IRI).

Conjugate-gradient preconditioning methods for shift-variant PET image reconstruction.

PubMed

Fessler, J A; Booth, S D

1999-01-01

Gradient-based iterative methods often converge slowly for tomographic image reconstruction and image restoration problems, but can be accelerated by suitable preconditioners. Diagonal preconditioners offer some improvement in convergence rate, but do not incorporate the structure of the Hessian matrices in imaging problems. Circulant preconditioners can provide remarkable acceleration for inverse problems that are approximately shift-invariant, i.e., for those with approximately block-Toeplitz or block-circulant Hessians. However, in applications with nonuniform noise variance, such as arises from Poisson statistics in emission tomography and in quantum-limited optical imaging, the Hessian of the weighted least-squares objective function is quite shift-variant, and circulant preconditioners perform poorly. Additional shift-variance is caused by edge-preserving regularization methods based on nonquadratic penalty functions. This paper describes new preconditioners that approximate more accurately the Hessian matrices of shift-variant imaging problems. Compared to diagonal or circulant preconditioning, the new preconditioners lead to significantly faster convergence rates for the unconstrained conjugate-gradient (CG) iteration. We also propose a new efficient method for the line-search step required by CG methods. Applications to positron emission tomography (PET) illustrate the method.

Hypoxia preconditioning protection of corneal stromal cells requires HIF1alpha but not VEGF.

PubMed

Xing, Dongmei; Bonanno, Joseph A

2009-05-18

Hypoxia preconditioning protects corneal stromal cells from stress-induced death. This study determined whether the transcription factor HIF-1alpha (Hypoxia Inducible Factor) is responsible and whether this is promulgated by VEGF (Vascular Endothelial Growth Factor). Cultured bovine stromal cells were preconditioned with hypoxia in the presence of cadmium chloride, a chemical inhibitor of HIF-1alpha, and HIF-1alpha siRNA to test if HIF-1alpha activity is needed for hypoxia preconditioning protection from UV-irradiation induced cell death. TUNEL assay was used to detect cell apoptosis after UV-irradiation. RT-PCR and western blot were used to detect the presence of HIF-1alpha and VEGF in transcriptional and translational levels. During hypoxia (0.5% O2), 5 muM cadmium chloride completely inhibited HIF-1alpha expression and reversed the protection by hypoxia preconditioning. HIF-1alpha siRNA (15 nM) reduced HIF-1alpha expression by 90% and produced a complete loss of protection provided by hypoxia preconditioning. Since VEGF is induced by hypoxia, can be HIF-1alpha dependent, and is often protective, we examined the changes in transcription of VEGF and its receptors after 4 h of hypoxia preconditioning. VEGF and its receptors Flt-1 and Flk-1 are up-regulated after hypoxia preconditioning. However, the transcription and translation of VEGF were paradoxically increased by siHIF-1alpha, suggesting that VEGF expression in stromal cells is not down-stream of HIF-1alpha. These findings demonstrate that hypoxia preconditioning protection in corneal stromal cells requires HIF-1alpha, but that VEGF is not a component of the protection.

The effect of brain death in rat steatotic and non-steatotic liver transplantation with previous ischemic preconditioning.

PubMed

Jiménez-Castro, Mónica B; Meroño, Noelia; Mendes-Braz, Mariana; Gracia-Sancho, Jordi; Martínez-Carreres, Laia; Cornide-Petronio, Maria Eugenia; Casillas-Ramirez, Araní; Rodés, Juan; Peralta, Carmen

2015-01-01

Most liver grafts undergoing transplantation derive from brain dead donors, which may also show hepatic steatosis, being both characteristic risk factors in liver transplantation. Ischemic preconditioning shows benefits when applied in non-brain dead clinical situations like hepatectomies, whereas it has been less promising in the transplantation from brain dead patients. This study examined how brain death affects preconditioned steatotic and non-steatotic liver grafts undergoing transplantation. Steatotic and non-steatotic grafts from non-brain dead and brain dead-donors were cold stored for 6h and then transplanted. After 2, 4, and 16 h of reperfusion, hepatic damage was analysed. In addition, two therapeutic strategies, ischemic preconditioning and/or acetylcholine pre-treatment, and their underlying mechanisms were characterized. Preconditioning benefits in non-brain dead donors were associated with nitric oxide and acetylcholine generation. In brain dead donors, preconditioning generated nitric oxide but did not promote acetylcholine upregulation, and this resulted in inflammation and damage. Acetylcholine treatment in brain dead donors, through PKC, increased antioxidants and reduced lipid peroxidation, nitrotyrosines and neutrophil accumulation, altogether protecting against damage. The combination of acetylcholine and preconditioning conferred stronger protection against damage, oxidative stress and neutrophil accumulation than acetylcholine treatment alone. These superior beneficial effects were due to a selective preconditioning-mediated generation of nitric oxide and regulation of PPAR and TLR4 pathways, which were not observed when acetylcholine was administered alone. Our findings propose the combination of acetylcholine+preconditioning as a feasible and highly protective strategy to reduce the adverse effects of brain death and to ultimately improve liver graft quality. Copyright © 2014 European Association for the Study of the Liver. Published by Elsevier B.V. All rights reserved.

Gadolinium and ruthenium red attenuate remote hind limb preconditioning-induced cardioprotection: possible role of TRP and especially TRPV channels.

PubMed

Randhawa, Puneet Kaur; Jaggi, Amteshwar Singh

2016-08-01

Remote ischemic preconditioning is a well reported therapeutic strategy that induces cardioprotective effects but the underlying intracellular mechanisms have not been widely explored. The current study was designed to investigate the involvement of TRP and especially TRPV channels in remote hind limb preconditioning-induced cardioprotection. Remote hind limb preconditioning stimulus (4 alternate cycles of inflation and deflation of 5 min each) was delivered using a blood pressure cuff tied on the hind limb of the anesthetized rat. Using Langendorff's system, the heart was perfused and subjected to 30-min ischemia and 120-min reperfusion. The myocardial injury was assessed by measuring infarct size, lactate dehydrogenase (LDH), creatine kinase (CK), LVDP, +dp/dtmax, -dp/dtmin, heart rate, and coronary flow rate. Gadolinium, TRP blocker, and ruthenium red, TRPV channel blocker, were employed as pharmacological tools. Remote hind limb preconditioning significantly reduced the infarct size, LDH release, CK release and improved coronary flow rate, hemodynamic parameters including LVDP, +dp/dtmax, -dp/dtmin, and heart rate. However, gadolinium (7.5 and 15 mg kg(-1)) and ruthenium red (4 and 8 mg kg(-1)) significantly attenuated the cardioprotective effects suggesting the involvement of TRP especially TRPV channels in mediating remote hind limb preconditioning-induced cardioprotection. Remote hind limb preconditioning stimulus possibly activates TRPV channels on the heart or sensory nerve fibers innervating the heart to induce cardioprotective effects. Alternatively, remote hind limb preconditioning stimulus may also activate the mechanosensitive TRP and especially TRPV channels on the sensory nerve fibers innervating the skeletal muscles to trigger cardioprotective neurogenic signaling cascade. The cardioprotective effects of remote hind limb preconditioning may be mediated via activation of mechanosensitive TRP and especially TRPV channels.

Giving rheumatology patients online home access to their electronic medical record (EMR): advantages, drawbacks and preconditions according to care providers.

PubMed

van der Vaart, Rosalie; Drossaert, Constance H C; Taal, Erik; van de Laar, Mart A F J

2013-09-01

Technology enables patients home access to their electronic medical record (EMR), via a patient portal. This study aims to analyse (dis)advantages, preconditions and suitable content for this service, according to rheumatology health professionals. A two-phase policy Delphi study was conducted. First, interviews were performed with nurses/nurse practitioners (n = 9) and rheumatologists (n = 13). Subsequently, collected responses were quantified, using a questionnaire among the interviewees. The following advantages of patient home access to the EMR were reported: (1) enhancement of patient participation in treatment, (2) increased knowledge and self-management, (3) improved patient-provider interaction, (4) increased patient safety, and (5) better communication with others. Foreseen disadvantages of the service included: (1) problems with interpretation of data, (2) extra workload, (3) a change in consultation content, and (4) disturbing the patient-provider interaction. Also, the following preconditions emerged from the data: (1) optimal security, (2) no extra record, but a patient-accessible section, (3) no access to clinical notes, and (4) a lag time on the release of lab data. Most respondents reported that data on diagnosis, medication, treatment plan and consultations could be released to patients. On releasing more complex data, such as bodily examinations, lab results and radiological images the opinions differed considerably. Providing patients home access to their medical record might be a valuable next step into patient empowerment and in service towards the patient, provided that security is optimal and content and presentation of data are carefully considered.

40 CFR 1065.518 - Engine preconditioning.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 33 2014-07-01 2014-07-01 false Engine preconditioning. 1065.518... CONTROLS ENGINE-TESTING PROCEDURES Performing an Emission Test Over Specified Duty Cycles § 1065.518 Engine preconditioning. (a) This section applies for engines where measured emissions are affected by prior operation...

GENE EXPRESSION CHANGES AFTER SEIZURE PRECONDITIONING IN THE THREE MAJOR HIPPOCAMPAL CELL LAYERS

PubMed Central

Borges, Karin; Shaw, Renee; Dingledine, Raymond

2008-01-01

Rodents experience hippocampal damage after status epilepticus (SE) mainly in pyramidal cells while sparing the dentate granule cell layer (DGCL). Hippocampal damage was prevented in rats that had been preconditioned by brief seizures on two consecutive days before SE. To identify neuroprotective genes and biochemical pathways changed after preconditioning we compared the effect of preconditioning on gene expression in the CA1 and CA3 pyramidal and DGCLs, harvested by laser capture microscopy. In the DGCL the expression of 632 genes was altered, compared to only 151 and 58 genes in CA1 and CA3 pyramidal cell layers. Most of the differentially expressed genes regulate tissue structure and intra- and extracellular signaling, including neurotransmission. A selective upregulation of energy metabolism transcripts occurred in CA1 pyramidal cells relative to the DGCL. These results reveal a broad transcriptional response of the DGCL to preconditioning, and suggest several mechanisms underlying the neuroprotective effect of preconditioning seizures. PMID:17239605

Analysis of physics-based preconditioning for single-phase subchannel equations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hansel, J. E.; Ragusa, J. C.; Allu, S.

2013-07-01

The (single-phase) subchannel approximations are used throughout nuclear engineering to provide an efficient flow simulation because the computational burden is much smaller than for computational fluid dynamics (CFD) simulations, and empirical relations have been developed and validated to provide accurate solutions in appropriate flow regimes. Here, the subchannel equations have been recast in a residual form suitable for a multi-physics framework. The Eigen spectrum of the Jacobian matrix, along with several potential physics-based preconditioning approaches, are evaluated, and the the potential for improved convergence from preconditioning is assessed. The physics-based preconditioner options include several forms of reduced equations that decouplemore » the subchannels by neglecting crossflow, conduction, and/or both turbulent momentum and energy exchange between subchannels. Eigen-scopy analysis shows that preconditioning moves clusters of eigenvalues away from zero and toward one. A test problem is run with and without preconditioning. Without preconditioning, the solution failed to converge using GMRES, but application of any of the preconditioners allowed the solution to converge. (authors)« less

Accounting for baseline differences and measurement error in the analysis of change over time.

PubMed

Braun, Julia; Held, Leonhard; Ledergerber, Bruno

2014-01-15

If change over time is compared in several groups, it is important to take into account baseline values so that the comparison is carried out under the same preconditions. As the observed baseline measurements are distorted by measurement error, it may not be sufficient to include them as covariate. By fitting a longitudinal mixed-effects model to all data including the baseline observations and subsequently calculating the expected change conditional on the underlying baseline value, a solution to this problem has been provided recently so that groups with the same baseline characteristics can be compared. In this article, we present an extended approach where a broader set of models can be used. Specifically, it is possible to include any desired set of interactions between the time variable and the other covariates, and also, time-dependent covariates can be included. Additionally, we extend the method to adjust for baseline measurement error of other time-varying covariates. We apply the methodology to data from the Swiss HIV Cohort Study to address the question if a joint infection with HIV-1 and hepatitis C virus leads to a slower increase of CD4 lymphocyte counts over time after the start of antiretroviral therapy. Copyright © 2013 John Wiley & Sons, Ltd.

Thermal preconditioning of mountain permafrost towards instability

NASA Astrophysics Data System (ADS)

Hauck, Christian; Etzelmüller, Bernd; Hilbich, Christin; Isaksen, Ketil; Mollaret, Coline; Pellet, Cécile; Westermann, Sebastian

2017-04-01

Warming permafrost has been detected worldwide in recent years and is projected to continue during the next century as shown in many modelling studies from the polar and mountain regions. In mountain regions, this can lead to potentially hazardous impacts on short time-scales by an increased tendency for slope instabilities. However, the time scale of permafrost thaw and the role of the ice content for determining the strength and rate of permafrost warming and degradation (= development of talik) are still unclear, especially in highly heterogeneous terrain. Observations of permafrost temperatures near the freezing point show complex inter-annual responses to climate forcing due to latent heat effects during thawing and the influence of the snow-cover, which is formed and modulated by highly non-linear processes itself. These effects are complicated by 3-dimensional hydrological processes and interactions between snow melt, infiltration and drainage which may also play an important role in the triggering of mass movements in steep permafrost slopes. In this contribution we demonstrate for the first time a preconditioning effect within near-surface layers in mountain permafrost that causes non-linear degradation and accelerates permafrost thaw. We hypothesise that an extreme regional or global temperature anomaly, such as the Central European summers 2003 and 2015 or the Northern European summers 2006 and 2014, will enhance permafrost degradation if the active layer and the top of the permafrost layer are already preconditioned, i.e. have reduced latent heat content. This preconditioning can already be effectuated by a singular warm year, leading to exceptionally strong melting of the ground ice in the near-surface layers. On sloping terrain and in a context of quasi-continuous atmospheric warming, this ice-loss can be considered as irreversible, as a large part of the melted water will drain/evaporate during the process, and the build-up of an equivalent amount of ice in following cold years does not happen on similar time-scales as the melting. Joint thermal and geophysical observations from permafrost sites in the Swiss Alps and Scandinavia suggest that the above process applies mostly to sites with low to intermediate ice contents, where singular anomalies can lead to sustained ice loss even at larger depths.

DEVELOPMENT OF LOW-DIFFUSION FLUX-SPLITTING METHODS FOR DENSE GAS-SOLID FLOWS

EPA Science Inventory

The development of a class of low-diffusion upwinding methods for computing dense gas-solid flows is presented in this work. An artificial compressibility/low-Mach preconditioning strategy is developed for a hyperbolic two-phase flow equation system consisting of separate solids ...

AMP-activated protein kinase (AMPK)-induced preconditioning in primary cortical neurons involves activation of MCL-1.

PubMed

Anilkumar, Ujval; Weisová, Petronela; Düssmann, Heiko; Concannon, Caoimhín G; König, Hans-Georg; Prehn, Jochen H M

2013-03-01

Neuronal preconditioning is a phenomenon where a previous exposure to a sub-lethal stress stimulus increases the resistance of neurons towards a second, normally lethal stress stimulus. Activation of the energy stress sensor, AMP-activated protein kinase (AMPK) has been shown to contribute to the protective effects of ischaemic and mitochondrial uncoupling-induced preconditioning in neurons, however, the molecular basis of AMPK-mediated preconditioning has been less well characterized. We investigated the effect of AMPK preconditioning using 5-aminoimidazole-4-carboxamide riboside (AICAR) in a model of NMDA-mediated excitotoxic injury in primary mouse cortical neurons. Activation of AMPK with low concentrations of AICAR (0.1 mM for 2 h) induced a transient increase in AMPK phosphorylation, protecting neurons against NMDA-induced excitotoxicity. Analysing potential targets of AMPK activation, demonstrated a marked increase in mRNA expression and protein levels of the anti-apoptotic BCL-2 family protein myeloid cell leukaemia sequence 1 (MCL-1) in AICAR-preconditioned neurons. Interestingly, over-expression of MCL-1 protected neurons against NMDA-induced excitotoxicity while MCL-1 gene silencing abolished the effect of AICAR preconditioning. Monitored intracellular Ca²⁺ levels during NMDA excitation revealed that MCL-1 over-expressing neurons exhibited improved bioenergetics and markedly reduced Ca²⁺ elevations, suggesting a potential mechanism through which MCL-1 confers neuroprotection. This study identifies MCL-1 as a key effector of AMPK-induced preconditioning in neurons. © 2012 International Society for Neurochemistry.

Effect of ozone oxidative preconditioning in preventing early radiation-induced lung injury in rats

PubMed Central

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. PMID:23969972

Assessing the feasibility of community health insurance in Uganda: A mixed-methods exploratory analysis.

PubMed

Biggeri, M; Nannini, M; Putoto, G

2018-03-01

Community health insurance (CHI) aims to provide financial protection and facilitate health care access among poor rural populations. Given common operational challenges that hamper the full development of the scheme, there is need to undertake systematic feasibility studies. These are scarce in the literature and usually they do not provide a comprehensive analysis of the local context. The present research intends to adopt a mixed-methods approach to assess ex-ante the feasibility of CHI. In particular, eight preconditions are proposed to inform the viability of introducing the micro insurance. A case study located in rural northern Uganda is presented to test the effectiveness of the mixed-methods procedure for the feasibility purpose. A household survey covering 180 households, 8 structured focus group discussions, and 40 key informant interviews were performed between October and December 2016 in order to provide a complete and integrated analysis of the feasibility preconditions. Through the data collected at the household level, the population health seeking behaviours and the potential insurance design were examined; econometric analyses were carried out to investigate the perception of health as a priority need and the willingness to pay for the scheme. The latter component, in particular, was analysed through a contingent valuation method. The results validated the relevant feasibility preconditions. Econometric estimates demonstrated that awareness of catastrophic health expenditures and the distance to the hospital play a critical influence on household priorities and willingness to pay. Willingness is also significantly affected by socio-economic status and basic knowledge of insurance principles. Overall, the mixed-methods investigation showed that a comprehensive feasibility analysis can shape a viable CHI model to be implemented in the local context. Copyright © 2018 Elsevier Ltd. All rights reserved.

Increased Agrobacterium-mediated transformation and rooting efficiencies in canola (Brassica napus L.) from hypocotyl segment explants

NASA Technical Reports Server (NTRS)

Cardoza, V.; Stewart, C. N.

2003-01-01

An efficient protocol for the production of transgenic Brassica napus cv. Westar plants was developed by optimizing two important parameters: preconditioning time and co-cultivation time. Agrobacterium tumefaciens-mediated transformation was performed using hypocotyls as explant tissue. Two variants of a green fluorescent protein (GFP)-encoding gene--mGFP5-ER and eGFP--both under the constitutive expression of the cauliflower mosaic virus 35S promoter, were used for the experiments. Optimizing the preconditioning time to 72 h and co-cultivation time with Agrobacterium to 48 h provided the increase in the transformation efficiency from a baseline of 4% to 25%. With mGFP5-ER, the transformation rate was 17% and with eGFP it was 25%. Transgenic shoots were selected on 200 mg/l kanamycin. Rooting efficiency was 100% on half-strength Murashige and Skoog medium with 10 g/l sucrose and 0.5 mg/l indole butyric acid in the presence of kanamycin.

40 CFR 92.125 - Pre-test procedures and preconditioning.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 20 2014-07-01 2013-07-01 true Pre-test procedures and preconditioning... PROGRAMS (CONTINUED) CONTROL OF AIR POLLUTION FROM LOCOMOTIVES AND LOCOMOTIVE ENGINES Test Procedures § 92.125 Pre-test procedures and preconditioning. (a) Locomotive testing. (1) Determine engine lubricating...

An iterative solver for the 3D Helmholtz equation

NASA Astrophysics Data System (ADS)

Belonosov, Mikhail; Dmitriev, Maxim; Kostin, Victor; Neklyudov, Dmitry; Tcheverda, Vladimir

2017-09-01

We develop a frequency-domain iterative solver for numerical simulation of acoustic waves in 3D heterogeneous media. It is based on the application of a unique preconditioner to the Helmholtz equation that ensures convergence for Krylov subspace iteration methods. Effective inversion of the preconditioner involves the Fast Fourier Transform (FFT) and numerical solution of a series of boundary value problems for ordinary differential equations. Matrix-by-vector multiplication for iterative inversion of the preconditioned matrix involves inversion of the preconditioner and pointwise multiplication of grid functions. Our solver has been verified by benchmarking against exact solutions and a time-domain solver.

Performance of a parallel thermal-hydraulics code TEMPEST

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fann, G.I.; Trent, D.S.

The authors describe the parallelization of the Tempest thermal-hydraulics code. The serial version of this code is used for production quality 3-D thermal-hydraulics simulations. Good speedup was obtained with a parallel diagonally preconditioned BiCGStab non-symmetric linear solver, using a spatial domain decomposition approach for the semi-iterative pressure-based and mass-conserved algorithm. The test case used here to illustrate the performance of the BiCGStab solver is a 3-D natural convection problem modeled using finite volume discretization in cylindrical coordinates. The BiCGStab solver replaced the LSOR-ADI method for solving the pressure equation in TEMPEST. BiCGStab also solves the coupled thermal energy equation. Scalingmore » performance of 3 problem sizes (221220 nodes, 358120 nodes, and 701220 nodes) are presented. These problems were run on 2 different parallel machines: IBM-SP and SGI PowerChallenge. The largest problem attains a speedup of 68 on an 128 processor IBM-SP. In real terms, this is over 34 times faster than the fastest serial production time using the LSOR-ADI solver.« less

Solution of the within-group multidimensional discrete ordinates transport equations on massively parallel architectures

NASA Astrophysics Data System (ADS)

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 thousands of processors. The PGS method does outperform SI DSA for the periodic heterogeneous layers (PHL) configuration problems. Although this demonstrates a relative strength/weakness between the two methods, the practicality of these problems is much less, further limiting instances where it would be beneficial to select ITMM over SI DSA. The results strongly indicate a need for a robust, stable, and efficient acceleration method (or preconditioner for PGMRES). The spatial multigrid (SMG) method is currently incomplete in that it does not work for all cases considered and does not effectively improve the convergence rate for all values of scattering ratio c or cell dimension h. Nevertheless, it does display the desired trend for highly scattering, optically thin problems. That is, it tends to lower the rate of growth of number of iterations with increasing number of processes, P, while not increasing the number of additional operations per iteration to the extent that the total execution time of the rapidly converging accelerated iterations exceeds that of the slower unaccelerated iterations. A predictive parallel performance model has been developed for the PBJ method. Timing tests were performed such that trend lines could be fitted to the data for the different components and used to estimate the execution times. Applied to the weak scaling results, the model notably underestimates construction time, but combined with a slight overestimation in iterative solution time, the model predicts total execution time very well for large P. It also does a decent job with the strong scaling results, closely predicting the construction time and time per iteration, especially as P increases. Although not shown to be competitive up to 1,024 processing elements with the current state of the art, the parallelized ITMM exhibits promising scaling trends. Ultimately, compared to the KBA method, the parallelized ITMM may be found to be a very attractive option for transport calculations spatially decomposed over several tens of thousands of processes. Acceleration/preconditioning of the parallelized ITMM once developed will improve the convergence rate and improve its competitiveness. (Abstract shortened by UMI.)

Implicit solvers for unstructured meshes

NASA Technical Reports Server (NTRS)

Venkatakrishnan, V.; Mavriplis, Dimitri J.

1991-01-01

Implicit methods were developed and tested for unstructured mesh computations. The approximate system which arises from the Newton linearization of the nonlinear evolution operator is solved by using the preconditioned GMRES (Generalized Minimum Residual) technique. Three different preconditioners were studied, namely, the incomplete LU factorization (ILU), block diagonal factorization, and the symmetric successive over relaxation (SSOR). The preconditioners were optimized to have good vectorization properties. SSOR and ILU were also studied as iterative schemes. The various methods are compared over a wide range of problems. Ordering of the unknowns, which affects the convergence of these sparse matrix iterative methods, is also studied. Results are presented for inviscid and turbulent viscous calculations on single and multielement airfoil configurations using globally and adaptively generated meshes.

PRIM: An Efficient Preconditioning Iterative Reweighted Least Squares Method for Parallel Brain MRI Reconstruction.

PubMed

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.

40 CFR 85.2218 - Preconditioned idle test-EPA 91.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 18 2011-07-01 2011-07-01 false Preconditioned idle test-EPA 91. 85.2218 Section 85.2218 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS... Tests § 85.2218 Preconditioned idle test—EPA 91. (a) General requirements—(1) Exhaust gas sampling...

40 CFR 86.1232-96 - Vehicle preconditioning.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 20 2012-07-01 2012-07-01 false Vehicle preconditioning. 86.1232-96... (CONTINUED) CONTROL OF EMISSIONS FROM NEW AND IN-USE HIGHWAY VEHICLES AND ENGINES (CONTINUED) Evaporative... Methanol-Fueled Heavy-Duty Vehicles § 86.1232-96 Vehicle preconditioning. (a) Fuel tank cap(s) of gasoline...

40 CFR 85.2218 - Preconditioned idle test-EPA 91.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 19 2012-07-01 2012-07-01 false Preconditioned idle test-EPA 91. 85... Tests § 85.2218 Preconditioned idle test—EPA 91. (a) General requirements—(1) Exhaust gas sampling algorithm. The analysis of exhaust gas concentrations begins ten seconds after the applicable test mode...

Adaptive truncation of matrix decompositions and efficient estimation of NMR relaxation distributions

NASA Astrophysics Data System (ADS)

Teal, Paul D.; Eccles, Craig

2015-04-01

The two most successful methods of estimating the distribution of nuclear magnetic resonance relaxation times from two dimensional data are data compression followed by application of the Butler-Reeds-Dawson algorithm, and a primal-dual interior point method using preconditioned conjugate gradient. Both of these methods have previously been presented using a truncated singular value decomposition of matrices representing the exponential kernel. In this paper it is shown that other matrix factorizations are applicable to each of these algorithms, and that these illustrate the different fundamental principles behind the operation of the algorithms. These are the rank-revealing QR (RRQR) factorization and the LDL factorization with diagonal pivoting, also known as the Bunch-Kaufman-Parlett factorization. It is shown that both algorithms can be improved by adaptation of the truncation as the optimization process progresses, improving the accuracy as the optimal value is approached. A variation on the interior method viz, the use of barrier function instead of the primal-dual approach, is found to offer considerable improvement in terms of speed and reliability. A third type of algorithm, related to the algorithm known as Fast iterative shrinkage-thresholding algorithm, is applied to the problem. This method can be efficiently formulated without the use of a matrix decomposition.

Application of preconditioned alternating direction method of multipliers in depth from focal stack

NASA Astrophysics Data System (ADS)

Javidnia, Hossein; Corcoran, Peter

2018-03-01

Postcapture refocusing effect in smartphone cameras is achievable using focal stacks. However, the accuracy of this effect is totally dependent on the combination of the depth layers in the stack. The accuracy of the extended depth of field effect in this application can be improved significantly by computing an accurate depth map, which has been an open issue for decades. To tackle this issue, a framework is proposed based on a preconditioned alternating direction method of multipliers for depth from the focal stack and synthetic defocus application. In addition to its ability to provide high structural accuracy, the optimization function of the proposed framework can, in fact, converge faster and better than state-of-the-art methods. The qualitative evaluation has been done on 21 sets of focal stacks and the optimization function has been compared against five other methods. Later, 10 light field image sets have been transformed into focal stacks for quantitative evaluation purposes. Preliminary results indicate that the proposed framework has a better performance in terms of structural accuracy and optimization in comparison to the current state-of-the-art methods.

Preconditioning results in S-nitrosylation of proteins involved in regulation of mitochondrial energetics and calcium transport.

PubMed

Sun, Junhui; Morgan, Meghan; Shen, Rong-Fong; Steenbergen, Charles; Murphy, Elizabeth

2007-11-26

Nitric oxide has been shown to be an important signaling messenger in ischemic preconditioning (IPC). Accordingly, we investigated whether protein S-nitrosylation occurs in IPC hearts and whether S-nitrosoglutathione (GSNO) elicits similar effects on S-nitrosylation and cardioprotection. Preceding 20 minutes of no-flow ischemia and reperfusion, hearts from C57BL/6J mice were perfused in the Langendorff mode and subjected to the following conditions: (1) control perfusion; (2) IPC; or (3) 0.1 mmol/L GSNO treatment. Compared with control, IPC and GSNO significantly improved postischemic recovery of left ventricular developed pressure and reduced infarct size. IPC and GSNO both significantly increased S-nitrosothiol contents and S-nitrosylation levels of the L-type Ca2+ channel alpha1 subunit in heart membrane fractions. We identified several candidate S-nitrosylated proteins by proteomic analysis following the biotin switch method, including the cardiac sarcoplasmic reticulum Ca2+-ATPase, alpha-ketoglutarate dehydrogenase, and the mitochondrial F1-ATPase alpha1 subunit. The activities of these enzymes were altered in a concentration-dependent manner by GSNO treatment. We further developed a 2D DyLight fluorescence difference gel electrophoresis proteomic method that used DyLight fluors and a modified biotin switch method to identify S-nitrosylated proteins. IPC and GSNO produced a similar pattern of S-nitrosylation modification and cardiac protection against ischemia/reperfusion injury, suggesting that protein S-nitrosylation may play an important cardioprotective role in heart.

Hypoxia preconditioning increases survival and decreases expression of Toll-like receptor 4 in pulmonary artery endothelial cells exposed to lipopolysaccharide.

PubMed

Ali, Irshad; Nanchal, Rahul; Husnain, Fouad; Audi, Said; Konduri, G Ganesh; Densmore, John C; Medhora, Meetha; Jacobs, Elizabeth R

2013-09-01

Abstract Pulmonary or systemic infections and hypoxemic respiratory failure are among the leading causes of admission to intensive care units, and these conditions frequently exist in sequence or in tandem. Inflammatory responses to infections are reproduced by lipopolysaccharide (LPS) engaging Toll-like receptor 4 (TLR4). Apoptosis is a hallmark of lung injury in sepsis. This study was conducted to determine whether preexposure to LPS or hypoxia modulated the survival of pulmonary artery endothelial cells (PAECs). We also investigated the role TLR4 receptor expression plays in apoptosis due to these conditions. Bovine PAECs were cultured in hypoxic or normoxic environments and treated with LPS. TLR4 antagonist TAK-242 was used to probe the role played by TLR4 receptors in cell survival. Cell apoptosis and survival were measured by caspase 3 activity and 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) incorporation. TLR4 expression and tumor necrosis factor α (TNF-α) production were also determined. LPS increased caspase 3 activity in a TAK-242-sensitive manner and decreased MTT incorporation. Apoptosis was decreased in PAECs preconditioned with hypoxia prior to LPS exposure. LPS increased TNF-α production, and hypoxic preconditioning blunted it. Hypoxic preconditioning reduced LPS-induced TLR4 messenger RNA and TLR4 protein. TAK-242 decreased to baseline the LPS-stimulated expression of TLR4 messenger RNA regardless of environmental conditions. In contrast, LPS followed by hypoxia substantially increased apoptosis and cell death. In conclusion, protection from LPS-stimulated PAEC apoptosis by hypoxic preconditioning is attributable in part to reduction in TLR4 expression. If these signaling pathways apply to septic patients, they may account for differing sensitivities of individuals to acute lung injury depending on oxygen tensions in PAECs in vivo.

Effects of ischemic preconditioning and iloprost on myocardial ischemia-reperfusion damage in rats.

PubMed

Ay, Yasin; Kara, Ibrahim; Aydin, Cemalettin; Ay, Nuray Kahraman; Teker, Melike Elif; Senol, Serkan; Inan, Bekir; Basel, Halil; Uysal, Omer; Zeybek, Rahmi

2013-01-01

This study investigates the effects of cardiac ischemic preconditioning and iloprost on reperfusion damage in rats with myocardial ischemia/reperfusion. 38 male Wistar Albino rats used in this study were divided into 5 groups. The control group (Group 1) (n=6), ischemia/reperfusion (IR) group (Group 2) (n=8), cardiac ischemic preconditioning (CIP) group (Group 3) (n=8), iloprost (ILO) group (Group 4) (n=8), and cardiac ischemic preconditioning + iloprost (CIP+ILO) group (Group 5) (n=8). Pre-ischemia, 15 minutes post-ischemia, 45 minutes post-reperfusion, mean blood pressure (MBP), and heart rates (HR) were recorded. The rate-pressure product (RPP) was calculated. Post-reperfusion plasma creatine kinase-MB (CK-MB), lactate dehydrogenase (LDH), troponin (cTn) vlaues, and infarct size/area at risk (IS/AAR) were calculated from myocardial tissue samples. Arrhythmia and ST segment elevations were evaluated during the ischemia and reperfusion stages. Although the MBP, HR, RPP values, biochemical parameters of CK-MB and LDH levels, IS/AAR rates, ST segment elevation values were found to be similar in CIP and CIP+ILO groups and the IR and ILO groups (p>0.05), CIP-containing group values had a positively meaningful difference (p<0.05) compared with the IR and ILO group. While mild-moderate findings of damage were observed in Group 3 and Group 5, severely findings of damage were releaved in Group 2 and Group 4. The arrhythmia score of the ILO group was meaningfully lower (F: 41.4, p<0.001) than the IR group. We can conclude that the effects of myocardial reperfusion damage can be reduced by cardiac ischemic preconditioning, intravenous iloprost reduced the incidence of ventricular arrhythmia associated with reperfusion, and its use with CIP caused no additional changes.

Comparison of bacterial attachment to platelet bags with and without preconditioning with plasma.

PubMed

Loza-Correa, M; Kalab, M; Yi, Q-L; Eltringham-Smith, L J; Sheffield, W P; Ramirez-Arcos, S

2017-07-01

Canadian Blood Services produces apheresis and buffy coat pooled platelet concentrates (PCs) stored in bags produced by two different manufacturers (A and B, respectively), both made of polyvinyl chloride-butyryl trihexyl citrate. This study was aimed at comparing Staphylococcus epidermidis adhesion to the inner surface of both bag types in the presence or absence of plasma factors. Sets (N = 2-6) of bags type A and B were left non-coated (control) or preconditioned with platelet-rich, platelet-poor or defibrinated plasma (PRP, PPP and DefibPPP, respectively). Each bag was inoculated with a 200-ml S. epidermidis culture adjusted to 0·5 colony-forming units/ml. Bags were incubated under platelet storage conditions for 7 days. After culture removal, bacteria attached to the plastic surface were either dislodged by sonication for bacterial quantification or examined in situ by scanning electron microscopy (SEM). Higher bacterial adhesion was observed to preconditioned PC bags than control containers for both bag types (P < 0·0001). Bacterial attachment to preconditioned bags was confirmed by SEM. Bacteria adhered equally to both types of containers in the presence of PRP, PPP and DefibPPP residues (P > 0·05). By contrast, a significant increase in bacterial adherence was observed to type A bags compared with type B bags in the absence of plasma (P < 0·05) [Correction added on 16 June 2017, after first online publication: this sentence has been corrected]. The ability of S. epidermidis to adhere to preconditioned platelet collection bags depends on the presence of plasma factors. Future efforts should be focused on reducing plasma proteins' attachment to platelet storage containers to decrease subsequent bacterial adhesion. © 2017 International Society of Blood Transfusion.

EXPOSURE METHOD CONSIDERATIONS FOR MEASURING VITELLOGENIN EXPRESSION IN LARVAL AND MALE FATHEAD MINNOWS (PIMEPHALES PROMELAS)

EPA Science Inventory

Our laboratory has developed methods for measuring the expression of the vitellogenin (Vg) gene in larval and adult male fathead minnows. During this development we found several conditions that affect background Vg levels and we observed preconditions for the expression of this...

40 CFR 51.100 - Definitions.

Code of Federal Regulations, 2011 CFR

2011-07-01

... inventory techniques similar to those described in the “AEROS Manual series, Vol. II AEROS User's Manual... emission control systems, at such time as the Administrator determines that such programs are feasible and... authority. (3) As a precondition to excluding these compounds as VOC or at any time thereafter, the...

40 CFR 51.100 - Definitions.

Code of Federal Regulations, 2013 CFR

2013-07-01

... inventory techniques similar to those described in the “AEROS Manual series, Vol. II AEROS User's Manual... emission control systems, at such time as the Administrator determines that such programs are feasible and... precondition to excluding these compounds as VOC or at any time thereafter, the enforcement authority may...

40 CFR 51.100 - Definitions.

Code of Federal Regulations, 2012 CFR

2012-07-01

... inventory techniques similar to those described in the “AEROS Manual series, Vol. II AEROS User's Manual... emission control systems, at such time as the Administrator determines that such programs are feasible and... authority. (3) As a precondition to excluding these compounds as VOC or at any time thereafter, the...

40 CFR 51.100 - Definitions.

Code of Federal Regulations, 2014 CFR

2014-07-01

... inventory techniques similar to those described in the “AEROS Manual series, Vol. II AEROS User's Manual... emission control systems, at such time as the Administrator determines that such programs are feasible and... precondition to excluding these compounds as VOC or at any time thereafter, the enforcement authority may...

40 CFR 51.100 - Definitions.

Code of Federal Regulations, 2010 CFR

2010-07-01

... inventory techniques similar to those described in the “AEROS Manual series, Vol. II AEROS User's Manual... emission control systems, at such time as the Administrator determines that such programs are feasible and... authority. (3) As a precondition to excluding these compounds as VOC or at any time thereafter, the...

High-order solution methods for grey discrete ordinates thermal radiative transfer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Maginot, Peter G., E-mail: maginot1@llnl.gov; Ragusa, Jean C., E-mail: jean.ragusa@tamu.edu; Morel, Jim E., E-mail: morel@tamu.edu

This work presents a solution methodology for solving the grey radiative transfer equations that is both spatially and temporally more accurate than the canonical radiative transfer solution technique of linear discontinuous finite element discretization in space with implicit Euler integration in time. We solve the grey radiative transfer equations by fully converging the nonlinear temperature dependence of the material specific heat, material opacities, and Planck function. The grey radiative transfer equations are discretized in space using arbitrary-order self-lumping discontinuous finite elements and integrated in time with arbitrary-order diagonally implicit Runge–Kutta time integration techniques. Iterative convergence of the radiation equation ismore » accelerated using a modified interior penalty diffusion operator to precondition the full discrete ordinates transport operator.« less

High-order solution methods for grey discrete ordinates thermal radiative transfer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Maginot, Peter G.; Ragusa, Jean C.; Morel, Jim E.

This paper presents a solution methodology for solving the grey radiative transfer equations that is both spatially and temporally more accurate than the canonical radiative transfer solution technique of linear discontinuous finite element discretization in space with implicit Euler integration in time. We solve the grey radiative transfer equations by fully converging the nonlinear temperature dependence of the material specific heat, material opacities, and Planck function. The grey radiative transfer equations are discretized in space using arbitrary-order self-lumping discontinuous finite elements and integrated in time with arbitrary-order diagonally implicit Runge–Kutta time integration techniques. Iterative convergence of the radiation equation ismore » accelerated using a modified interior penalty diffusion operator to precondition the full discrete ordinates transport operator.« less

High-order solution methods for grey discrete ordinates thermal radiative transfer

DOE PAGES

Maginot, Peter G.; Ragusa, Jean C.; Morel, Jim E.

2016-09-29

This paper presents a solution methodology for solving the grey radiative transfer equations that is both spatially and temporally more accurate than the canonical radiative transfer solution technique of linear discontinuous finite element discretization in space with implicit Euler integration in time. We solve the grey radiative transfer equations by fully converging the nonlinear temperature dependence of the material specific heat, material opacities, and Planck function. The grey radiative transfer equations are discretized in space using arbitrary-order self-lumping discontinuous finite elements and integrated in time with arbitrary-order diagonally implicit Runge–Kutta time integration techniques. Iterative convergence of the radiation equation ismore » accelerated using a modified interior penalty diffusion operator to precondition the full discrete ordinates transport operator.« less

Acoustic and elastic waveform inversion best practices

NASA Astrophysics Data System (ADS)

Modrak, Ryan T.

Reaching the global minimum of a waveform misfit function requires careful choices about the nonlinear optimization, preconditioning and regularization methods underlying an inversion. Because waveform inversion problems are susceptible to erratic convergence, one or two test cases are not enough to reliably inform such decisions. We identify best practices instead using two global, one regional and four near-surface acoustic test problems. To obtain meaningful quantitative comparisons, we carry out hundreds acoustic inversions, varying one aspect of the implementation at a time. Comparing nonlinear optimization algorithms, we find that L-BFGS provides computational savings over nonlinear conjugate gradient methods in a wide variety of test cases. Comparing preconditioners, we show that a new diagonal scaling derived from the adjoint of the forward operator provides better performance than two conventional preconditioning schemes. Comparing regularization strategies, we find that projection, convolution, Tikhonov regularization, and total variation regularization are effective in different contexts. Besides these issues, reliability and efficiency in waveform inversion depend on close numerical attention and care. Implementation details have a strong effect on computational cost, regardless of the chosen material parameterization or nonlinear optimization algorithm. Building on the acoustic inversion results, we carry out elastic experiments with four test problems, three objective functions, and four material parameterizations. The choice of parameterization for isotropic elastic media is found to be more complicated than previous studies suggests, with "wavespeed-like'' parameters performing well with phase-based objective functions and Lame parameters performing well with amplitude-based objective functions. Reliability and efficiency can be even harder to achieve in transversely isotropic elastic inversions because rotation angle parameters describing fast-axis direction are difficult to recover. Using Voigt or Chen-Tromp parameters avoids the need to include rotation angles explicitly and provides an effective strategy for anisotropic inversion. The need for flexible and portable workflow management tools for seismic inversion also poses a major challenge. In a final chapter, the software used to the carry out the above experiments is described and instructions for reproducing experimental results are given.

Spectral multigrid methods for elliptic equations 2

NASA Technical Reports Server (NTRS)

Zang, T. A.; Wong, Y. S.; Hussaini, M. Y.

1983-01-01

A detailed description of spectral multigrid methods is provided. This includes the interpolation and coarse-grid operators for both periodic and Dirichlet problems. The spectral methods for periodic problems use Fourier series and those for Dirichlet problems are based upon Chebyshev polynomials. An improved preconditioning for Dirichlet problems is given. Numerical examples and practical advice are included.

Tackling bioactive glass excessive in vitro bioreactivity: Preconditioning approaches for cell culture tests.

PubMed

Ciraldo, Francesca E; Boccardi, Elena; Melli, Virginia; Westhauser, Fabian; Boccaccini, Aldo R

2018-05-21

Bioactive glasses (BGs) are being increasingly considered for biomedical applications in bone and soft tissue replacement approaches thanks to their ability to form strong bonding with tissues. However, due to their high reactivity once in contact with water-based solutions BGs rapidly exchange ions with the surrounding environment leading in most cases to an undesired increase of the pH under static in vitro conditions (due to alkaline ion "burst release"), making difficult or even impossible to perform cell culture studies. Several pre-conditioning treatments have been therefore proposed in laboratories worldwide to limit this problem. This paper presents an overview of the different strategies that have been put forward to pre-treat BG samples to tackle the pH raise issue in order to enable cell biology studies. The paper also discusses the relevant criteria that determine the selection of the optimal pre-treatment depending on the BG composition and morphology (e.g. particles, scaffolds). Bioactive glasses (BGs), since their discovery in 1971 by L.L Hench, have been widely used for bone replacement and repair, and, more recently, they are becoming highly attractive for bone and soft tissue engineering applications. BGs have in fact the ability to form a strong bond with both hard and soft tissues once in contact with biological fluid. The enhanced interaction of BGs with the biological environment is based on their significant surface bioreactivity. This surface effect of BGs is, on the other hand, problematic for cell biology studies by standard (static) cell culture methods: an excessive bioreactivity leads in most cases to a rapid and dramatic increase of the pH of the surrounding medium, which results in cell death and makes cell culture tests on BG samples impossible. The BG research community has been aware of this for many years and numerous pre-treatments have been proposed by different groups worldwide to limit this problem. For the first time, we have reviewed in this paper the variety of surface preconditioning treatments that have been put forward over the years, we provide a summary of such pre-treatments used in laboratory practice, discussing and offering criteria that can be used for the determination of the optimal pre-treatment depending on BG composition and morphology of the sample tested (bulk, particulate, scaffolds). The information and discussion provided in this review should support best research practice when testing bioactive glasses in cell culture. Copyright © 2018 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

On conjugate gradient type methods and polynomial preconditioners for a class of complex non-Hermitian matrices

NASA Technical Reports Server (NTRS)

Freund, Roland

1988-01-01

Conjugate gradient type methods are considered for the solution of large linear systems Ax = b with complex coefficient matrices of the type A = T + i(sigma)I where T is Hermitian and sigma, a real scalar. Three different conjugate gradient type approaches with iterates defined by a minimal residual property, a Galerkin type condition, and an Euclidian error minimization, respectively, are investigated. In particular, numerically stable implementations based on the ideas behind Paige and Saunder's SYMMLQ and MINRES for real symmetric matrices are proposed. Error bounds for all three methods are derived. It is shown how the special shift structure of A can be preserved by using polynomial preconditioning. Results on the optimal choice of the polynomial preconditioner are given. Also, some numerical experiments for matrices arising from finite difference approximations to the complex Helmholtz equation are reported.

Sensory Preconditioning in Newborn Rabbits: From Common to Distinct Odor Memories

ERIC Educational Resources Information Center

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…

40 CFR 85.2220 - Preconditioned two speed idle test-EPA 91.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 18 2010-07-01 2010-07-01 false Preconditioned two speed idle test-EPA... Warranty Short Tests § 85.2220 Preconditioned two speed idle test—EPA 91. (a) General requirements—(1...-speed mode followed immediately by a first-chance idle mode. (ii) The second-chance test as described...

40 CFR 85.2220 - Preconditioned two speed idle test-EPA 91.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 18 2011-07-01 2011-07-01 false Preconditioned two speed idle test-EPA... Warranty Short Tests § 85.2220 Preconditioned two speed idle test—EPA 91. (a) General requirements—(1...-speed mode followed immediately by a first-chance idle mode. (ii) The second-chance test as described...

Neuroprotective effects of ischemic preconditioning on hippocampal CA1 pyramidal neurons through maintaining calbindin D28k immunoreactivity following subsequent transient cerebral ischemia

PubMed Central

Kim, In Hye; Jeon, Yong Hwan; Lee, Tae-Kyeong; Cho, Jeong Hwi; Lee, Jae-Chul; Park, Joon Ha; Ahn, Ji Hyeon; Shin, Bich-Na; Kim, Yang Hee; Hong, Seongkweon; Yan, Bing Chun; Won, Moo-Ho; Lee, Yun Lyul

2017-01-01

Ischemic preconditioning elicited by a non-fatal brief occlusion of blood flow has been applied for an experimental therapeutic strategy against a subsequent fatal ischemic insult. In this study, we investigated the neuroprotective effects of ischemic preconditioning (2-minute transient cerebral ischemia) on calbindin D28k immunoreactivity in the gerbil hippocampal CA1 area following a subsequent fatal transient ischemic insult (5-minute transient cerebral ischemia). A large number of pyramidal neurons in the hippocampal CA1 area died 4 days after 5-minute transient cerebral ischemia. Ischemic preconditioning reduced the death of pyramidal neurons in the hippocampal CA1 area. Calbindin D28k immunoreactivity was greatly attenuated at 2 days after 5-minute transient cerebral ischemia and it was hardly detected at 5 days post-ischemia. Ischemic preconditioning maintained calbindin D28k immunoreactivity after transient cerebral ischemia. These findings suggest that ischemic preconditioning can attenuate transient cerebral ischemia-caused damage to the pyramidal neurons in the hippocampal CA1 area through maintaining calbindin D28k immunoreactivity. PMID:28761424

S{sub 2}SA preconditioning for the S{sub n} equations with strictly non negative spatial discretization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bruss, D. E.; Morel, J. E.; Ragusa, J. C.

2013-07-01

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{sub 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 amore » linear diffusion equation has important implications for preconditioning the S{sub n} equations with a strictly non negative spatial discretization in multiple dimensions. (authors)« less

Remote ischemic preconditioning with a specialized protocol activates the non-neuronal cardiac cholinergic system and increases ATP content in the heart.

PubMed

Oikawa, Shino; Mano, Asuka; Takahashi, Rina; Kakinuma, Yoshihiko

2015-11-01

Ischemic preconditioning (IPC) renders the targeted organ resistant to prolonged ischemic insults, leading to organoprotection. Among several means to achieve IPC, we reported that remote ischemic preconditioning (RIPC) activates the non-neuronal cardiac cholinergic system (NNCCS) to accelerate de novo ACh synthesis in cardiomyocytes. In the current study, we aimed to optimize a specific protocol to most efficiently activate NNCCS using RIPC. In this study, we elucidated that the protocol with 3 min of ischemia repeated three times increased cardiac ChAT expression (139.2 ± 0.4%; P < 0.05) as well as ACh (14.2 ± 2.0× 10(-8) M; P< 0.05) and ATP content (2.13 ± 0.19 μmol/g tissue; P < 0.05) in the heart. Moreover, in the specific protocol, several characteristic responses against energy starvation and for obtaining adequate energy were observed; therefore, it is suggested that RIPC evokes a robust response by the heart to activate NNCCS through the modification of energy metabolism. Copyright © 2015 Elsevier B.V. All rights reserved.

Preconditioning with the traditional Chinese medicine Huang-Lian-Jie-Du-Tang initiates HIF-1α-dependent neuroprotection against cerebral ischemia in rats.

PubMed

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 reserved.

Evidence that the adenosine A3 receptor may mediate the protection afforded by preconditioning in the isolated rabbit heart.

PubMed

Liu, G S; Richards, S C; Olsson, R A; Mullane, K; Walsh, R S; Downey, J M

1994-07-01

Agonists selective for the A1 adenosine receptor mimic the protective effect of ischaemic preconditioning against infarction in the rabbit heart. Unselective adenosine antagonists block this protection but, paradoxically, the A1 adenosine receptor selective antagonist 8-cyclopentyl- 1,3-dipropylxanthine (DPCPX) does not. The aim of this study was to test the hypothesis that the newly described A3 adenosine receptor, which has an agonist profile similar to the A1 receptor but is insensitive to DPCPX, might mediate preconditioning. Isolated rabbit hearts perfused with Krebs buffer experienced 30 min of regional ischaemia followed by 120 min of reperfusion. Infarct size was measured by tetrazolium staining. In control hearts infarction was 32.2(SEM 1.5)% of the risk zone. Preconditioning by 5 min ischaemia and 10 min reperfusion reduced infarct size to 8.8(2.3)%. Replacing the regional ischaemia with 5 min perfusion with 10 microM adenosine or 65 nM N6-[2-(4-aminophenyl)ethyl]adenosine (APNEA), an adenosine A3 receptor agonist, was equally protective. The unselective antagonist 8-p-sulphophenyl theophylline at 100 microM abolished protection by preconditioning, adenosine, and APNEA, but 200 nM DPCPX did not block protection by any of the interventions. Likewise the potent but unselective A3 receptor antagonist 8-(4-carboxyethenylphenyl)-1,3-dipropylxanthine (BW A1433) completely blocked protection from ischaemic preconditioning. Because protection against infarction afforded by ischaemic preconditioning, adenosine, or the A3 receptor agonist APNEA could not be blocked by DPCPX and because the potent A3 receptor antagonist BW A1433 blocked protection from ischaemic preconditioning, these data indicate that the protection of preconditioning is not exclusively mediated by the adenosine A1 receptor in rabbit heart and could involve the A3 receptor.

Scalable algorithms for 3D extended MHD.

NASA Astrophysics Data System (ADS)

Chacon, Luis

2007-11-01

In the modeling of plasmas with extended MHD (XMHD), the challenge is to resolve long time scales while rendering the whole simulation manageable. In XMHD, this is particularly difficult because fast (dispersive) waves are supported, resulting in a very stiff set of PDEs. In explicit schemes, such stiffness results in stringent numerical stability time-step constraints, rendering them inefficient and algorithmically unscalable. In implicit schemes, it yields very ill-conditioned algebraic systems, which are difficult to invert. In this talk, we present recent theoretical and computational progress that demonstrate a scalable 3D XMHD solver (i.e., CPU ˜N, with N the number of degrees of freedom). The approach is based on Newton-Krylov methods, which are preconditioned for efficiency. The preconditioning stage admits suitable approximations without compromising the quality of the overall solution. In this work, we employ optimal (CPU ˜N) multilevel methods on a parabolized XMHD formulation, which renders the whole algorithm scalable. The (crucial) parabolization step is required to render XMHD multilevel-friendly. Algebraically, the parabolization step can be interpreted as a Schur factorization of the Jacobian matrix, thereby providing a solid foundation for the current (and future extensions of the) approach. We will build towards 3D extended MHDootnotetextL. Chac'on, Comput. Phys. Comm., 163 (3), 143-171 (2004)^,ootnotetextL. Chac'on et al., 33rd EPS Conf. Plasma Physics, Rome, Italy, 2006 by discussing earlier algorithmic breakthroughs in 2D reduced MHDootnotetextL. Chac'on et al., J. Comput. Phys. 178 (1), 15- 36 (2002) and 2D Hall MHD.ootnotetextL. Chac'on et al., J. Comput. Phys., 188 (2), 573-592 (2003)

Preconditioned Mixed Spectral Element Methods for Elasticity and Stokes Problems

NASA Technical Reports Server (NTRS)

Pavarino, Luca F.

1996-01-01

Preconditioned iterative methods for the indefinite systems obtained by discretizing the linear elasticity and Stokes problems with mixed spectral elements in three dimensions are introduced and analyzed. The resulting stiffness matrices have the structure of saddle point problems with a penalty term, which is associated with the Poisson ratio for elasticity problems or with stabilization techniques for Stokes problems. The main results of this paper show that the convergence rate of the resulting algorithms is independent of the penalty parameter, the number of spectral elements Nu and mildly dependent on the spectral degree eta via the inf-sup constant. The preconditioners proposed for the whole indefinite system are block-diagonal and block-triangular. Numerical experiments presented in the final section show that these algorithms are a practical and efficient strategy for the iterative solution of the indefinite problems arising from mixed spectral element discretizations of elliptic systems.

Numerical Investigation of a Model Scramjet Combustor Using DDES

NASA Astrophysics Data System (ADS)

Shin, Junsu; Sung, Hong-Gye

2017-04-01

Non-reactive flows moving through a model scramjet were investigated using a delayed detached eddy simulation (DDES), which is a hybrid scheme combining Reynolds averaged Navier-Stokes scheme and a large eddy simulation. The three dimensional Navier-Stokes equations were solved numerically on a structural grid using finite volume methods. An in-house was developed. This code used a monotonic upstream-centered scheme for conservation laws (MUSCL) with an advection upstream splitting method by pressure weight function (AUSMPW+) for space. In addition, a 4th order Runge-Kutta scheme was used with preconditioning for time integration. The geometries and boundary conditions of a scramjet combustor operated by DLR, a German aerospace center, were considered. The profiles of the lower wall pressure and axial velocity obtained from a time-averaged solution were compared with experimental results. Also, the mixing efficiency and total pressure recovery factor were provided in order to inspect the performance of the combustor.

Estimation of Organic Vapor Breakthrough in Humidified Activated Carbon Beds: -Application of Wheeler-Jonas Equation, NIOSH MultiVapor™ and RBT (Relative Breakthrough Time)

PubMed Central

Abiko, Hironobu; Furuse, Mitsuya; Takano, Tsuguo

2016-01-01

Objectives: In the use of activated carbon beds as adsorbents for various types of organic vapor in respirator gas filters, water adsorption of the bed and test gas humidity are expected to alter the accuracy in the estimation of breakthrough data. There is increasing interest in the effects of moisture on estimation methods, and this study has investigated the effects with actual breakthrough data. Methods: We prepared several activated carbon beds preconditioned by equilibration with moisture at different relative humidities (RH=40%-70%) and a constant temperature of 20°C. Then, we measured breakthrough curves in the early region of breakthrough time for 10 types of organic vapor, and investigated the effects of moisture on estimation using the Wheeler-Jonas equation, the simulation software NIOSH MultiVapor™ 2.2.3, and RBT (Relative Breakthrough Time) proposed by Tanaka et al. Results: The Wheeler-Jonas equation showed good accordance with breakthrough curves at all RH in this study. However, the correlation coefficient decreased gradually with increasing RH regardless of type of organic vapor. Estimation of breakthrough time by MultiVapor showed good accordance with experimental data at RH=50%. In contrast, it showed discordance at high RH (>50%). RBTs reported previously were consistent with experimental data at RH=50%. On the other hand, the values of RBT changed markedly with increasing RH. Conclusions: The results of each estimation method showed good accordance with experimental data under comparatively dry conditions (RH≤50%). However, there were discrepancies under high humidified conditions, and further studies are warranted. PMID:27725483

40 CFR 86.153-98 - Vehicle and canister preconditioning; refueling test.

Code of Federal Regulations, 2012 CFR

2012-07-01

... controlled to 50±25 grains of water vapor per pound of dry air) maintained at a nominal flow rate of 0.8 cfm... preconditioning; refueling test. (a) Vehicle and canister preconditioning. Vehicles and vapor storage canisters... at least 1200 canister bed volumes of ambient air (with humidity controlled to 50±25 grains of water...

40 CFR 86.153-98 - Vehicle and canister preconditioning; refueling test.

Code of Federal Regulations, 2011 CFR

2011-07-01

... controlled to 50±25 grains of water vapor per pound of dry air) maintained at a nominal flow rate of 0.8 cfm... preconditioning; refueling test. (a) Vehicle and canister preconditioning. Vehicles and vapor storage canisters... at least 1200 canister bed volumes of ambient air (with humidity controlled to 50±25 grains of water...

40 CFR 86.153-98 - Vehicle and canister preconditioning; refueling test.

Code of Federal Regulations, 2014 CFR

2014-07-01

... controlled to 50±25 grains of water vapor per pound of dry air) maintained at a nominal flow rate of 0.8 cfm... preconditioning; refueling test. (a) Vehicle and canister preconditioning. Vehicles and vapor storage canisters... at least 1200 canister bed volumes of ambient air (with humidity controlled to 50±25 grains of water...

40 CFR 86.153-98 - Vehicle and canister preconditioning; refueling test.

Code of Federal Regulations, 2010 CFR

2010-07-01

... controlled to 50±25 grains of water vapor per pound of dry air) maintained at a nominal flow rate of 0.8 cfm... preconditioning; refueling test. (a) Vehicle and canister preconditioning. Vehicles and vapor storage canisters... at least 1200 canister bed volumes of ambient air (with humidity controlled to 50±25 grains of water...

40 CFR 86.153-98 - Vehicle and canister preconditioning; refueling test.

Code of Federal Regulations, 2013 CFR

2013-07-01

... controlled to 50±25 grains of water vapor per pound of dry air) maintained at a nominal flow rate of 0.8 cfm... preconditioning; refueling test. (a) Vehicle and canister preconditioning. Vehicles and vapor storage canisters... at least 1200 canister bed volumes of ambient air (with humidity controlled to 50±25 grains of water...

Thermal inactivation kinetics of Bacillus coagulans spores in tomato juice.

PubMed

Peng, Jing; Mah, Jae-Hyung; Somavat, Romel; Mohamed, Hussein; Sastry, Sudhir; Tang, Juming

2012-07-01

The thermal characteristics of the spores and vegetative cells of three strains of Bacillus coagulans (ATCC 8038, ATCC 7050, and 185A) in tomato juice were evaluated. B. coagulans ATCC 8038 was chosen as the target microorganism for thermal processing of tomato products due to its spores having the highest thermal resistance among the three strains. The thermal inactivation kinetics of B. coagulans ATCC 8038 spores in tomato juice between 95 and 115°C were determined independently in two different laboratories using two different heating setups. The results obtained from both laboratories were in general agreement, with z-values (z-value is defined as the change in temperature required for a 10-fold reduction of the D-value, which is defined as the time required at a certain temperature for a 1-log reduction of the target microorganisms) of 8.3 and 8.7°C, respectively. The z-value of B. coagulans 185A spores in tomato juice (pH 4.3) was found to be 10.2°C. The influence of environmental factors, including cold storage time, pH, and preconditioning, upon the thermal resistance of these bacterial spores is discussed. The results obtained showed that a storage temperature of 4°C was appropriate for maintaining the viability and thermal resistance of B. coagulans ATCC 8038 spores. Acidifying the pH of tomato juice decreased the thermal resistance of these spores. A 1-h exposure at room temperature was considered optimal for preconditioning B. coagulans ATCC 8038 spores in tomato juice.

The least-squares finite element method for low-mach-number compressible viscous flows

NASA Technical Reports Server (NTRS)

Yu, Sheng-Tao

1994-01-01

The present paper reports the development of the Least-Squares Finite Element Method (LSFEM) for simulating compressible viscous flows at low Mach numbers in which the incompressible flows pose as an extreme. Conventional approach requires special treatments for low-speed flows calculations: finite difference and finite volume methods are based on the use of the staggered grid or the preconditioning technique; and, finite element methods rely on the mixed method and the operator-splitting method. In this paper, however, we show that such difficulty does not exist for the LSFEM and no special treatment is needed. The LSFEM always leads to a symmetric, positive-definite matrix through which the compressible flow equations can be effectively solved. Two numerical examples are included to demonstrate the method: first, driven cavity flows at various Reynolds numbers; and, buoyancy-driven flows with significant density variation. Both examples are calculated by using full compressible flow equations.

A Kronecker product splitting preconditioner for two-dimensional space-fractional diffusion equations

NASA Astrophysics Data System (ADS)

Chen, Hao; Lv, Wen; Zhang, Tongtong

2018-05-01

We study preconditioned iterative methods for the linear system arising in the numerical discretization of a two-dimensional space-fractional diffusion equation. Our approach is based on a formulation of the discrete problem that is shown to be the sum of two Kronecker products. By making use of an alternating Kronecker product splitting iteration technique we establish a class of fixed-point iteration methods. Theoretical analysis shows that the new method converges to the unique solution of the linear system. Moreover, the optimal choice of the involved iteration parameters and the corresponding asymptotic convergence rate are computed exactly when the eigenvalues of the system matrix are all real. The basic iteration is accelerated by a Krylov subspace method like GMRES. The corresponding preconditioner is in a form of a Kronecker product structure and requires at each iteration the solution of a set of discrete one-dimensional fractional diffusion equations. We use structure preserving approximations to the discrete one-dimensional fractional diffusion operators in the action of the preconditioning matrix. Numerical examples are presented to illustrate the effectiveness of this approach.

Characteristics and frequency of large submarine landslides at the western tip of the Gulf of Corinth

NASA Astrophysics Data System (ADS)

Beckers, Arnaud; Hubert-Ferrari, Aurelia; Beck, Christian; Papatheodorou, George; de Batist, Marc; Sakellariou, Dimitris; Tripsanas, Efthymios; Demoulin, Alain

2018-05-01

Coastal and submarine landslides are frequent at the western tip of the Gulf of Corinth, where small to medium failure events (106-107 m3) occur on average every 30-50 years. These landslides trigger tsunamis and consequently represent a significant hazard. We use here a dense grid of high-resolution seismic profiles to realize an inventory of the large mass transport deposits (MTDs) that result from these submarine landslides. Six large mass wasting events are identified, and their associated deposits locally represent 30 % of the sedimentation since 130 ka in the main western basin. In the case of a large MTD of ˜ 1 km3 volume, the simultaneous occurrence of different slope failures is inferred and suggests an earthquake triggering. However, the overall temporal distribution of MTDs would result from the time-dependent evolution of pre-conditioning factors rather than from the recurrence of external triggers. Two likely main pre-conditioning factors are (1) the reloading time of slopes, which varied with the sedimentation rate, and (2) dramatic changes in water depth and water circulation that occurred 10-12 ka ago during the last post-glacial transgression. Such sliding events likely generated large tsunami waves in the whole Gulf of Corinth, possibly larger than those reported in historical sources considering the observed volume of the MTDs.

UPLC-QTOFMS-based metabolomic analysis of the serum of hypoxic preconditioning mice

PubMed Central

Liu, Jie; Zhang, Gang; Chen, Dewei; Chen, Jian; Yuan, Zhi-Bin; Zhang, Er-Long; Gao, Yi-Xing; Xu, Gang; Sun, Bing-Da; Liao, Wenting; Gao, Yu-Qi

2017-01-01

Hypoxic preconditioning (HPC) is well-known to exert a protective effect against hypoxic injury; however, the underlying molecular mechanism remains unclear. The present study utilized a serum metabolomics approach to detect the alterations associated with HPC. In the present study, an animal model of HPC was established by exposing adult BALB/c mice to acute repetitive hypoxia four times. The serum samples were collected by orbital blood sampling. Metabolite profiling was performed using ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-QTOFMS), in conjunction with univariate and multivariate statistical analyses. The results of the present study confirmed that the HPC mouse model was established and refined, suggesting significant differences between the control and HPC groups at the molecular levels. HPC caused significant metabolic alterations, as represented by the significant upregulation of valine, methionine, tyrosine, isoleucine, phenylalanine, lysophosphatidylcholine (LysoPC; 16:1), LysoPC (22:6), linoelaidylcarnitine, palmitoylcarnitine, octadecenoylcarnitine, taurine, arachidonic acid, linoleic acid, oleic acid and palmitic acid, and the downregulation of acetylcarnitine, malate, citrate and succinate. Using MetaboAnalyst 3.0, a number of key metabolic pathways were observed to be acutely perturbed, including valine, leucine and isoleucine biosynthesis, in addition to taurine, hypotaurine, phenylalanine, linoleic acid and arachidonic acid metabolism. The results of the present study provided novel insights into the mechanisms involved in the acclimatization of organisms to hypoxia, and demonstrated the protective mechanism of HPC. PMID:28901489

Progressive exercise preconditioning protects against circulatory shock during experimental heatstroke.

PubMed

Hung, Ching-Hsia; Chang, Nen-Chung; Cheng, Bor-Chih; Lin, Mao-Tsun

2005-05-01

Heat shock protein (HSP) 72 expression protects against arterial hypotension in rat heatstroke. HSP72 can also be induced in multiple organs, including hearts from rats with endurance exercise. We validated the hypothesis that progressive exercise preconditioning may confer cardiovascular protection during heatstroke by inducing the overexpression of HSP72 in multiple organs. To deal with the matter, we assessed the effects of heatstroke on mean arterial pressure, heart rate, cardiac output, stroke volume, total peripheral vascular resistance, colonic temperature, blood gases, and serum or tissue levels of tumor necrosis factor-alpha (TNF-alpha) in urethane-anesthetized rats pretreated without or with progressive exercise training for 1, 2, or 3 weeks. In addition, HSP72 expression in multiple organs was determined in different groups of animals. Heatstroke was induced by exposing the rats to a high blanket temperature (43 degrees C); the moment at which mean arterial pressure decreased from the peak value was taken as the time of heatstroke onset. Previous exercise training for 3 weeks, but not 1 or 2 weeks, conferred significant protection against hyperthermia, arterial hypotension, decreased cardiac output, decreased stroke volume, decreased peripheral vascular resistance, and increased levels of serum or tissue TNF-alpha during heatstroke and correlated with overexpression of HSP72 in multiple organs, including heart, liver, and adrenal gland. However, 10 days after 3 weeks of progressive exercise training, when HSP72 expression in multiple organs returned to basal values, the beneficial effects exerted by 3 weeks of exercise training were no longer observed. These results strongly suggest that HSP72 preconditioning with progressive exercise training protects against hyperthermia, circulatory shock, and TNF-alpha overproduction during heatstroke.

Considerations in detecting CDC select agents under field conditions

NASA Astrophysics Data System (ADS)

Spinelli, Charles; Soelberg, Scott; Swanson, Nathaneal; Furlong, Clement; Baker, Paul

2008-04-01

Surface Plasmon Resonance (SPR) has become a widely accepted technique for real-time detection of interactions between receptor molecules and ligands. Antibody may serve as receptor and can be attached to the gold surface of the SPR device, while candidate analyte fluids contact the detecting antibody. Minute, but detectable, changes in refractive indices (RI) indicate that analyte has bound to the antibody. A decade ago, an inexpensive, robust, miniature and fully integrated SPR chip, called SPREETA, was developed. University of Washington (UW) researchers subsequently developed a portable, temperature-regulated instrument, called SPIRIT, to simultaneously use eight of these three-channel SPREETA chips. A SPIRIT prototype instrument was tested in the field, coupled to a remote reporting system on a surrogate unmanned aerial vehicle (UAV). Two target protein analytes were released sequentially as aerosols with low analyte concentration during each of three flights and were successfully detected and verified. Laboratory experimentation with a more advanced SPIRIT instrument demonstrated detection of very low levels of several select biological agents that might be employed by bioterrorists. Agent detection under field-like conditions is more challenging, especially as analyte concentrations are reduced and complex matricies are introduced. Two different sample preconditioning protocols have been developed for select agents in complex matrices. Use of these preconditioning techniques has allowed laboratory detection in spiked heavy mud of Francisella tularensis at 10 3 CFU/ml, Bacillus anthracis spores at 10 3 CFU/ml, Staphylococcal enterotoxin B (SEB) at 1 ng/ml, and Vaccinia virus (a smallpox simulant) at 10 5 PFU/ml. Ongoing experiments are aimed at simultaneous detection of multiple agents in spiked heavy mud, using a multiplex preconditioning protocol.

Rapamycin preconditioning attenuates transient focal cerebral ischemia/reperfusion injury in mice.

PubMed

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.

Effect of proximal versus distal 50% enterectomy on nutritional parameters in rats preconditioned with a high-fat diet or regular chow.

PubMed

Yanala, Ujwal R; Reidelberger, Roger D; Thompson, Jon S; Shostrom, Valerie K; Carlson, Mark A

2015-11-27

Obesity may protect against the nutritional consequences of short bowel syndrome. We hypothesized that rats preconditioned with an obesogenic diet would have better outcomes after surgical induction of short bowel syndrome compared to rats on regular chow. Rats were fed a high-fat diet or regular rat chow for six months, and then underwent 50% proximal, 50% distal, or sham enterectomy. Food intake, weight, and body composition were monitored before and for 4 weeks after surgery. The high-fat diet consistently produced obesity (>25% body fat). All procedures induced weight loss, but there was no discernable difference between resection vs. sham resection. Rats on the high-fat diet had a greater post-resection loss of body fat compared to rats on chow (36 vs. 26 g, respectively). There was a nonsignificant trend of less lean mass loss in the former compared to the latter rats (16 vs. 33 g, respectively). Enterectomy moderated serum ghrelin, GIP, PPY, insulin, and leptin. Intestinal adaptation was not different between obese vs. non-obese rats. Rats preconditioned with the high-fat diet may have had better retention of lean body mass after a surgical procedure compared to rats on chow. The effect of 50% enterectomy was less than expected.

Time rescaling and pattern formation in biological evolution.

PubMed

Igamberdiev, Abir U

2014-09-01

Biological evolution is analyzed as a process of continuous measurement in which biosystems interpret themselves in the environment resulting in changes of both. This leads to rescaling of internal time (heterochrony) followed by spatial reconstructions of morphology (heterotopy). The logical precondition of evolution is the incompleteness of biosystem's internal description, while the physical precondition is the uncertainty of quantum measurement. The process of evolution is based on perpetual changes in interpretation of information in the changing world. In this interpretation the external biospheric gradients are used for establishment of new features of organization. It is concluded that biological evolution involves the anticipatory epigenetic changes in the interpretation of genetic symbolism which cannot generally be forecasted but can provide canalization of structural transformations defined by the existing organization and leading to predictable patterns of form generation. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Geographical and temporal differences in electric vehicle range due to cabin conditioning energy consumption

NASA Astrophysics Data System (ADS)

Kambly, Kiran; Bradley, Thomas H.

2015-02-01

Electric vehicles (EVs) are vehicles that are propelled by electric motors powered by rechargeable battery. They are generally asserted to have GHG emissions, driveability and life cycle cost benefits over conventional vehicles. Despite this, EVs face significant challenges due to their limited on-board energy storage capacity. In addition to providing energy for traction, the energy storage device operates HVAC systems for cabin conditioning. This results in reduced driving range. The factors such as local ambient temperature, local solar radiation, local humidity, duration and thermal soak have been identified to affect the cabin conditions. In this paper, the development of a detailed system-level approach to HVAC energy consumption in EVs as a function of transient environmental parameters is described. The resulting vehicle thermal comfort model is used to address several questions such as 1) How does day to day environmental conditions affect EV range? 2) How does frequency of EV range change geographically? 3) How does trip start time affect EV range? 4) Under what conditions does cabin preconditioning assist in increasing the EV range? 5) What percentage increase in EV range can be expected due to cabin preconditioning at a given location?

Ischemic preconditioning of the lower extremity attenuates the normal hypoxic increase in pulmonary artery systolic pressure.

PubMed

Foster, Gary P; Westerdahl, Daniel E; Foster, Laura A; Hsu, Jeffrey V; Anholm, James D

2011-12-15

Ischemic pre-condition of an extremity (IPC) induces effects on local and remote tissues that are protective against ischemic injury. To test the effects of IPC on the normal hypoxic increase in pulmonary pressures and exercise performance, 8 amateur cyclists were evaluated under normoxia and hypoxia (13% F(I)O(2)) in a randomized cross-over trial. IPC was induced using an arterial occlusive cuff to one thigh for 5 min followed by deflation for 5 min for 4 cycles. In the control condition, the resting pulmonary artery systolic pressure (PASP) increased from a normoxic value of 25.6±2.3 mmHg to 41.8±7.2 mmHg following 90 min of hypoxia. In the IPC condition, the PASP increased to only 32.4±3.1 mmHg following hypoxia, representing a 72.8% attenuation (p=0.003). No significant difference was detected in cycle ergometer time trial duration between control and IPC conditions with either normoxia or hypoxia. IPC administered prior to hypoxic exposure was associated with profound attenuation of the normal hypoxic increase of pulmonary artery systolic pressure. Published by Elsevier B.V.

The sustainability of healthcare innovations: a concept analysis.

PubMed

Fleiszer, Andrea R; Semenic, Sonia E; Ritchie, Judith A; Richer, Marie-Claire; Denis, Jean-Louis

2015-07-01

To report on an analysis of the concept of the sustainability of healthcare innovations. While there have been significant empirical, theoretical and practical contributions made towards the development and implementation of healthcare innovations, there has been less attention paid to their sustainability. Yet many desired healthcare innovations are not sustained over the long term. There is a need to increase clarity around the concept of innovation sustainability to guide the advancement of knowledge on this topic. Concept analysis. We included literature reviews, theoretical and empirical articles, books and grey literature obtained through database searching (ABI/INFORM, Academic Search Complete, Business Source Complete, CINAHL, Embase, MEDLINE and Web of Science) from 1996-May 2014, reference harvesting and citation searching. We examined sources according to terms and definitions, characteristics, preconditions, outcomes and boundaries to evaluate the maturity of the concept. This concept is partially mature. Healthcare innovation sustainability remains a multi-dimensional, multi-factorial notion that is used inconsistently or ambiguously and takes on different meanings at different times in different contexts. We propose a broad conceptualization that consists of three characteristics: benefits, routinization or institutionalization, and development. We also suggest that sustained innovations are influenced by a variety of preconditions or factors, which are innovation-, context-, leadership- and process-related. Further conceptual development is essential to continue advancing our understanding of the sustainability of healthcare innovations, especially in nursing where this topic remains largely unexplored. © 2015 John Wiley & Sons Ltd.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lin, Paul T.; Shadid, John N.; Tsuji, Paul H.

Here, this study explores the performance and scaling of a GMRES Krylov method employed as a smoother for an algebraic multigrid (AMG) preconditioned Newton- Krylov solution approach applied to a fully-implicit variational multiscale (VMS) nite element (FE) resistive magnetohydrodynamics (MHD) formulation. In this context a Newton iteration is used for the nonlinear system and a Krylov (GMRES) method is employed for the linear subsystems. The efficiency of this approach is critically dependent on the scalability and performance of the AMG preconditioner for the linear solutions and the performance of the smoothers play a critical role. Krylov smoothers are considered inmore » an attempt to reduce the time and memory requirements of existing robust smoothers based on additive Schwarz domain decomposition (DD) with incomplete LU factorization solves on each subdomain. Three time dependent resistive MHD test cases are considered to evaluate the method. The results demonstrate that the GMRES smoother can be faster due to a decrease in the preconditioner setup time and a reduction in outer GMRESR solver iterations, and requires less memory (typically 35% less memory for global GMRES smoother) than the DD ILU smoother.« less

Preconditioning principles for preventing sports injuries in adolescents and children.

PubMed

Dollard, Mark D; Pontell, David; Hallivis, Robert

2006-01-01

Preseason preconditioning can be accomplished well over a 4-week period with a mandatory period of rest as we have discussed. Athletic participation must be guided by a gradual increase of skills performance in the child assessed after a responsible preconditioning program applying physiologic parameters as outlined. Clearly, designing a preconditioning program is a dynamic process when accounting for all the variables in training discussed so far. Despite the physiologic demands of sport and training, we still need to acknowledge the psychologic maturity and welfare of the child so as to ensure that the sport environment is a wholesome and emotionally rewarding experience.

Effects of exercise preconditioning on intestinal ischemia-reperfusion injury.

PubMed

Gokbel, H; Oz, M; Okudan, N; Belviranli, M; Esen, H

2014-01-01

To investigate the effects of exercise preconditioning on oxidative injury in the intestinal tissue of rats. Sixty male Wistar rats were randomly divided into six groups as sham (n = 10), ischemia-reperfusion (n = 10), exercise (n = 10), exercise plus ischemia-reperfusion (n = 10), ischemic preconditioning (n = 10), and ischemic preconditioning plus ischemia-reperfusion groups (n = 10). Tissue levels of malondialdehyde and activities of myeloperoxidase and superoxide dismutase, and serum levels of tumor necrosis factor-alpha and interleukin-6 were measured. Intestinal tissue histopathology was also evaluated by light microscopy. Tumor necrosis factor-alpha concentrations significantly decreased in the exercise group compared to the sham group (p < 0.05). Myeloperoxidase activity significantly increased and superoxide dismutase activity significantly decreased in ischemia-reperfusion group compared to the sham group (p < 0.05). Superoxide dismutase activity in the ischemic preconditioning and ischemic preconditioning plus ischemia-reperfusion groups were significantly higher compared to the ischemia-reperfusion and exercise groups (p < 0.05). Histopathologically, intestinal injury significantly attenuated in the exercise plus ischemia-reperfusion group compared to the ischemia-reperfusion group. The results of the present study indicate that exercise training seems to have a protective role against intestinal ischemia-reperfusion injury (Tab. 3, Fig. 1, Ref. 35).

Benchmarking the Multidimensional Stellar Implicit Code MUSIC

NASA Astrophysics Data System (ADS)

Goffrey, T.; Pratt, J.; Viallet, M.; Baraffe, I.; Popov, M. V.; Walder, R.; Folini, D.; Geroux, C.; Constantino, T.

2017-04-01

We present the results of a numerical benchmark study for the MUltidimensional Stellar Implicit Code (MUSIC) based on widely applicable two- and three-dimensional compressible hydrodynamics problems relevant to stellar interiors. MUSIC is an implicit large eddy simulation code that uses implicit time integration, implemented as a Jacobian-free Newton Krylov method. A physics based preconditioning technique which can be adjusted to target varying physics is used to improve the performance of the solver. The problems used for this benchmark study include the Rayleigh-Taylor and Kelvin-Helmholtz instabilities, and the decay of the Taylor-Green vortex. Additionally we show a test of hydrostatic equilibrium, in a stellar environment which is dominated by radiative effects. In this setting the flexibility of the preconditioning technique is demonstrated. This work aims to bridge the gap between the hydrodynamic test problems typically used during development of numerical methods and the complex flows of stellar interiors. A series of multidimensional tests were performed and analysed. Each of these test cases was analysed with a simple, scalar diagnostic, with the aim of enabling direct code comparisons. As the tests performed do not have analytic solutions, we verify MUSIC by comparing it to established codes including ATHENA and the PENCIL code. MUSIC is able to both reproduce behaviour from established and widely-used codes as well as results expected from theoretical predictions. This benchmarking study concludes a series of papers describing the development of the MUSIC code and provides confidence in future applications.

An optimization-based approach for solving a time-harmonic multiphysical wave problem with higher-order schemes

NASA Astrophysics Data System (ADS)

Mönkölä, Sanna

2013-06-01

This study considers developing numerical solution techniques for the computer simulations of time-harmonic fluid-structure interaction between acoustic and elastic waves. The focus is on the efficiency of an iterative solution method based on a controllability approach and spectral elements. We concentrate on the model, in which the acoustic waves in the fluid domain are modeled by using the velocity potential and the elastic waves in the structure domain are modeled by using displacement. Traditionally, the complex-valued time-harmonic equations are used for solving the time-harmonic problems. Instead of that, we focus on finding periodic solutions without solving the time-harmonic problems directly. The time-dependent equations can be simulated with respect to time until a time-harmonic solution is reached, but the approach suffers from poor convergence. To overcome this challenge, we follow the approach first suggested and developed for the acoustic wave equations by Bristeau, Glowinski, and Périaux. Thus, we accelerate the convergence rate by employing a controllability method. The problem is formulated as a least-squares optimization problem, which is solved with the conjugate gradient (CG) algorithm. Computation of the gradient of the functional is done directly for the discretized problem. A graph-based multigrid method is used for preconditioning the CG algorithm.

Effects of in vitro low oxygen tension preconditioning of adipose stromal cells on their in vivo chondrogenic potential: application in cartilage tissue repair.

PubMed

Portron, Sophie; Merceron, Christophe; Gauthier, Olivier; Lesoeur, Julie; Sourice, Sophie; Masson, Martial; Fellah, Borhane Hakim; Geffroy, Olivier; Lallemand, Elodie; Weiss, Pierre; Guicheux, Jérôme; Vinatier, Claire

2013-01-01

Multipotent stromal cell (MSC)-based regenerative strategy has shown promise for the repair of cartilage, an avascular tissue in which cells experience hypoxia. Hypoxia is known to promote the early chondrogenic differentiation of MSC. The aim of our study was therefore to determine whether low oxygen tension could be used to enhance the regenerative potential of MSC for cartilage repair. MSC from rabbit or human adipose stromal cells (ASC) were preconditioned in vitro in control or chondrogenic (ITS and TGF-β) medium and in 21 or 5% O2. Chondrogenic commitment was monitored by measuring COL2A1 and ACAN expression (real-time PCR). Preconditioned rabbit and human ASC were then incorporated into an Si-HPMC hydrogel and injected (i) into rabbit articular cartilage defects for 18 weeks or (ii) subcutaneously into nude mice for five weeks. The newly formed tissue was qualitatively and quantitatively evaluated by cartilage-specific immunohistological staining and scoring. The phenotype of ASC cultured in a monolayer or within Si-HPMC in control or chondrogenic medium and in 21 or 5% O2 was finally evaluated using real-time PCR. 5% O2 increased the in vitro expression of chondrogenic markers in ASC cultured in induction medium. Cells implanted within Si-HPMC hydrogel and preconditioned in chondrogenic medium formed a cartilaginous tissue, regardless of the level of oxygen. In addition, the 3D in vitro culture of ASC within Si-HPMC hydrogel was found to reinforce the pro-chondrogenic effects of the induction medium and 5% O2. These data together indicate that although 5% O2 enhances the in vitro chondrogenic differentiation of ASC, it does not enhance their in vivo chondrogenesis. These results also highlight the in vivo chondrogenic potential of ASC and their potential value in cartilage repair.

Spherical and hyperspherical harmonics representation of van der Waals aggregates

NASA Astrophysics Data System (ADS)

Lombardi, Andrea; Palazzetti, Federico; Aquilanti, Vincenzo; Grossi, Gaia; Albernaz, Alessandra F.; Barreto, Patricia R. P.; Cruz, Ana Claudia P. S.

2016-12-01

The representation of the potential energy surfaces of atom-molecule or molecular dimers interactions should account faithfully for the symmetry properties of the systems, preserving at the same time a compact analytical form. To this aim, the choice of a proper set of coordinates is a necessary precondition. Here we illustrate a description in terms of hyperspherical coordinates and the expansion of the intermolecular interaction energy in terms of hypersherical harmonics, as a general method for building potential energy surfaces suitable for molecular dynamics simulations of van der Waals aggregates. Examples for the prototypical case diatomic-molecule-diatomic-molecule interactions are shown.

Methodenvergleich zur Bestimmung der hydraulischen Durchlässigkeit

NASA Astrophysics Data System (ADS)

Storz, Katharina; Steger, Hagen; Wagner, Valentin; Bayer, Peter; Blum, Philipp

2017-06-01

Knowing the hydraulic conductivity (K) is a precondition for understanding groundwater flow processes in the subsurface. Numerous laboratory and field methods for the determination of hydraulic conductivity exist, which can lead to significantly different results. In order to quantify the variability of these various methods, the hydraulic conductivity was examined for an industrial silica sand (Dorsilit) using four different methods: (1) grain-size analysis, (2) Kozeny-Carman approach, (3) permeameter tests and (4) flow rate experiments in large-scale tank experiments. Due to the large volume of the artificially built aquifer, the tank experiment results are assumed to be the most representative. Hydraulic conductivity values derived from permeameter tests show only minor deviation, while results of the empirically evaluated grain-size analysis are about one magnitude higher and show great variances. The latter was confirmed by the analysis of several methods for the determination of K-values found in the literature, thus we generally question the suitability of grain-size analyses and strongly recommend the use of permeameter tests.

Preconditioning for the Navier-Stokes equations with finite-rate chemistry

NASA Technical Reports Server (NTRS)

Godfrey, Andrew G.

1993-01-01

The extension of Van Leer's preconditioning procedure to generalized finite-rate chemistry is discussed. Application to viscous flow is begun with the proper preconditioning matrix for the one-dimensional Navier-Stokes equations. Eigenvalue stiffness is resolved and convergence-rate acceleration is demonstrated over the entire Mach-number range from nearly stagnant flow to hypersonic. Specific benefits are realized at the low and transonic flow speeds typical of complete propulsion-system simulations. The extended preconditioning matrix necessarily accounts for both thermal and chemical nonequilibrium. Numerical analysis reveals the possible theoretical improvements from using a preconditioner for all Mach number regimes. Numerical results confirm the expectations from the numerical analysis. Representative test cases include flows with previously troublesome embedded high-condition-number areas. Van Leer, Lee, and Roe recently developed an optimal, analytic preconditioning technique to reduce eigenvalue stiffness over the full Mach-number range. By multiplying the flux-balance residual with the preconditioning matrix, the acoustic wave speeds are scaled so that all waves propagate at the same rate, an essential property to eliminate inherent eigenvalue stiffness. This session discusses a synthesis of the thermochemical nonequilibrium flux-splitting developed by Grossman and Cinnella and the characteristic wave preconditioning of Van Leer into a powerful tool for implicitly solving two and three-dimensional flows with generalized finite-rate chemistry. For finite-rate chemistry, the state vector of unknowns is variable in length. Therefore, the preconditioning matrix extended to generalized finite-rate chemistry must accommodate a flexible system of moving waves. Fortunately, no new kind of wave appears in the system. The only existing waves are entropy and vorticity waves, which move with the fluid, and acoustic waves, which propagate in Mach number dependent directions. The nonequilibrium vibrational energies and species densities in the unknown state vector act strictly as convective waves. The essential concept for extending the preconditioning to generalized chemistry models is determining the differential variables which symmetrize the flux Jacobians. The extension is then straight-forward. This algorithm research effort will be released in a future version of the production level computational code coined the General Aerodynamic Simulation Program (GASP), developed by Walters, Slack, and McGrory.

Effect of hyperbaric oxygen preconditioning on peri-hemorrhagic focal edema and aquaporin-4 expression.

PubMed

Fang, Jinyong; Li, Hongling; Li, Guanglei; Wang, Lichun

2015-08-01

The aim of the present study was to investigate the effect of hyperbaric oxygen preconditioning (HBO-PC) on peri-hemorrhagic focal edema and aquaporin-4 (AQP-4) expression in an experimental intracerebral hemorrhage (ICH) rat model. Sixty-six Sprague Dawley® rats were divided into three groups: The sham-surgery group (SHG; n=6); the control group (A-ICH; n=30), in which the rats were injected with autologous blood; and the experimental HBO-PC group (P-HBO; n=30). The rats underwent brain edema and AQP-4 detection at 5 postoperative time-points (24, 48 and 72 h and 5 and 7 days). The water content in the brain tissues of the A-ICH animals was higher than that in the brain tissues of the SHG rats at each time-point (P<0.05), and the edema in the P-HBO was significantly more severe 24 and 48 h postoperatively than that at 7 days postoperatively (P<0.05). The difference between the P-HBO and A-ICH was significant at 48 and 72 h postoperatively (P<0.05). AQP-4 was expressed in the post-hemorrhagic rat brains of all groups; the SHG animals exhibited low expression, while the A-ICH animals exhibited an increased expression 24 h postoperatively. In the A-ICH, expression peaked at 48 h postoperatively and began to decrease gradually after 72 h. At the 7-day time-point, the expression level in the A-ICH was closer to but still higher than that of the SHG animals (P<0.05). The differences between the P-HBO and A-ICH animals at the postoperative 24-h, 48-h and 7-day time-points were statistically significant (P<0.05). In conclusion, HBO-PC may downregulate AQP-4 expression to reduce the intracerebral edema, thus strengthening tolerance to ICH and protecting the nerves.

Identifying hydrological pre-conditions and rainfall triggers of slope failures for 2014 storm events in the Ialomita Subcarpathians, Romania

NASA Astrophysics Data System (ADS)

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.

Remote ischaemic postconditioning protects the heart during acute myocardial infarction in pigs

PubMed Central

Andreka, Gyorgy; Vertesaljai, Marton; Szantho, Gergely; Font, Gusztav; Piroth, Zsolt; Fontos, Geza; Juhasz, Eszter D; Szekely, Laszlo; Szelid, Zsolt; Turner, Mark S; Ashrafian, Houman; Frenneaux, Michael P

2007-01-01

Background Ischaemic preconditioning results in a reduction in ischaemic‐reperfusion injury to the heart. This beneficial effect is seen both with direct local preconditioning of the myocardium and with remote preconditioning of easily accessible distant non‐vital limb tissue. Ischaemic postconditioning with a comparable sequence of brief periods of local ischaemia, when applied immediately after the ischaemic insult, confers benefits similar to preconditioning. Objective To test the hypothesis that limb ischaemia induces remote postconditioning and hence reduces experimental myocardial infarct size in a validated swine model of acute myocardial infarction. Methods Acute myocardial infarction was induced in 24 pigs with 90 min balloon inflations of the left anterior descending coronary artery. Remote ischaemic postconditioning was induced in 12 of the pigs by four 5 min cycles of blood pressure cuff inflation applied to the lower limb immediately after the balloon deflation. Infarct size was assessed by measuring 72 h creatinine kinase release, MRI scan and immunohistochemical analysis. Results Area under the curve of creatinine kinase release was significantly reduced in the postconditioning group compared with the control group with a 26% reduction in the infarct size (p<0.05). This was confirmed by MRI scanning and immunohistochemical analysis that revealed a 22% (p<0.05) and a 47.52% (p<0.01) relative reduction in the infarct size, respectively. Conclusion Remote ischaemic postconditioning is a simple technique to reduce infarct size without the hazards and logistics of multiple coronary artery balloon inflations. This type of conditioning promises clear clinical potential. PMID:17449499

The anti-apoptotic effect of fluid mechanics preconditioning by cells membrane and mitochondria in rats brain microvascular endothelial cells.

PubMed

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.

A Chebyshev Collocation Method for Moving Boundaries, Heat Transfer, and Convection During Directional Solidification

NASA Technical Reports Server (NTRS)

Zhang, Yiqiang; Alexander, J. I. D.; Ouazzani, J.

1994-01-01

Free and moving boundary problems require the simultaneous solution of unknown field variables and the boundaries of the domains on which these variables are defined. There are many technologically important processes that lead to moving boundary problems associated with fluid surfaces and solid-fluid boundaries. These include crystal growth, metal alloy and glass solidification, melting and name propagation. The directional solidification of semi-conductor crystals by the Bridgman-Stockbarger method is a typical example of such a complex process. A numerical model of this growth method must solve the appropriate heat, mass and momentum transfer equations and determine the location of the melt-solid interface. In this work, a Chebyshev pseudospectra collocation method is adapted to the problem of directional solidification. Implementation involves a solution algorithm that combines domain decomposition, finite-difference preconditioned conjugate minimum residual method and a Picard type iterative scheme.

Flow Applications of the Least Squares Finite Element Method

NASA Technical Reports Server (NTRS)

Jiang, Bo-Nan

1998-01-01

The main thrust of the effort has been towards the development, analysis and implementation of the least-squares finite element method (LSFEM) for fluid dynamics and electromagnetics applications. In the past year, there were four major accomplishments: 1) special treatments in computational fluid dynamics and computational electromagnetics, such as upwinding, numerical dissipation, staggered grid, non-equal order elements, operator splitting and preconditioning, edge elements, and vector potential are unnecessary; 2) the analysis of the LSFEM for most partial differential equations can be based on the bounded inverse theorem; 3) the finite difference and finite volume algorithms solve only two Maxwell equations and ignore the divergence equations; and 4) the first numerical simulation of three-dimensional Marangoni-Benard convection was performed using the LSFEM.

Advancing parabolic operators in thermodynamic MHD models: Explicit super time-stepping versus implicit schemes with Krylov solvers

NASA Astrophysics Data System (ADS)

Caplan, R. M.; Mikić, Z.; Linker, J. A.; Lionello, R.

2017-05-01

We explore the performance and advantages/disadvantages of using unconditionally stable explicit super time-stepping (STS) algorithms versus implicit schemes with Krylov solvers for integrating parabolic operators in thermodynamic MHD models of the solar corona. Specifically, we compare the second-order Runge-Kutta Legendre (RKL2) STS method with the implicit backward Euler scheme computed using the preconditioned conjugate gradient (PCG) solver with both a point-Jacobi and a non-overlapping domain decomposition ILU0 preconditioner. The algorithms are used to integrate anisotropic Spitzer thermal conduction and artificial kinematic viscosity at time-steps much larger than classic explicit stability criteria allow. A key component of the comparison is the use of an established MHD model (MAS) to compute a real-world simulation on a large HPC cluster. Special attention is placed on the parallel scaling of the algorithms. It is shown that, for a specific problem and model, the RKL2 method is comparable or surpasses the implicit method with PCG solvers in performance and scaling, but suffers from some accuracy limitations. These limitations, and the applicability of RKL methods are briefly discussed.

Starch Accumulation in the Bundle Sheaths of C3 Plants: A Possible Pre-Condition for C4 Photosynthesis.

PubMed

Miyake, Hiroshi

2016-05-01

C4 plants have evolved >60 times from their C3 ancestors. C4 photosynthesis requires a set of closely co-ordinated anatomical and biochemical characteristics. However, it is now recognized that the evolution of C4 plants requires fewer changes than had ever been considered, because of the genetic, biochemical and anatomical pre-conditions of C3 ancestors that were recruited into C4 photosynthesis. Therefore, the pre-conditions in C3 plants are now being actively investigated to clarify the evolutionary trajectory from C3 to C4 plants and to engineer C4 traits efficiently into C3 crops. In the present mini review, the anatomical characteristics of C3 and C4 plants are briefly reviewed and the importance of the bundle sheath for the evolution of C4 photosynthesis is described. For example, while the bundle sheath of C3 rice plants accumulates large amounts of starch in the developing leaf blade and at the lamina joint of the mature leaf, the starch sheath function is also observed during leaf development in starch accumulator grasses regardless of photosynthetic type. The starch sheath function of C3 plants is therefore also implicated as a possible pre-condition for the evolution of C4 photosynthesis. The phylogenetic relationships between the types of storage carbohydrates and of photosynthesis need to be clarified in the future. © The Author 2016. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Cerenkov luminescence tomography based on preconditioning orthogonal matching pursuit

NASA Astrophysics Data System (ADS)

Liu, Haixiao; Hu, Zhenhua; Wang, Kun; Tian, Jie; Yang, Xin

2015-03-01

Cerenkov luminescence imaging (CLI) is a novel optical imaging method and has been proved to be a potential substitute of the traditional radionuclide imaging such as positron emission tomography (PET) and single-photon emission computed tomography (SPECT). This imaging method inherits the high sensitivity of nuclear medicine and low cost of optical molecular imaging. To obtain the depth information of the radioactive isotope, Cerenkov luminescence tomography (CLT) is established and the 3D distribution of the isotope is reconstructed. However, because of the strong absorption and scatter, the reconstruction of the CLT sources is always converted to an ill-posed linear system which is hard to be solved. In this work, the sparse nature of the light source was taken into account and the preconditioning orthogonal matching pursuit (POMP) method was established to effectively reduce the ill-posedness and obtain better reconstruction accuracy. To prove the accuracy and speed of this algorithm, a heterogeneous numerical phantom experiment and an in vivo mouse experiment were conducted. Both the simulation result and the mouse experiment showed that our reconstruction method can provide more accurate reconstruction result compared with the traditional Tikhonov regularization method and the ordinary orthogonal matching pursuit (OMP) method. Our reconstruction method will provide technical support for the biological application for Cerenkov luminescence.

TIGAR contributes to ischemic tolerance induced by cerebral preconditioning through scavenging of reactive oxygen species and inhibition of apoptosis

PubMed Central

Zhou, Jun-Hao; Zhang, Tong-Tong; Song, Dan-Dan; Xia, Yun-Fei; Qin, Zheng-Hong; Sheng, Rui

2016-01-01

Previous study showed that TIGAR (TP53-induced glycolysis and apoptosis regulator) protected ischemic brain injury via enhancing pentose phosphate pathway (PPP) flux and preserving mitochondria function. This study was aimed to study the role of TIGAR in cerebral preconditioning. The ischemic preconditioning (IPC) and isoflurane preconditioning (ISO) models were established in primary cultured cortical neurons and in mice. Both IPC and ISO increased TIGAR expression in cortical neurons. Preconditioning might upregulate TIGAR through SP1 transcription factor. Lentivirus mediated knockdown of TIGAR significantly abolished the ischemic tolerance induced by IPC and ISO. ISO also increased TIGAR in mouse cortex and hippocampus and alleviated subsequent brain ischemia-reperfusion injury, while the ischemic tolerance induced by ISO was eliminated with TIGAR knockdown in mouse brain. ISO increased the production of NADPH and glutathione (GSH), and scavenged reactive oxygen species (ROS), while TIGAR knockdown decreased GSH and NADPH production and increased the level of ROS. Supplementation of ROS scavenger NAC and PPP product NADPH effectively rescue the neuronal injury caused by TIGAR deficiency. Notably, TIGAR knockdown inhibited ISO-induced anti-apoptotic effects in cortical neurons. These results suggest that TIGAR participates in the cerebral preconditioning through reduction of ROS and subsequent cell apoptosis. PMID:27256465

Integrity of Cerebellar Fastigial Nucleus Intrinsic Neurons Is Critical for the Global Ischemic Preconditioning

PubMed Central

Regnier-Golanov, Angelique S.; Britz, Gavin W.

2017-01-01

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”. PMID:28934119

Super-low dose endotoxin pre-conditioning exacerbates sepsis mortality.

PubMed

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.

Hypoxia preconditioning increases survival and decreases expression of Toll-like receptor 4 in pulmonary artery endothelial cells exposed to lipopolysaccharide

PubMed Central

Nanchal, Rahul; Audi, Said; Konduri, G. Ganesh; Medhora, Meetha

2013-01-01

Abstract Pulmonary or systemic infections and hypoxemic respiratory failure are among the leading causes of admission to intensive care units, and these conditions frequently exist in sequence or in tandem. Inflammatory responses to infections are reproduced by lipopolysaccharide (LPS) engaging Toll-like receptor 4 (TLR4). Apoptosis is a hallmark of lung injury in sepsis. This study was conducted to determine whether preexposure to LPS or hypoxia modulated the survival of pulmonary artery endothelial cells (PAECs). We also investigated the role TLR4 receptor expression plays in apoptosis due to these conditions. Bovine PAECs were cultured in hypoxic or normoxic environments and treated with LPS. TLR4 antagonist TAK-242 was used to probe the role played by TLR4 receptors in cell survival. Cell apoptosis and survival were measured by caspase 3 activity and 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) incorporation. TLR4 expression and tumor necrosis factor α (TNF-α) production were also determined. LPS increased caspase 3 activity in a TAK-242-sensitive manner and decreased MTT incorporation. Apoptosis was decreased in PAECs preconditioned with hypoxia prior to LPS exposure. LPS increased TNF-α production, and hypoxic preconditioning blunted it. Hypoxic preconditioning reduced LPS-induced TLR4 messenger RNA and TLR4 protein. TAK-242 decreased to baseline the LPS-stimulated expression of TLR4 messenger RNA regardless of environmental conditions. In contrast, LPS followed by hypoxia substantially increased apoptosis and cell death. In conclusion, protection from LPS-stimulated PAEC apoptosis by hypoxic preconditioning is attributable in part to reduction in TLR4 expression. If these signaling pathways apply to septic patients, they may account for differing sensitivities of individuals to acute lung injury depending on oxygen tensions in PAECs in vivo. PMID:24618542

Chronic active Epstein-Barr virus infection with mosquito allergy successfully treated with reduced-intensity unrelated allogeneic bone marrow transplantation in a boy.

PubMed

Matsunaga, Takayuki; Kurosawa, Hidemitsu; Okuya, Mayuko; Nakajima, Daisuke; Hagisawa, Susumu; Sato, Yuya; Fukushima, Keitaro; Sugita, Kenichi; Arisaka, Osamu

2009-03-01

EBV-infected T-/NK cells play an important role in the pathogenesis of mosquito allergy, and the prognosis of most patients with mosquito allergy is poor without proper treatment. We describe a 13-yr-old boy who had CAEBV with mosquito allergy and was successfully treated with BMT from an unrelated donor after reduced-intensity preconditioning. Because combination chemotherapy failed to achieve CR, we performed unrelated BMT to reconstitute normal immunity and eradicate any residual EBV-infected cells. To reduce complications after BMT, we selected a reduced-intensity preconditioning regimen consisting of fludarabine, l-phenylalanine mustard, and antithymocyte Ig instead of a conventional myeloablative preconditioning. Although grade II acute GVHD developed, it was successfully controlled with immunosuppressive therapy. After 27 months, the patient has been well without any signs of CAEBV, and the EBV DNA has been undetectable with real-time PCR analysis. We conclude that RIST from the bone marrow of an unrelated donor is indicated for some patients who have CAEBV that is refractory to chemotherapy and who have no HLA-matched related donors or cord blood as a source of stem cells.

Linear solver performance in elastoplastic problem solution on GPU cluster

NASA Astrophysics Data System (ADS)

Khalevitsky, Yu. V.; Konovalov, A. V.; Burmasheva, N. V.; Partin, A. S.

2017-12-01

Applying the finite element method to severe plastic deformation problems involves solving linear equation systems. While the solution procedure is relatively hard to parallelize and computationally intensive by itself, a long series of large scale systems need to be solved for each problem. When dealing with fine computational meshes, such as in the simulations of three-dimensional metal matrix composite microvolume deformation, tens and hundreds of hours may be needed to complete the whole solution procedure, even using modern supercomputers. In general, one of the preconditioned Krylov subspace methods is used in a linear solver for such problems. The method convergence highly depends on the operator spectrum of a problem stiffness matrix. In order to choose the appropriate method, a series of computational experiments is used. Different methods may be preferable for different computational systems for the same problem. In this paper we present experimental data obtained by solving linear equation systems from an elastoplastic problem on a GPU cluster. The data can be used to substantiate the choice of the appropriate method for a linear solver to use in severe plastic deformation simulations.

Hyperbaric oxygen preconditioning protects against traumatic brain injury at high altitude.

PubMed

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.

Gradient-Based Aerodynamic Shape Optimization Using ADI Method for Large-Scale Problems

NASA Technical Reports Server (NTRS)

Pandya, Mohagna J.; Baysal, Oktay

1997-01-01

A gradient-based shape optimization methodology, that is intended for practical three-dimensional aerodynamic applications, has been developed. It is based on the quasi-analytical sensitivities. The flow analysis is rendered by a fully implicit, finite volume formulation of the Euler equations.The aerodynamic sensitivity equation is solved using the alternating-direction-implicit (ADI) algorithm for memory efficiency. A flexible wing geometry model, that is based on surface parameterization and platform schedules, is utilized. The present methodology and its components have been tested via several comparisons. Initially, the flow analysis for for a wing is compared with those obtained using an unfactored, preconditioned conjugate gradient approach (PCG), and an extensively validated CFD code. Then, the sensitivities computed with the present method have been compared with those obtained using the finite-difference and the PCG approaches. Effects of grid refinement and convergence tolerance on the analysis and shape optimization have been explored. Finally the new procedure has been demonstrated in the design of a cranked arrow wing at Mach 2.4. Despite the expected increase in the computational time, the results indicate that shape optimization, which require large numbers of grid points can be resolved with a gradient-based approach.

40 CFR 85.2219 - Idle test with loaded preconditioning-EPA 91.

Code of Federal Regulations, 2012 CFR

2012-07-01

... concentration of CO plus CO2 falls below 6 percent or the vehicle's engine stalls at any time during the test... the overall maximum test time. (b) Test sequence. (1) The test sequence consists of a first-chance... indicator or road-load controller. (ii) The vehicle is tested in as-received condition with all accessories...

40 CFR 85.2219 - Idle test with loaded preconditioning-EPA 91.

Code of Federal Regulations, 2013 CFR

2013-07-01

... concentration of CO plus CO2 falls below 6 percent or the vehicle's engine stalls at any time during the test... the overall maximum test time. (b) Test sequence. (1) The test sequence consists of a first-chance... indicator or road-load controller. (ii) The vehicle is tested in as-received condition with all accessories...

High-intensity interval training (HIIT) increases insulin-like growth factor-I (IGF-I) in sedentary aging men but not masters' athletes: an observational study.

PubMed

Herbert, Peter; Hayes, Lawrence D; Sculthorpe, Nicholas; Grace, Fergal M

2017-03-01

The aim of this investigation was to examine the impact high-intensity interval training (HIIT) on serum insulin-like growth factor-I (IGF-I) in active compared with sedentary aging men. 22 lifetime sedentary (SED; 62 ± 2 years) and 17 masters' athletes (LEX; 60 ± 5 years) were recruited to the study. As HIIT requires preconditioning exercise in sedentary cohorts, the study required three assessment phases; enrollment (phase A), following preconditioning exercise (phase B), and post-HIIT (phase C). Serum IGF-I was determined by electrochemiluminescent immunoassay. IGF-I was higher in LEX compared to SED at baseline (p = 0.007, Cohen's d = 0.91), and phase B (p = 0.083, Cohen's d = 0.59), with only a small difference at C (p = 0.291, Cohen's d = 0.35). SED experienced a small increase in IGF-I following preconditioning from 13.1 ± 4.7 to 14.2 ± 6.0 μg·dl -1 (p = 0.376, Cohen's d = 0.22), followed by a larger increase post-HIIT (16.9 ± 4.4 μg·dl -1 ), which was significantly elevated compared with baseline (p = 0.002, Cohen's d = 0.85), and post-preconditioning (p = 0.005, Cohen's d = 0.51). LEX experienced a trivial changes in IGF-I from A to B (18.2 ± 6.4 to 17.2 ± 3.7 μg·dl -1 [p = 0.538, Cohen's d = 0.19]), and a small change post-HIIT (18.4 ± 4.1 μg·dl -1 [p = 0.283, Cohen's d = 0.31]). Small increases were observed in fat-free mass in both groups following HIIT (p < 0.05, Cohen's d = 0.32-0.45). In conclusion, HIIT with preconditioning exercise abrogates the age associated difference in IGF-I between SED and LEX, and induces small improvements in fat-free mass in both SED and LEX.

Time-trial Performance in Elite Speed Skaters After Remote Ischemic Preconditioning.

PubMed

Richard, Philippe; Billaut, François

2018-05-10

Speed skating leads to blood-flow restriction and deoxygenation in the lower limbs (especially the right leg) that may affect performance. Although the acute influence of such deoxygenation is not clearly understood, we tested whether remote ischemic preconditioning (RIPC) could modify muscular oxygenation and improve time-trial performance in that sport. Using a randomized, single-blind, placebo-controlled, crossover design, 9 elite speed skaters performed 1000-m on-ice time-trials preceded by either RIPC of the upper limbs (3x5-min compression/5-min reperfusion cycles at 30 mmHg > arterial systolic pressure) or SHAM (10 mmHg). Changes in tissue saturation index (TSI), oxyhemoglobin-oxymyoglobine ([O2HbMb]), deoxyhemoglobin-deoxymyoglobine ([HHbMb]) and total hemoglobin-myoglobine ([THbMb]) in the right vastus lateralis muscle were monitored by near-infrared spectroscopy (NIRS). Differences between RIPC and SHAM were analyzed using Cohen's effect size (ES) ± 90% confidence limits and magnitude-based inferences. Compared with SHAM, RIPC had negligible effect on performance and NIRS variables. However, in a subgroup of sprinters (n=5) RIPC likely lowered TSI at the beginning of the time-trial (-6.1%; ES -0.65) and likely increased [HHbMb] at the beginning (3%; ES 0.39), middle (2.9%; ES 0.37) and end of the trial (-2.1%, ES 0.27). In the middle section of the trial, these metabolic changes were concomitant with a possible increase in [THbMb]. RIPC has no practical ergogenic impact on 1000-m long-track speed-skating performance in elite athletes. The relevance of using RIPC during training to increase physiological stress in sprinters particularly deserves further investigation.

Enhanced cell volume regulation: a key protective mechanism of ischemic preconditioning in rabbit ventricular myocytes.

PubMed

Diaz, Roberto J; Armstrong, Stephen C; Batthish, Michelle; Backx, Peter H; Ganote, Charles E; Wilson, Gregory J

2003-01-01

Accumulation of osmotically active metabolites, which create an osmotic gradient estimated at ~60 mOsM, and cell swelling are prominent features of ischemic myocardial cell death. This study tests the hypothesis that reduction of ischemic swelling by enhanced cell volume regulation is a key mechanism in the delay of ischemic myocardial cell death by ischemic preconditioning (IPC). Experimental protocols address whether: (i) IPC triggers a cell volume regulation mechanism that reduces cardiomyocyte swelling during subsequent index ischemia; (ii) this reduction in ischemic cell swelling is sufficient in magnitude to account for the IPC protection; (iii) the molecular mechanism that mediates IPC also mediates cell volume regulation. Two experimental models with rabbit ventricular myocytes were studied: freshly isolated pelleted myocytes and 48-h cultured myocytes. Myocytes were preconditioned either by distinct short simulated ischemia (SI)/simulated reperfusion protocols (IPC), or by subjecting myocytes to a pharmacological preconditioning (PPC) protocol (1 microM calyculin A, or 1 microM N(6)-2-(4-aminophenyl)ethyladenosine (APNEA), prior to subjecting them to either different durations of long SI or 30 min hypo-osmotic stress. Cell death (percent blue square myocytes) was monitored by trypan blue staining. Cell swelling was determined by either the bromododecane cell flotation assay (qualitative) or video/confocal microscopy (quantitative). Simulated ischemia induced myocyte swelling in both the models. In pelleted myocytes, IPC or PPC with either calyculin A or APNEA produced a marked reduction of ischemic cell swelling as determined by the cell floatation assay. In cultured myocytes, IPC substantially reduced ischemic cell swelling (P < 0.001). This IPC effect on ischemic cell swelling was related to an IPC and PPC (with APNEA) mediated triggering of cell volume regulatory decrease (RVD). IPC and APNEA also significantly (P < 0.001) reduced hypo-osmotic cell swelling. This IPC and APNEA effect was blocked by either adenosine receptor, PKC or Cl(-) channel inhibition. The osmolar equivalent for IPC protection approximated 50-60 mOsM, an osmotic gradient similar to the estimated ischemic osmotic load for preconditioned and non-preconditioned myocytes. The results suggest that cell volume regulation is a key mechanism that accounts for most of the IPC protection in cardiomyocytes.

GPU-based acceleration of computations in nonlinear finite element deformation analysis.

PubMed

Mafi, Ramin; Sirouspour, Shahin

2014-03-01

The physics of deformation for biological soft-tissue is best described by nonlinear continuum mechanics-based models, which then can be discretized by the FEM for a numerical solution. However, computational complexity of such models have limited their use in applications requiring real-time or fast response. In this work, we propose a graphic processing unit-based implementation of the FEM using implicit time integration for dynamic nonlinear deformation analysis. This is the most general formulation of the deformation analysis. It is valid for large deformations and strains and can account for material nonlinearities. The data-parallel nature and the intense arithmetic computations of nonlinear FEM equations make it particularly suitable for implementation on a parallel computing platform such as graphic processing unit. In this work, we present and compare two different designs based on the matrix-free and conventional preconditioned conjugate gradients algorithms for solving the FEM equations arising in deformation analysis. The speedup achieved with the proposed parallel implementations of the algorithms will be instrumental in the development of advanced surgical simulators and medical image registration methods involving soft-tissue deformation. Copyright © 2013 John Wiley & Sons, Ltd.

A 3D finite-difference BiCG iterative solver with the Fourier-Jacobi preconditioner for the anisotropic EIT/EEG forward problem.

PubMed

Turovets, Sergei; Volkov, Vasily; Zherdetsky, Aleksej; Prakonina, Alena; Malony, Allen D

2014-01-01

The Electrical Impedance Tomography (EIT) and electroencephalography (EEG) forward problems in anisotropic inhomogeneous media like the human head belongs to the class of the three-dimensional boundary value problems for elliptic equations with mixed derivatives. We introduce and explore the performance of several new promising numerical techniques, which seem to be more suitable for solving these problems. The proposed numerical schemes combine the fictitious domain approach together with the finite-difference method and the optimally preconditioned Conjugate Gradient- (CG-) type iterative method for treatment of the discrete model. The numerical scheme includes the standard operations of summation and multiplication of sparse matrices and vector, as well as FFT, making it easy to implement and eligible for the effective parallel implementation. Some typical use cases for the EIT/EEG problems are considered demonstrating high efficiency of the proposed numerical technique.

Influence of the dentinal wall on the pH of sodium hypochlorite during root canal irrigation.

PubMed

Macedo, Ricardo Gomes; Herrero, Noemi Pascual; Wesselink, Paul; Versluis, Michel; van der Sluis, Luc

2014-07-01

The purpose of this study was to evaluate the influence of dentin on the pH levels of different concentrations of sodium hypochlorite (NaOCl) solutions over time and to evaluate if preconditioning of dentin with 17% EDTA or agitation of the NaOCl solution influences these pH levels. A novel clinically representative model that scales with the ratio of the irrigant volume to the dentin surface area of a human root canal was used. Three standardized bovine dentin bars (2 × 2 × 10 mm) were placed in a plastic test tube. A total of 150 tubes were distributed in 29 groups. In the first experiment, the pH of various NaOCl solutions, with different concentrations (3%, 6%, and 9%) and starting pH levels (5 and 12), was monitored during exposure to dentin between 10 and 300 seconds. In a second experiment, the effect of agitation (45 Hz) and pretreatment of dentin with 17% EDTA on the pH levels of various NaOCl solutions was studied after 30 seconds of exposure to dentin. The short-term chemical stability of the tested solutions was assessed for both the concentration and the pH. The exposure time (P < .001) and concentration of the NaOCl solution (P < .011) significantly influence the pH level after exposure to dentin. However, the change in pH is too small to induce a change in the irrigant antimicrobial/tissue dissolution capacity. Agitation of the irrigant and preconditioning of the dentin did not alter the pH (P > .05). Both the pH 5 and pH 12 solutions were chemically stable for 1 hour. Copyright © 2014 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

Biodegradation of 3,4 dichloroaniline by fungal isolated from the preconditioning phase of winery wastes subjected to vermicomposting.

PubMed

Castillo, Jean Manuel; Nogales, Rogelio; Romero, Esperanza

2014-02-28

A hazardous contaminant, 3,4-dichloroaniline (DCA) is widespread in the environment due to its extensive use in the manufacture of chemicals and its application in different sectors. The ability of fungi grow on in winery wastes in the preconditioning period of vermicomposting to degrade DCA was investigated. Three filamentous fungi (F1, F2, and F3) were isolated and one identified as Aspergillus niger and two as Fusarium sp. strains. The culture media with the fungus alone or in consortium (Fmix) with DCA as the nitrogen source were analyzed by solid-phase microextraction and gas chromatography-mass spectrometry (SPME-GC/MS). The fastest degradation rate was measured in Fmix with a DT50 of 0.85day(-1). Fusarium sp. and A. niger differed in the metabolism of DCA. Five metabolites were identified as a result of oxidation, co-denitrification, N-acetylation, and polymerization reactions. The major metabolites were 3,4-dichloroacetanilide and dichloroquinolines. The azo-metabolites tetrachloroazobenzene and tetracloroazoxybenzene and 3,4-dichloronitrobenzene were found in minor amounts but appeared to be the most persistent in the Fusarium cultures (half-lives ranging from 8.3 to 30.9 days). This study highlights the metabolic potential of microorganisms in the preconditioning period of the vermicomposting process and its possible application for in situ bioremediation strategies. Copyright © 2014 Elsevier B.V. All rights reserved.

ONRASIA Scientific Information Bulletin. Volume 8, Number 3, July- September 1993

DTIC Science & Technology

1993-09-01

the Ninth Symposium on Preconditioned Conjugate Dr. Steven F. Ashby Gradient Methods , which he organized. Computing Sciences Department Computing...ditioned Conjugate Gradient Methods , held at Keio chines and is currently a topic of considerable University (Yokohama). During this meeting, I interest...in the United States. In Japan, on the other discussed iterative methods for linear systems with hand, this technique does not appear to be too well

Interannual variability (1979-2013) of the North-Western Mediterranean deep water mass formation: past observation reanalysis and coupled ocean-atmosphere high-resolution modelling

NASA Astrophysics Data System (ADS)

Somot, Samuel; Houpert, Loic; Sevault, Florence; Testor, Pierre; Bosse, Anthony; Durrieu de Madron, Xavier; Dubois, Clotilde; Herrmann, Marine; Waldman, Robin; Bouin, Marie-Noëlle; Cassou, Christophe

2015-04-01

The North-Western Mediterranean Sea is known as one of the only place in the world where open-sea deep convection occurs (often up to more than 2000m) with the formation of the Western Mediterranean Deep Water (WMDW). This phenomena is mostly driven by local preconditioning of the water column and strong buoyancy losses during Winter. At the event scale, the WMDW formation is characterized by different phases (preconditioning, strong mixing, restratification and spreading), intense air-sea interaction and strong meso-scale activity but, on a longer time scale, it also shows a large interannual variability and may be strongly affected by climate change with impact on the regional biogeochemistry. Therefore observing, simulating and understanding the long-term temporal variability of the North-Western Mediterranean deep water formation is still today a very challenging task. We try here to tackle those issues thanks to (1) a thorough reanalysis of past in-situ observations (CTD, Argo, surface and deep moorings, gliders) and (2) an ERA-Interim driven simulation using a recently-developed fully coupled Regional Climate System Model (CNRM-RCSM4, Sevault et al. 2014). The multi-decadal simulation (1979-2013) is designed to be temporally and spatially homogeneous with a realistic chronology, a high resolution representation of both the regional ocean and atmosphere, specific initial conditions, a long-term spin-up and a full ocean-atmosphere coupling without constraint at the air-sea interface. The observation reanalysis allows to reconstruct interannual time series of deep water formation indicators (ocean surface variables, mixed layer depth, surface of the convective area, dense water volumes and characteristics of the deep water). Using the observation-based indicators and the model outputs, the 34 Winters of the period 1979-2013 are analysed in terms of weather regimes, related Winter air-sea fluxes, ocean preconditioning, mixed layer depth, surface of the convective area, deep water formation rate and long-term evolution of the deep water hydrology.

Transport synthetic acceleration with opposing reflecting boundary conditions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zika, M.R.; Adams, M.L.

2000-02-01

The transport synthetic acceleration (TSA) scheme is extended to problems with opposing reflecting boundary conditions. This synthetic method employs a simplified transport operator as its low-order approximation. A procedure is developed that allows the use of the conjugate gradient (CG) method to solve the resulting low-order system of equations. Several well-known transport iteration algorithms are cast in a linear algebraic form to show their equivalence to standard iterative techniques. Source iteration in the presence of opposing reflecting boundary conditions is shown to be equivalent to a (poorly) preconditioned stationary Richardson iteration, with the preconditioner defined by the method of iteratingmore » on the incident fluxes on the reflecting boundaries. The TSA method (and any synthetic method) amounts to a further preconditioning of the Richardson iteration. The presence of opposing reflecting boundary conditions requires special consideration when developing a procedure to realize the CG method for the proposed system of equations. The CG iteration may be applied only to symmetric positive definite matrices; this condition requires the algebraic elimination of the boundary angular corrections from the low-order equations. As a consequence of this elimination, evaluating the action of the resulting matrix on an arbitrary vector involves two transport sweeps and a transmission iteration. Results of applying the acceleration scheme to a simple test problem are presented.« less

Efficient preconditioning of the electronic structure problem in large scale ab initio molecular dynamics simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schiffmann, Florian; VandeVondele, Joost, E-mail: Joost.VandeVondele@mat.ethz.ch

2015-06-28

We present an improved preconditioning scheme for electronic structure calculations based on the orbital transformation method. First, a preconditioner is developed which includes information from the full Kohn-Sham matrix but avoids computationally demanding diagonalisation steps in its construction. This reduces the computational cost of its construction, eliminating a bottleneck in large scale simulations, while maintaining rapid convergence. In addition, a modified form of Hotelling’s iterative inversion is introduced to replace the exact inversion of the preconditioner matrix. This method is highly effective during molecular dynamics (MD), as the solution obtained in earlier MD steps is a suitable initial guess. Filteringmore » small elements during sparse matrix multiplication leads to linear scaling inversion, while retaining robustness, already for relatively small systems. For system sizes ranging from a few hundred to a few thousand atoms, which are typical for many practical applications, the improvements to the algorithm lead to a 2-5 fold speedup per MD step.« less

A Generalized Sampling and Preconditioning Scheme for Sparse Approximation of Polynomial Chaos Expansions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jakeman, John D.; Narayan, Akil; Zhou, Tao

We propose an algorithm for recovering sparse orthogonal polynomial expansions via collocation. A standard sampling approach for recovering sparse polynomials uses Monte Carlo sampling, from the density of orthogonality, which results in poor function recovery when the polynomial degree is high. Our proposed approach aims to mitigate this limitation by sampling with respect to the weighted equilibrium measure of the parametric domain and subsequently solves a preconditionedmore » $$\\ell^1$$-minimization problem, where the weights of the diagonal preconditioning matrix are given by evaluations of the Christoffel function. Our algorithm can be applied to a wide class of orthogonal polynomial families on bounded and unbounded domains, including all classical families. We present theoretical analysis to motivate the algorithm and numerical results that show our method is superior to standard Monte Carlo methods in many situations of interest. In conclusion, numerical examples are also provided to demonstrate that our proposed algorithm leads to comparable or improved accuracy even when compared with Legendre- and Hermite-specific algorithms.« less

A Generalized Sampling and Preconditioning Scheme for Sparse Approximation of Polynomial Chaos Expansions

DOE PAGES

Jakeman, John D.; Narayan, Akil; Zhou, Tao

2017-06-22

We propose an algorithm for recovering sparse orthogonal polynomial expansions via collocation. A standard sampling approach for recovering sparse polynomials uses Monte Carlo sampling, from the density of orthogonality, which results in poor function recovery when the polynomial degree is high. Our proposed approach aims to mitigate this limitation by sampling with respect to the weighted equilibrium measure of the parametric domain and subsequently solves a preconditionedmore » $$\\ell^1$$-minimization problem, where the weights of the diagonal preconditioning matrix are given by evaluations of the Christoffel function. Our algorithm can be applied to a wide class of orthogonal polynomial families on bounded and unbounded domains, including all classical families. We present theoretical analysis to motivate the algorithm and numerical results that show our method is superior to standard Monte Carlo methods in many situations of interest. In conclusion, numerical examples are also provided to demonstrate that our proposed algorithm leads to comparable or improved accuracy even when compared with Legendre- and Hermite-specific algorithms.« less

A new preconditioner update strategy for the solution of sequences of linear systems in structural mechanics: application to saddle point problems in elasticity

NASA Astrophysics Data System (ADS)

Mercier, Sylvain; Gratton, Serge; Tardieu, Nicolas; Vasseur, Xavier

2017-12-01

Many applications in structural mechanics require the numerical solution of sequences of linear systems typically issued from a finite element discretization of the governing equations on fine meshes. The method of Lagrange multipliers is often used to take into account mechanical constraints. The resulting matrices then exhibit a saddle point structure and the iterative solution of such preconditioned linear systems is considered as challenging. A popular strategy is then to combine preconditioning and deflation to yield an efficient method. We propose an alternative that is applicable to the general case and not only to matrices with a saddle point structure. In this approach, we consider to update an existing algebraic or application-based preconditioner, using specific available information exploiting the knowledge of an approximate invariant subspace or of matrix-vector products. The resulting preconditioner has the form of a limited memory quasi-Newton matrix and requires a small number of linearly independent vectors. Numerical experiments performed on three large-scale applications in elasticity highlight the relevance of the new approach. We show that the proposed method outperforms the deflation method when considering sequences of linear systems with varying matrices.

Improving multi-objective reservoir operation optimization with sensitivity-informed dimension reduction

NASA Astrophysics Data System (ADS)

Chu, J.; Zhang, C.; Fu, G.; Li, Y.; Zhou, H.

2015-08-01

This study investigates the effectiveness of a sensitivity-informed method for multi-objective operation of reservoir systems, which uses global sensitivity analysis as a screening tool to reduce computational demands. Sobol's method is used to screen insensitive decision variables and guide the formulation of the optimization problems with a significantly reduced number of decision variables. This sensitivity-informed method dramatically reduces the computational demands required for attaining high-quality approximations of optimal trade-off relationships between conflicting design objectives. The search results obtained from the reduced complexity multi-objective reservoir operation problems are then used to pre-condition the full search of the original optimization problem. In two case studies, the Dahuofang reservoir and the inter-basin multi-reservoir system in Liaoning province, China, sensitivity analysis results show that reservoir performance is strongly controlled by a small proportion of decision variables. Sensitivity-informed dimension reduction and pre-conditioning are evaluated in their ability to improve the efficiency and effectiveness of multi-objective evolutionary optimization. Overall, this study illustrates the efficiency and effectiveness of the sensitivity-informed method and the use of global sensitivity analysis to inform dimension reduction of optimization problems when solving complex multi-objective reservoir operation problems.

The epidemiology of bovine respiratory disease: What is the evidence for preventive measures?

PubMed Central

Taylor, Jared D.; Fulton, Robert W.; Lehenbauer, Terry W.; Step, Douglas L.; Confer, Anthony W.

2010-01-01

Bovine respiratory disease (BRD) is the most common and costly disease of beef cattle in North America. Despite extensive research, industry practices are often more informed by dogma than by fact. Frequently advocated interventions, including vaccination, various processing procedures, and nutritional manipulation, have limited impact on morbidity and mortality. Evidence for use of oral antimicrobials, either in feed or water, appears to be equivocal. In contrast, preconditioning and metaphylaxis have significant scientific evidence of efficacy, with weaning prior to sale potentially being the most important component of preconditioning. The inability to reach more definitive conclusions in preventing BRD may be attributable to difficulties in investigating the disease. Study challenges include potential for extensive confounding, tremendous variability, the multi-factorial nature of the disease, and inadequate methods for diagnosis. PMID:21358927

[Effects of BNP preconditioning on myocardial cell apoptosis and expressions of bcl-2 and Bax during myocardial ischemia-reperfusion injury in rats].

PubMed

Deng, Yu-Jun; Tan, Ning; Zeng, Hong-Ke; Fu, Yong-Heng; Dong, Xiao-Li

2010-12-28

To study the effects of B-type natriuretic peptide (BNP) preconditioning on the apoptosis and expressions of Bcl-2 and Bax in rat cardiomyocytes during myocardial ischemia-reperfusion. Twenty-one male Sprague-Dawley rats weighing (250 ± 50) g were randomly divided into 3 groups of sham operation (SHAM), ischemia-reperfusion (I/R) and B-type natriuretic peptide (BNP). A rat model of in vivo myocardial ischemia-reperfusion injury was established by ligating the left anterior descending coronary artery for 35 minutes and then reperfusing for 240 minutes. The apoptosis of myocardial cell was determined by terminal deoxynucleotidyl transferase mediated dUTP-biotin nick end-labeling (TUNEL) method. Real-time polymerase chain reaction and Western blot were used to detect the expression changes of Bcl-2 and Bax in rat ischemia myocardium. The apoptotic indices of SHAM, BNP and I/R groups were 5.4% ± 4.2%, 22.5% ± 9.5% and 45.2% ± 13.0% respectively (P < 0.05). The Bcl-2 protein expression of SHAM, BNP and I/R groups were 0.87 ± 0.09, 0.70 ± 0.07 and 0.38 ± 0.09 respectively (P < 0.05). The Bax protein expression of SHAM, BNP and I/R groups were 0.08 ± 0.04, 0.39 ± 0.09 and 0.71 ± 0.18 respectively (P < 0.01). The Bcl-2/Bax mRNA ratio of SHAN, BNP and I/R groups were 0.763 ± 0.154, 0.099 ± 0.025 and 0.022 ± 0.024 respectively (P < 0.05). The BNP preconditioning can decrease the myocardial apoptosis induced by ischemia-reperfusion injury. The mechanisms may be associated with an elevated expression of Bcl-2, an increased ratio of Bcl-2/Bax and a lowered expression of Bax.

High-performance equation solvers and their impact on finite element analysis

NASA Technical Reports Server (NTRS)

Poole, Eugene L.; Knight, Norman F., Jr.; Davis, D. Dale, Jr.

1990-01-01

The role of equation solvers in modern structural analysis software is described. Direct and iterative equation solvers which exploit vectorization on modern high-performance computer systems are described and compared. The direct solvers are two Cholesky factorization methods. The first method utilizes a novel variable-band data storage format to achieve very high computation rates and the second method uses a sparse data storage format designed to reduce the number of operations. The iterative solvers are preconditioned conjugate gradient methods. Two different preconditioners are included; the first uses a diagonal matrix storage scheme to achieve high computation rates and the second requires a sparse data storage scheme and converges to the solution in fewer iterations that the first. The impact of using all of the equation solvers in a common structural analysis software system is demonstrated by solving several representative structural analysis problems.

High-performance equation solvers and their impact on finite element analysis

NASA Technical Reports Server (NTRS)

Poole, Eugene L.; Knight, Norman F., Jr.; Davis, D. D., Jr.

1992-01-01

The role of equation solvers in modern structural analysis software is described. Direct and iterative equation solvers which exploit vectorization on modern high-performance computer systems are described and compared. The direct solvers are two Cholesky factorization methods. The first method utilizes a novel variable-band data storage format to achieve very high computation rates and the second method uses a sparse data storage format designed to reduce the number od operations. The iterative solvers are preconditioned conjugate gradient methods. Two different preconditioners are included; the first uses a diagonal matrix storage scheme to achieve high computation rates and the second requires a sparse data storage scheme and converges to the solution in fewer iterations that the first. The impact of using all of the equation solvers in a common structural analysis software system is demonstrated by solving several representative structural analysis problems.

Kelch-like ECH-associated Protein 1-dependent Nuclear Factor-E2-related Factor 2 Activation in Relation to Antioxidation Induced by Sevoflurane Preconditioning.

PubMed

Cai, Min; Tong, Li; Dong, Beibei; Hou, Wugang; Shi, Likai; Dong, Hailong

2017-03-01

The authors have reported that antioxidative effects play a crucial role in the volatile anesthetic-induced neuroprotection. Accumulated evidence shows that endogenous antioxidation could be up-regulated by nuclear factor-E2-related factor 2 through multiple pathways. However, whether nuclear factor-E2-related factor 2 activation is modulated by sevoflurane preconditioning and, if so, what is the signaling cascade underlying upstream of this activation are still unknown. Sevoflurane preconditioning in mice was performed with sevoflurane (2.5%) 1 h per day for five consecutive days. Focal cerebral ischemia/reperfusion injury was induced by middle cerebral artery occlusion. Expression of nuclear factor-E2-related factor 2, kelch-like ECH-associated protein 1, manganese superoxide dismutase, thioredoxin-1, and nicotinamide adenine dinucleotide phosphate quinolone oxidoreductase-1 was detected (n = 6). The antioxidant activities and oxidative product expression were also examined. To determine the role of kelch-like ECH-associated protein 1 inhibition-dependent nuclear factor-E2-related factor 2 activation in sevoflurane preconditioning-induced neuroprotection, the kelch-like ECH-associated protein 1-nuclear factor-E2-related factor 2 signal was modulated by nuclear factor-E2-related factor 2 knockout, kelch-like ECH-associated protein 1 overexpression lentivirus, and kelch-like ECH-associated protein 1 deficiency small interfering RNA (n = 8). The infarct volume, neurologic scores, and cellular apoptosis were assessed. Sevoflurane preconditioning elicited neuroprotection and increased nuclear factor-E2-related factor 2 nuclear translocation, which in turn up-regulated endogenous antioxidation and reduced oxidative injury. Sevoflurane preconditioning reduced kelch-like ECH-associated protein 1 expression. Nuclear factor-E2-related factor 2 ablation abolished neuroprotection and reversed sevoflurane preconditioning by mediating the up-regulation of antioxidants. Kelch-like ECH-associated protein 1 overexpression reversed nuclear factor-E2-related factor 2 up-regulation and abolished the neuroprotection induced by sevoflurane preconditioning. Kelch-like ECH-associated protein 1 small interfering RNA administration improved nuclear factor-E2-related factor 2 expression and the outcome of mice subjected to ischemia/reperfusion injury. Kelch-like ECH-associated protein 1 down-regulation-dependent nuclear factor-E2-related factor 2 activation underlies the ability of sevoflurane preconditioning to activate the endogenous antioxidant response, which elicits its neuroprotection.

Involvement of SIRT1 in hypoxic down-regulation of c-Myc and β-catenin and hypoxic preconditioning effect of polyphenols

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hong, Kyung-Soo; Research Center for Ischemic Tissue regeneration, Pusan National University School of Medicine, Yangsan; Park, Jun-Ik

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-cateninmore » 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-exposed or hypoxic preconditioned cells. ► SIRT1 deacetylates c-Myc and β-catenin ► HIF-1α is up-regulated by down-regulation of c-Myc and β-catenin expression. ► Polyphenolic SIRT1 activators mimics hypoxic preconditioning.« less

Isotope dilution ICP-MS with laser-assisted sample introduction for direct determination of sulfur in petroleum products.

PubMed

Boulyga, Sergei F; Heilmann, Jens; Heumann, Klaus G

2005-08-01

Inductively coupled plasma isotope dilution mass spectrometry (ICP-IDMS) with direct laser-assisted introduction of isotope-diluted samples into the plasma, using a laser ablation system with high ablation rates, was developed for accurate sulfur determinations in different petroleum products such as 'sulfur-free' premium gasoline, diesel fuel, and heating oil. Two certified gas oil reference materials were analyzed for method validation. Two different 34S-enriched spike compounds, namely, elementary sulfur dissolved in xylene and dibenzothiophene in hexane, were synthesized and tested for their usefulness in this isotope dilution technique. The isotope-diluted sample was adsorbed on a filter-paper-like material, which was fixed in a special holder for irradiation by the laser beam. Under these conditions no time-dependent spike/analyte fractionation was only observed for the dibenzothiophene spike during the laser ablation process, which means that the measured 34S/32S isotope ratio of the isotope-diluted sample remained constant-a necessary precondition for accurate results with the isotope dilution technique. A comparison of LA-ICP-IDMS results with the certified values of the gas oil reference materials and with results obtained from ICP-IDMS analyses with wet sample digestion demonstrated the accuracy of the new LA-ICP-IDMS method in the concentration range of 9.2 microg g(-1) ('sulfur-free' premium gasoline) to 10.4 mg g(-1) (gas oil reference material BCR 107). The detection limit for sulfur by LA-ICP-IDMS is 0.04 microg g(-1) and the analysis time is only about 10 min, which therefore also qualifies this method for accurate determinations of low sulfur contents in petroleum products on a routine level.

[Comparison of pharmacological renal preconditioning with dalargin and lithium ions in the model of gentamycin-induced acute renal failure].

PubMed

Cherpakov, R A; Grebenchikov, O A; Plotnikov, E Ju; Likhvantsev, V V

2015-01-01

To examine the efficacy of renal preconditioning effect of dalargin and lithium ions by observing the model of gentamycin-induced acute renalfailure. The experiments were performed on white rats, male. The influence of dalargin and lithium ions on the development of gentamycin-induced acute renalfailure was studied in vivo. On the first 24 hours after dalargin injections were terminated, the rats were euthanized humanly. After this we took the blood for a biochemistry study and a renal culture for biochemical test and also for the test of gsk-3β activity. Concentrations of creatinine and urea were studied in serum. The culture samples of renal tubular epithelium before insertion of gentamycin were incubated in dalargin or lithium ions in different concentrations. After that the substratum was immediately changed to gentamycin in different concentrations also and the incubated for 24 hours. After all the standards MTT-test was performed (based on the ability of living cells to reduce the unpainted form by 3-4,5-dimethylthiazol-2-yl-2,5-difenilterarazola to blue crystalline farmazan). Lithium precondition leads to the 250% increase of gsk-3β concentration (p = 0.035). The same results were observed after injection of dalargin in 50 mcg/kg concentration. Concentration of creatinine was 44% lower in the dalargin group than in the control group (p = 0.022). Concentration of creatinine was 32% lower in the lithium group than in the control group (p = 0.030). Concentration of urea was 27% lower in the lithium group than in the control group (p = 0.049). Morphological inflammatory changes in the control group were more significant also. In vitro studies showed the maximum efficacy in the lithium group. The most effective dalargin concentration was 5 mg/ml. Lithium and dalargine preconditioning lowers the signs of gentamycine induced acute renal failure and damage rate of renal parenchyma in vivo and in vitro.

Changes in dissolved organic matter quality in a peatland and forest headwater stream as a function of seasonality and hydrologic conditions

NASA Astrophysics Data System (ADS)

Broder, Tanja; Knorr, Klaus-Holger; Biester, Harald

2017-04-01

Peatlands and peaty riparian zones are major sources of dissolved organic matter (DOM), but are poorly understood in terms of export dynamics and controls thereof. Thereby quality of DOM affects function and behavior of DOM in aquatic ecosystems, but DOM quality can also help to track DOM sources and their export dynamics under specific hydrologic preconditions. The objective of this study was to elucidate controls on temporal variability in DOM concentration and quality in stream water draining a bog and a forested peaty riparian zone, particularly considering drought and storm flow events. DOM quality was monitored using spectrofluorometric indices for aromaticity (SUVA254), apparent molecular size (SR) and precursor organic material (FI), as well as PARAFAC modeling of excitation emission matrices (EEMs). Indices for DOM quality exhibited major changes due to different hydrologic conditions, but patterns were also dependent on season. Stream water at the forested site with mineral, peaty soils generally exhibited higher variability in DOM concentrations and quality compared to the outflow of an ombrotrophic bog, where DOM was less susceptible to changes in hydrologic conditions. During snowmelt and spring events, near-surface protein-like DOM pools were exported. A microbial DOM fraction originating from groundwater and deep peat layers was increasing during drought, while a strongly microbially altered DOM fraction was also exported by discharge events with dry preconditions at the forested site. This might be due to accelerated microbial activity in the peaty riparian zone of the forested site under these preconditions. Our study demonstrated that DOM export dynamics are not only a passive mixing of different hydrological sources, but monitoring studies have to consider that DOM quality depends on hydrologic preconditions and season. Moreover, the forested peaty riparian zone generated the most variability in headwater DOM quantity and quality, as could be tracked by the used spectrofluorometric indices.

Hypoxia preconditioning of mesenchymal stromal cells enhances PC3 cell lymphatic metastasis accompanied by VEGFR-3/CCR7 activation.

PubMed

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.

The involvement of protein kinase C-ε in isoflurane induced preconditioning of human embryonic stem cell--derived Nkx2.5(+) cardiac progenitor cells.

PubMed

Song, In-Ae; Oh, Ah-Young; Kim, Jin-Hee; Choi, Young-Min; Jeon, Young-Tae; Ryu, Jung-Hee; Hwang, Jung-Won

2016-02-20

Anesthetic preconditioning can improve survival of cardiac progenitor cells exposed to oxidative stress. We investigated the role of protein kinase C and isoform protein kinase C-ε in isoflurane-induced preconditioning of cardiac progenitor cells exposed to oxidative stress. Cardiac progenitor cells were obtained from undifferentiated human embryonic stem cells. Immunostaining with anti-Nkx2.5 was used to confirm the differentiated cardiac progenitor cells. Oxidative stress was induced by H2O2 and FeSO4. For anesthetic preconditioning, cardiac progenitor cells were exposed to 0.25, 0.5, and 1.0 mM of isoflurane. PMA and chelerythrine were used for protein kinase C activation and inhibition, while εψRACK and εV1-2 were used for protein kinase C -ε activation and inhibition, respectively. Isoflurane-preconditioning decreased the death rate of Cardiac progenitor cells exposed to oxidative stress (death rates isoflurane 0.5 mM 12.7 ± 9.3%, 1.0 mM 12.0 ± 7.7% vs. control 31.4 ± 10.2%). Inhibitors of both protein kinase C and protein kinase C -ε abolished the preconditioning effect of isoflurane 0.5 mM (death rates 27.6 ± 13.5% and 25.9 ± 8.7% respectively), and activators of both protein kinase C and protein kinase C - ε had protective effects from oxidative stress (death rates 16.0 ± 3.2% and 10.6 ± 3.8% respectively). Both PKC and PKC-ε are involved in isoflurane-induced preconditioning of human embryonic stem cells -derived Nkx2.5(+) Cardiac progenitor cells under oxidative stress.

Effects and interaction, of cariporide and preconditioning on cardiac arrhythmias and infarction in rat in vivo

PubMed Central

Aye, Nu Nu; Komori, Sadayoshi; Hashimoto, Keitaro

1999-01-01

Although Na+-H+ exchange (NHE) inhibitors are reported to protect the myocardium against ischaemic injury, NHE activation has also been proposed as a potential mechanism of ischaemic preconditioning-induced protection. This study was performed to test any modifiable effect of cariporide, an NHE inhibitor, on cardioprotective effects of preconditioning.Anaesthetized rats were subjected to 30 min of coronary artery occlusion and 150 min of reperfusion. The preconditioning (PC) was induced by 3 min of ischaemia and 10 min of reperfusion (1PC) or three episodes of 3 min ischaemia and 5 min reperfusion (3PC). Cariporide (0.3 mg kg−1) an NHE inhibitor, was administered 30 min (cari(30)) or 45 min (cari(45)) before coronary ligation (n=8–11 for each group).Ventricular arrhythmias during 30 min ischaemia and infarct size (measured by triphenyltetrazolium (TTC) and expressed as a per cent area at risk (%AAR)) were determined. Cari(30) reduced ventricular fibrillation (VF) incidence and infarct size (from 45 to 0% and 34±4 to 9±2%; each P<0.05), whereas cari(45) did not. Likewise, 3PC reduced these variables (to 0% and 10±2%; P<0.05 in each case) whereas 1PC did not. Moreover, subthreshold preconditioning (1PC) and cariporide (cari(45)), when combined, reduced VF incidence and infarct size (to 0% and 15+3%; each P<0.05).In conclusion, changes in NHE activity do not seem to be responsible for the cardioprotective action of ischaemic preconditioning. Protective effects of NHE inhibition and subthreshold preconditioning appear to act additively. PMID:10433514

Cardioprotection of ischaemic preconditioning is associated with inhibition of translocation of MLKL within the plasma membrane.

PubMed

Szobi, Adrián; Farkašová-Ledvényiová, Veronika; Lichý, Martin; Muráriková, Martina; Čarnická, Slávka; Ravingerová, Tatiana; Adameová, Adriana

2018-06-19

Necroptosis, a form of cell loss involving the RIP1-RIP3-MLKL axis, has been identified in cardiac pathologies while its inhibition is cardioprotective. We investigated whether the improvement of heart function because of ischaemic preconditioning is associated with mitigation of necroptotic signaling, and these effects were compared with a pharmacological antinecroptotic approach targeting RIP1. Langendorff-perfused rat hearts were subjected to ischaemic preconditioning with or without a RIP1 inhibitor (Nec-1s). Necroptotic signaling and the assessment of oxidative damage and a putative involvement of CaMKII in this process were analysed in whole tissue and subcellular fractions. Ischaemic preconditioning, Nec-1s and their combination improved postischaemic heart function recovery and reduced infarct size to a similar degree what was in line with the prevention of MLKL oligomerization and translocation to the membrane. On the other hand, membrane peroxidation and apoptosis were unchanged by either approach. Ischaemic preconditioning failed to ameliorate ischaemia-reperfusion-induced increase in RIP1 and RIP3 while pSer229-RIP3 levels were reduced only by Nec-1s. In spite of the additive phosphorylation of CaMKII and PLN because of ditherapy, the postischaemic contractile force and relaxation was comparably improved in all the intervention groups while antiarrhythmic effects were observed in the ischaemic preconditioning group only. Necroptosis inhibition seems to be involved in cardioprotection of ischaemic preconditioning and is comparable but not intensified by an anti-RIP1 agent. Changes in oxidative stress nor CaMKII signaling are unlikely to explain the beneficial effects. © 2018 Comenius University in Bratislava, Faculty of Pharmacy. Journal of Cellular and Molecular Medicine published by John Wiley & Sons Ltd and Foundation for Cellular and Molecular Medicine.

On a model of three-dimensional bursting and its parallel implementation

NASA Astrophysics Data System (ADS)

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.

Configuration complexity assessment of convergent supply chain systems

NASA Astrophysics Data System (ADS)

Modrak, Vladimir; Marton, David

2014-07-01

System designers usually generate alternative configurations of supply chains (SCs) by varying especially fixed assets to satisfy a desired production scope and rate. Such alternatives often vary in associated costs and other facets including degrees of complexity. Hence, a measure of configuration complexity can be a tool for comparison and decision-making. This paper presents three approaches to assessment of configuration complexity and their applications to designing convergent SC systems. Presented approaches are conceptually distinct ways of measuring structural complexity parameters based on different preconditions and circumstances of assembly systems which are typical representatives of convergent SCs. There are applied two similar approaches based on different preconditions that are related to demand shares. Third approach does not consider any special condition relating to character of final product demand. Subsequently, we propose a framework for modeling of assembly SC models, which are dividing to classes.

Complex wet-environments in electronic-structure calculations

NASA Astrophysics Data System (ADS)

Fisicaro, Giuseppe; Genovese, Luigi; Andreussi, Oliviero; Marzari, Nicola; Goedecker, Stefan

The computational study of chemical reactions in complex, wet environments is critical for applications in many fields. It is often essential to study chemical reactions in the presence of an applied electrochemical potentials, including complex electrostatic screening coming from the solvent. In the present work we present a solver to handle both the Generalized Poisson and the Poisson-Boltzmann equation. A preconditioned conjugate gradient (PCG) method has been implemented for the Generalized Poisson and the linear regime of the Poisson-Boltzmann, allowing to solve iteratively the minimization problem with some ten iterations. On the other hand, a self-consistent procedure enables us to solve the Poisson-Boltzmann problem. The algorithms take advantage of a preconditioning procedure based on the BigDFT Poisson solver for the standard Poisson equation. They exhibit very high accuracy and parallel efficiency, and allow different boundary conditions, including surfaces. The solver has been integrated into the BigDFT and Quantum-ESPRESSO electronic-structure packages and it will be released as a independent program, suitable for integration in other codes. We present test calculations for large proteins to demonstrate efficiency and performances. This work was done within the PASC and NCCR MARVEL projects. Computer resources were provided by the Swiss National Supercomputing Centre (CSCS) under Project ID s499. LG acknowledges also support from the EXTMOS EU project.

On the relevance of source effects in geomagnetic pulsations for induction soundings

NASA Astrophysics Data System (ADS)

Neska, Anne; Tadeusz Reda, Jan; Leszek Neska, Mariusz; Petrovich Sumaruk, Yuri

2018-03-01

This study is an attempt to close a gap between recent research on geomagnetic pulsations and their usage as source signals in electromagnetic induction soundings (i.e., magnetotellurics, geomagnetic depth sounding, and magnetovariational sounding). The plane-wave assumption as a precondition for the proper performance of these methods is partly violated by the local nature of field line resonances which cause a considerable portion of pulsations at mid latitudes. It is demonstrated that and explained why in spite of this, the application of remote reference stations in quasi-global distances for the suppression of local correlated-noise effects in induction arrows is possible in the geomagnetic pulsation range. The important role of upstream waves and of the magnetic equatorial region for such applications is emphasized. Furthermore, the principal difference between application of reference stations for local transfer functions (which result in sounding curves and induction arrows) and for inter-station transfer functions is considered. The preconditions for the latter are much stricter than for the former. Hence a failure to estimate an inter-station transfer function to be interpreted in terms of electromagnetic induction, e.g., because of field line resonances, does not necessarily prohibit use of the station pair for a remote reference estimation of the impedance tensor.

An experimental evaluation of the effect of homogenization quality as a preconditioning on oil-water two-phase volume fraction measurement accuracy using gamma-ray attenuation technique

NASA Astrophysics Data System (ADS)

Sharifzadeh, M.; Hashemabadi, S. H.; Afarideh, H.; Khalafi, H.

2018-02-01

The problem of how to accurately measure multiphase flow in the oil/gas industry remains as an important issue since the early 80 s. Meanwhile, oil-water two-phase flow rate measurement has been regarded as an important issue. Gamma-ray attenuation is one of the most commonly used methods for phase fraction measurement which is entirely dependent on the flow regime variations. The peripheral strategy applied for removing the regime dependency problem, is using a homogenization system as a preconditioning tool, as this research work demonstrates. Here, at first, TPFHL as a two-phase flow homogenizer loop has been introduced and verified by a quantitative assessment. In the wake of this procedure, SEMPF as a static-equivalent multiphase flow with an additional capability for preparing a uniform mixture has been explained. The proposed idea in this system was verified by Monte Carlo simulations. Finally, the different water-gas oil two-phase volume fractions fed to the homogenizer loop and injected into the static-equivalent system. A comparison between performance of these two systems by using gamma-ray attenuation technique, showed not only an extra ability to prepare a homogenized mixture but a remarkably increased measurement accuracy for the static-equivalent system.

Personalized Medicine in the U.S. and Germany: Awareness, Acceptance, Use and Preconditions for the Wide Implementation into the Medical Standard

PubMed Central

Kichko, Kateryna; Marschall, Paul; Flessa, Steffen

2016-01-01

The aim of our research was to collect comprehensive data about the public and physician awareness, acceptance and use of Personalized Medicine (PM), as well as their opinions on PM reimbursement and genetic privacy protection in the U.S. and Germany. In order to give a better overview, we compared our survey results with the results from other studies and discussed Personalized Medicine preconditions for its wide implementation into the medical standard. For the data collection, using the same methodology, we performed several surveys in Pennsylvania (U.S.) and Bavaria (Germany). Physicians were contacted via letter, while public representatives in person. Survey results, analyzed by means of descriptive and non-parametric statistic methods, have shown that awareness, acceptance, use and opinions on PM aspects in Pennsylvania and Bavaria were not significantly different. In both states there were strong concerns about genetic privacy protection and no support of one genetic database. The costs for Personalized Medicine were expected to be covered by health insurances and governmental funds. Summarizing, we came to the conclusion that for PM wide implementation there will be need to adjust the healthcare reimbursement system, as well as adopt new laws which protect against genetic misuse and simultaneously enable voluntary data provision. PMID:27144585

AdVEGF-All6A+ Preconditioning of Murine Ischemic Skin Flaps Is Comparable to Surgical Delay

PubMed Central

Gersch, Robert P.; Fourman, Mitchell S.; Phillips, Brett T.; Nasser, Ahmed; McClain, Steve A.; Khan, Sami U.; Dagum, Alexander B.

2015-01-01

Background: Surgical flap delay is commonly used in preconditioning reconstructive flaps to prevent necrosis. However, staged procedures are not ideal. Pharmacologic up-regulation of angiogenic and arteriogenic factors before flap elevation poses a nonsurgical approach to improve flap survival. Methods: Male Sprague Dawley rats were divided into control (n = 16), surgical delay (Delay), AdNull, AdEgr-1, and AdVEGF (n ≥ 9/group) groups. Delay rats had a 9 cm × 3 cm cranial based pedicle skin flap incised 10 days prior to elevation. Adenoviral groups received 28 intradermal injections (109 pu/animal total) throughout the distal two thirds of the flap 1 week prior to elevation. At postoperative day (POD) 0 flaps were elevated and silicone sheeting was placed between flap and wound bed. Perfusion analysis in arbitrary perfusion units of the ischemic middle third of the flap using laser Doppler imaging was conducted preoperatively and on POD 0, 3, and 7. Clinical and histopathologic assessments of the skin flaps were performed on POD 7. Results: AdVEGF (50.8 ± 10.9 APU) and AdEgr-1 (39.3 ± 10.6 APU) perfusion levels were significantly higher than controls (16.5 ± 4.2 APU) on POD 7. Delay models were equivalent to controls (25.9 ± 6.8 APU). AdVEGF and Delay animals showed significantly more viable surface area on POD 7 (14.4 ± 1.3 cm2, P < 0.01 and 12.4 ± 1.2 cm2, P < 0.05, respectively) compared with Controls (8.7 ± 0.7 cm2). Conclusions: AdVEGF preconditioning resulted in flap survival comparable to surgical delay. Adenoviral preconditioning maintained perfusion levels postoperatively while surgical delay did not. PMID:26495207

Females transplanted with ovaries subjected to hypoxic preconditioning show impair of ovarian function

PubMed Central

2014-01-01

Background Cryopreservation of the ovarian tissue has shown promising results. However, there remain controversial issues such as the short half-life of grafts. In this aspect, there are some evidences that preconditioning the ovarian tissue before transplantation is beneficial. Objective To determine the effect of hypoxic preconditioning in vitro on ovarian tissue prior to transplantation. Methods Eighteen female adult Wistar rats, were sorted into three experimental groups. Ovaries were maintained in DMEM low glucose serum free at 37°C with 5% CO2, at atmospheric oxigen concentration (normoxia) or 1% O2 (hypoxia) for 16 hours. Oxigen concentration was determined by injection of nitrogen in the incubator. Animals submitted to ovarian transplantation immediately after oophorectomy were the Control Group (C). After this, the ovaries were implanted in the retroperitoneum with nonabsorbable suture and animals evaluated for thirty days after transplantation. Beginning on postoperative (PO) day 11, a daily collection of vaginal smear was carried out. Analyses comprised morphological, morphometric (counting ovarian follicles and corpora lutea) and immunohistochemistry for cleaved caspase-3 (apoptosis). Results In normoxia and control groups all animals recovered their estrous cycles, while in the hypoxia group, two animals did not ovulate but, among those which did, resumption took longer than in the other groups (p < 0.05). The number of ovarian follicles and corpora lutea decreased significantly in the hypoxia group when compared to the other two groups (p < 0.001) and apoptosis was increased in the few ovarian follicles which remained viable (p < 0.001). Conclusion The hypoxic preconditioning in vitro was not beneficial to the graft and worsened their viability, compromising its functionality or delaying the return of this. PMID:24655551

Simplified methods of determining treatment retention in Malawi: ART cohort reports vs. pharmacy stock cards.

PubMed

Chan, A K; Singogo, E; Changamire, R; Ratsma, Y E C; Tassie, J-M; Harries, A D

2012-06-21

Rapid scale-up of antiretroviral therapy (ART) has challenged the health system in Malawi to monitor large numbers of patients effectively. To compare two methods of determining retention on treatment: quarterly ART clinic data aggregation vs. pharmacy stock cards. Between October 2010 and March 2011, data on ART outcomes were extracted from monitoring tools at five facilities. Pharmacy data on ART consumption were extracted. Workload for each method was observed and timed. We used intraclass correlation and Bland-Altman plots to compare the agreeability of both methods to determine treatment retention. There is wide variability between ART clinic cohort data and pharmacy data to determine treatment retention due to divergence in data at sites with large numbers of patients. However, there is a non-significant trend towards agreeability between the two methods (intraclass correlation coefficient > 0.9; P > 0.05). Pharmacy stock card monitoring is more time-efficient than quarterly ART data aggregation (81 min vs. 573 min). In low-resource settings, pharmacy records could be used to improve drug forecasting and estimate ART retention in a more time-efficient manner than quarterly data aggregation; however, a necessary precondition would be capacity building around pharmacy data management, particularly for large-sized cohorts.

A clinically observed discrepancy between image-based and log-based MLC positions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Neal, Brian, E-mail: bpn2p@virginia.edu; Ahmed, Mahmoud; Kathuria, Kunal

2016-06-15

Purpose: To present a clinical case in which real-time intratreatment imaging identified an multileaf collimator (MLC) leaf to be consistently deviating from its programmed and logged position by >1 mm. Methods: An EPID-based exit-fluence dosimetry system designed to prevent gross delivery errors was used to capture cine during treatment images. The author serendipitously visually identified a suspected MLC leaf displacement that was not otherwise detected. The leaf position as recorded on the EPID images was measured and log-files were analyzed for the treatment in question, the prior day’s treatment, and for daily MLC test patterns acquired on those treatment days.more » Additional standard test patterns were used to quantify the leaf position. Results: Whereas the log-file reported no difference between planned and recorded positions, image-based measurements showed the leaf to be 1.3 ± 0.1 mm medial from the planned position. This offset was confirmed with the test pattern irradiations. Conclusions: It has been clinically observed that log-file derived leaf positions can differ from their actual position by >1 mm, and therefore cannot be considered to be the actual leaf positions. This cautions the use of log-based methods for MLC or patient quality assurance without independent confirmation of log integrity. Frequent verification of MLC positions through independent means is a necessary precondition to trust log-file records. Intratreatment EPID imaging provides a method to capture departures from MLC planned positions.« less

Retinal metabolic events in preconditioning light stress as revealed by wide-spectrum targeted metabolomics.

PubMed

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.

Teko: A block preconditioning capability with concrete example applications in Navier--Stokes and MHD

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cyr, Eric C.; Shadid, John N.; Tuminaro, Raymond S.

This study describes the design of Teko, an object-oriented C++ library for implementing advanced block preconditioners. Mathematical design criteria that elucidate the needs of block preconditioning libraries and techniques are explained and shown to motivate the structure of Teko. For instance, a principal design choice was for Teko to strongly reflect the mathematical statement of the preconditioners to reduce development burden and permit focus on the numerics. Additional mechanisms are explained that provide a pathway to developing an optimized production capable block preconditioning capability with Teko. Finally, Teko is demonstrated on fluid flow and magnetohydrodynamics applications. In addition to highlightingmore » the features of the Teko library, these new results illustrate the effectiveness of recent preconditioning developments applied to advanced discretization approaches.« less

Teko: A block preconditioning capability with concrete example applications in Navier--Stokes and MHD

DOE PAGES

Cyr, Eric C.; Shadid, John N.; Tuminaro, Raymond S.

2016-10-27

This study describes the design of Teko, an object-oriented C++ library for implementing advanced block preconditioners. Mathematical design criteria that elucidate the needs of block preconditioning libraries and techniques are explained and shown to motivate the structure of Teko. For instance, a principal design choice was for Teko to strongly reflect the mathematical statement of the preconditioners to reduce development burden and permit focus on the numerics. Additional mechanisms are explained that provide a pathway to developing an optimized production capable block preconditioning capability with Teko. Finally, Teko is demonstrated on fluid flow and magnetohydrodynamics applications. In addition to highlightingmore » the features of the Teko library, these new results illustrate the effectiveness of recent preconditioning developments applied to advanced discretization approaches.« less

Decentralised control of continuous Petri nets

NASA Astrophysics Data System (ADS)

Wang, Liewei; Wang, Xu

2017-05-01

This paper focuses on decentralised control of systems modelled by continuous Petri nets, in which a target marking control problem is discussed. In some previous works, an efficient ON/OFF strategy-based minimum-time controller was developed. Nevertheless, the convergence is only proved for subclasses like Choice-Free nets. For a general net, the pre-conditions of applying the ON/OFF strategy are not given; therefore, the application scope of the method is unclear. In this work, we provide two sufficient conditions of applying the ON/OFF strategy-based controller to general nets. Furthermore, an extended algorithm for general nets is proposed, in which control laws are computed based on some limited information, without knowing the detailed structure of subsystems.

Feedback from video for virtual reality Navigation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tsap, L V

2000-10-27

Important preconditions for wide acceptance of virtual reality (VR) systems include their comfort, ease and naturalness to use. Most existing trackers super from discomfort-related issues. For example, body-based trackers (hand controllers, joysticks, helmet attachments, etc.) restrict spontaneity and naturalness of motion, while ground-based devices (e.g., hand controllers) limit the workspace by literally binding an operator to the ground. There are similar problems with controls. This paper describes using real-time video with registered depth information (from a commercially available camera) for virtual reality navigation. Camera-based setup can replace cumbersome trackers. The method includes selective depth processing for increased speed, and amore » robust skin-color segmentation for accounting illumination variations.« less

Transfusion of Plasma Collected at Late Phase after Preconditioning Reduces Myocardial Infarct Size Induced by Ischemia-reperfusion in Rats In vivo.

PubMed

Zhao, Yang; Zheng, Zhi-Nan; Cheung, Chi-Wai; Zuo, Zhi-Yi; Jin, San-Qing

2017-02-05

Plasma transfusion is a common clinical practice. Remote ischemic preconditioning (RIPC) protects organs against ischemia-reperfusion (IR) injury. Whether preconditioned plasma (PP), collected at late phase after RIPC, could protect organs against IR injury in vivo is unknown. This study explored whether transfusion of PP could reduce myocardial infarct size (IS) after IR in rat in vivo. Eighty Lewis rats were randomized to eight groups (n = 10 for each group). Two groups of plasma donor rats donated plasma at 48 h after transient limb ischemia (PP) or control protocol (nonpreconditioned plasma [NPP]). Six groups of recipient rats received normal saline (NS; NS-IR 1, and NS-IR 24 groups), NPP (NPP-IR 1 and NPP-IR 24 groups), or PP (PP-IR 1 and PP-IR 24 groups) at one or 24 h before myocardial IR. Myocardial IR consisted of 30-min left anterior descending (LAD) coronary artery occlusion and 180-min reperfusion. The area at risk (AAR) and infarct area were determined by double-staining with Evans blue and triphenyltetrazolium chloride. IS was calculated by infarct area divided by AAR. This was a 3 × 2 factorial design study, and factorial analysis was used to evaluate the data. If an interaction between the fluid and transfusion time existed, one-way analysis of variance with Bonferroni correction for multiple comparisons was used to analyze the single effects of fluid type when the transfusion time was fixed. IS in the NPP-IR 1 and PP-IR 1 groups was smaller than in the NS-IR 1 group (F = 6.838, P = 0.005; NPP-IR 1: 57 ± 8% vs. NS-IR1: 68 ± 6%, t = 2.843, P = 0.020; PP-IR 1: 56 ± 8% vs. NS-IR 1: 68 ± 6%, t = 3.102, P = 0.009), but no significant difference was detected between the NPP-IR 1 and PP-IR 1 groups (57 ± 8% vs. 56 ± 8%, t = 0.069, P = 1.000). IS in the NPP-IR 24 and PP-IR 24 groups was smaller than in the NS-IR 24 group (F = 24.796, P< 0.001; NPP-IR 24: 56% ± 7% vs. NS-IR 24: 68 ± 7%, t = 3.102, P = 0.026; PP-IR 24: 40 ± 9% vs. NS-IR 24: 68 ± 7%, t = 7.237, P< 0.001); IS in the PP-IR 24 group was smaller than in the NPP-IR 24 group (40 ± 9% vs. 56 ± 7%, t = 4.135, P = 0.002). Transfusion of PP collected at late phase after remote ischemic preconditioning could reduce IS, suggesting that late-phase cardioprotection was transferable in vivo.

Effects of conditioners on microshear bond strength to enamel after carbamide peroxide bleaching and/or casein phosphopeptide-amorphous calcium phosphate (CPP-ACP) treatment.

PubMed

Adebayo, O A; Burrow, M F; Tyas, M J

2007-11-01

To evaluate (a) the enamel microshear bond strength (MSBS) of a universal adhesive and (b) the effects of conditioning with a self-etching primer adhesive with/without prior bleaching and/or casein phosphopeptide-amorphous calcium phosphate (CPP-ACP) application. Thirty-five molars were cut into four sections, assigned randomly to four groups (no treatment; 16% carbamide peroxide bleaching; CPP-ACP-containing paste (Tooth Mousse, TM); bleaching and TM) and treated accordingly. Specimens were divided into two for bonding with either a self-etching primer (Clearfil SE Bond, CSE) or a total-etch adhesive (Single Bond, SB). Specimens for CSE bonding were subdivided for one of four preconditioning treatments (no conditioning; 30-40% phosphoric acid (PA); 15% EDTA; 20% polyacrylic acid conditioner (Cavity conditioner, CC) and treated. The adhesives were applied and resin composite bonded to the enamel using microtubes (internal diameter 0.75mm). Bonds were stressed in shear until failure, mean MSBS calculated and data analysed using ANOVA with Tukey's HSD test (alpha=0.05). The modes of bond failure were assessed and classified. Two-way ANOVA revealed significant differences between treatments (P<0.0001), conditioners (P<0.0001) and a significant interaction between treatments and conditioners (P=0.001). One-way ANOVA revealed no significant differences in MSBS following any of the treatments for SB; following TM application for CSE without preconditioning; and significant differences in MSBS following bleaching with and without TM application for CSE. With preconditioning, applying PA before CSE post-bleaching and either PA or CC before CSE post-TM application, resulted in significant differences in MSBS (P<0.05). The use of conditioners prior to bonding with the self-etching primer adhesive system on treated enamel may significantly improve bond strengths.

Effect of micronisation of pre-conditioned cowpeas on cooking time and sensory properties of cooked cowpeas.

PubMed

Kayitesi, Eugénie; Duodu, Kwaku Gyebi; Minnaar, Amanda; de Kock, Henriette L

2013-03-15

Cowpea is mostly utilised as cooked whole seeds. This is often achieved only after boiling for up to 2 h, resulting in high energy consumption and a long time for food preparation. Micronisation of pre-conditioned cowpeas reduces their cooking time. Micronisation changes the physicochemical properties of cowpea seeds, which may affect the sensory properties of cooked cowpeas. Consumer acceptance and utilisation of micronised cowpeas depend on their sensory properties. Micronised and unmicronised samples of Blackeye, Bechuana white, Glenda and Dr Saunders cowpeas were subjected to cooking time, descriptive sensory and colour analyses. Micronisation significantly reduced cowpea cooking time by 28-49%. There were significant (P < 0.05) increases in roasted aroma and flavour, mushy texture and splitting in all micronised samples. Bechuana white was more mushy and split than others. There were significant decreases in firmness, mealiness and coarseness after micronisation for all cowpea types. Micronised cowpeas were darker (lower L* values) than unmicronised cooked cowpeas. Darkening was more evident in light-coloured than dark-coloured cowpeas. Micronisation reduces cowpea cooking time but also affects sensory properties of cowpeas such as introducing roasted flavours that may not be familiar to consumers. This might have an influence on consumer acceptance of micronised cowpeas. © 2012 Society of Chemical Industry.

Effect of Hypoglycemic Agents on Ischemic Preconditioning in Patients With Type 2 Diabetes and Symptomatic Coronary Artery Disease

PubMed Central

Rahmi, Rosa Maria; Uchida, Augusto Hiroshi; Rezende, Paulo Cury; Lima, Eduardo Gomes; Garzillo, Cibele Larrosa; Favarato, Desiderio; Strunz, Celia M.C.; Takiuti, Myrthes; Girardi, Priscyla; Hueb, Whady; Kalil Filho, Roberto; Ramires, José A.F.

2013-01-01

OBJECTIVE To assess the effect of two hypoglycemic drugs on ischemic preconditioning (IPC) patients with type 2 diabetes and coronary artery disease (CAD). RESEARCH DESIGN AND METHODS We performed a prospective study of 96 consecutive patients allocated into two groups: 42 to group repaglinide (R) and 54 to group vildagliptin (V). All patients underwent two consecutive exercise tests (ET1 and ET2) in phase 1 without drugs. In phase 2, 1 day after ET1 and -2, 2 mg repaglinide three times daily or 50 mg vildagliptin twice daily was given orally to patients in the respective group for 6 days. On the seventh day, 60 min after 6 mg repaglinide or 100 mg vildagliptin, all patients underwent two consecutive exercise tests (ET3 and ET4). RESULTS In phase 1, IPC was demonstrated by improvement in the time to 1.0 mm ST-segment depression and rate pressure product (RPP). All patients developed ischemia in ET3; however, 83.3% of patients in group R experienced ischemia earlier in ET4, without significant improvement in RPP, indicating the cessation of IPC (P < 0.0001). In group V, only 28% of patients demonstrated IPC cessation, with 72% still having the protective effect (P < 0.0069). CONCLUSIONS Repaglinide eliminated myocardial IPC, probably by its effect on the KATP channel. Vildagliptin did not damage this protective mechanism in a relevant way in patients with type 2 diabetes and CAD, suggesting a good alternative treatment in this population. PMID:23250803

Modeling the intense 2012-2013 dense water formation event in the northwestern Mediterranean Sea: Evaluation with an ensemble simulation approach

NASA Astrophysics Data System (ADS)

Waldman, Robin; Somot, Samuel; Herrmann, Marine; Bosse, Anthony; Caniaux, Guy; Estournel, Claude; Houpert, Loic; Prieur, Louis; Sevault, Florence; Testor, Pierre

2017-02-01

The northwestern Mediterranean Sea is a well-observed ocean deep convection site. Winter 2012-2013 was an intense and intensely documented dense water formation (DWF) event. We evaluate this DWF event in an ensemble configuration of the regional ocean model NEMOMED12. We then assess for the first time the impact of ocean intrinsic variability on DWF with a novel perturbed initial state ensemble method. Finally, we identify the main physical mechanisms driving water mass transformations. NEMOMED12 reproduces accurately the deep convection chronology between late January and March, its location off the Gulf of Lions although with a southward shift and its magnitude. It fails to reproduce the Western Mediterranean Deep Waters salinification and warming, consistently with too strong a surface heat loss. The Ocean Intrinsic Variability modulates half of the DWF area, especially in the open-sea where the bathymetry slope is low. It modulates marginally (3-5%) the integrated DWF rate, but its increase with time suggests its impact could be larger at interannual timescales. We conclude that ensemble frameworks are necessary to evaluate accurately numerical simulations of DWF. Each phase of DWF has distinct diapycnal and thermohaline regimes: during preconditioning, the Mediterranean thermohaline circulation is driven by exchanges with the Algerian basin. During the intense mixing phase, surface heat fluxes trigger deep convection and internal mixing largely determines the resulting deep water properties. During restratification, lateral exchanges and internal mixing are enhanced. Finally, isopycnal mixing was shown to play a large role in water mass transformations during the preconditioning and restratification phases.

Stress alters asenapine-induced Fos expression in the Meynert's nucleus: response of adjacent hypocretin and melanin-concentrating hormone neurons in rat.

PubMed

Majercikova, Z; Kiss, A

2016-01-01

Asenapine (ASE), an atypical antipsychotic drug used in the treatment of schizophrenia, induces Fos expression in forebrain. Effect of ASE on activity of basal nucleus of Meynert (NBM) cells, a part of the striatal-cortical circuits, was studied. We were also interested to reveal whether a chronic unpredictable variable mild stress (CMS) preconditioning might affect the ASE impact. Rats were divided into as follows: controls-vehicle, controls-ASE, stressed-vehicle and stressed-ASE groups. CMS included restrain, social isolation, crowding, swimming and cold applied for 21 days. On the 22nd day, rats were subcutaneously injected with ASE (0.3 mg/kg) or vehicle (saline 300 μl/rat), 90 min prior euthanizing. After transcardial fixation, brains were cut into 30 μm thick coronal sections. Fos protein presence, as indicator of cell activity, was detected by ABC immunohistochemistry. Hypocretin (Hcrt) and melanin-concentrating hormone (MCH) containing cells were visualized with fluorescent dyes. ASE induced significant increase in Fos expression in NBM in both controls and CMS preconditioned rats in comparison with the related vehicle-treated controls. CMS preconditioning, however, significantly lowered the Fos response to ASE in NBM. From Hrct and MCH cells, only Hcrt ones displayed Fos presence in response to ASE. This study demonstrates for the first time that ASE may target a special group of cells occupying NBM, which effect can be modulated by CMS preconditioning. This finding extends a view that ASE impact may extend beyond the classical forebrain target areas common for the action of all antipsychotics and might be helpful in the identification of sites and side effects of its therapeutic actions.

Reperfusion kinase phosphorylation is essential but not sufficient in the mediation of pharmacological preconditioning: Characterisation in the bi-phasic profile of early and late protection.

PubMed

Bell, Robert M; Clark, James E; Hearse, David J; Shattock, Michael J

2007-01-01

Pharmacological preconditioning (PPC) triggers early (ePPC) and delayed protection (dPPC), occurring within 1 h or after 24 h following the preconditioning stimulus, respectively, through recruitment of protein kinase signalling. Angiotensin II (ATII) is a recognised trigger of PPC, recruiting kinases and transcription factors known to be involved in both phases of protection. Our objectives were to determine whether ATII is capable of triggering dPPC and whether recruitment of pro-survival kinases, Akt and extracellular signal-regulated kinase (ERK), following the injurious ischaemic insult is essential for the mediation of PPC. In a mouse Langendorff model of ischaemia/reperfusion injury, we undertook to determine whether ATII triggers both ePPC and dPPC. Western blot analysis was used to determine kinase phosphorylation at reperfusion, and kinase inhibitors wortmannin and PD98059 were used to ascertain the significance of kinase regulation. We demonstrated that ATII triggered PPC with attenuation of infarction at 1 and 24 h (19+/-4% and 25+/-4% versus control, 35+/-4% of risk zone, p < 0.05), consistent with the ePPC and dPPC time-course. This bi-phasic protection was associated with significant post-ischaemic phosphorylation of both Akt and ERK within the first 5 min of reperfusion. Akt and ERK phosphorylation was increased following ePPC by 4.5+/-0.5 and 1.9+/-0.6 fold, respectively (p < 0.001), and dPPC by 24+/-2.0 and 2.1+/-0.1 fold, respectively (p < 0.001). Both wortmannin and PD98059 administered during reperfusion ameliorated the phosphorylation of Akt and ERK and abrogated the resistance to infarction resulting from both ePPC and dPPC (33+/-3% and 35+/-4%, respectively, versus controls 33+/-4% and 33+/-5%, p = NS). There was no evidence of augmented phosphorylation of either p38 kinase or JNK at either time point. We demonstrate that PPC results in a clearly delineated time-course of bi-phasic protection against injurious ischemic injury that is correlated with reperfusion kinase phosphorylation of both Akt and ERK. These data indicate a novel mechanism of early and particularly delayed preconditioning.

Equivalent cardioprotection induced by ischemic and hypoxic preconditioning.

PubMed

Xiang, Xujin; Lin, Haixia; Liu, Jin; Duan, Zeyan

2013-04-01

We aimed to compare cardioprotection induced by various hypoxic preconditioning (HPC) and ischemic preconditioning (IPC) protocols. Isolated rat hearts were randomly divided into 7 groups (n = 7 per group) and received 3 or 5 cycles of 3-minute ischemia or hypoxia followed by 3-minute reperfusion (IPC33 or HPC33 or IPC53 or HPC53 group), 3 cycles of 5-minute ischemia or hypoxia followed by 5-minute reperfusion (IPC35 group or HPC35 group), or 30-minute perfusion (ischemic/reperfusion group), respectively. Then all the hearts were subjected to 50-minute ischemia and 120-minute reperfusion. Cardiac function, infarct size, and coronary flow rate (CFR) were evaluated. Recovery of cardiac function and CFR in IPC35, HPC35, and HPC53 groups was significantly improved as compared with I/R group (p < 0.01). There were no significant differences in cardiac function parameters between IPC35 and HPC35 groups. Consistently, infarct size was significantly reduced in IPC35, HPC35, and HPC53 groups compared with ischemic/reperfusion group. Multiple-cycle short duration HPC exerted cardioprotection, which was as powerful as that of IPC. Georg Thieme Verlag KG Stuttgart · New York.

Preconditioning crush increases the survival rate of motor neurons after spinal root avulsion

PubMed Central

Li, Lin; Zuo, Yizhi; He, Jianwen

2014-01-01

In a previous study, heat shock protein 27 was persistently upregulated in ventral motor neurons following nerve root avulsion or crush. Here, we examined whether the upregulation of heat shock protein 27 would increase the survival rate of motor neurons. Rats were divided into two groups: an avulsion-only group (avulsion of the L4 lumbar nerve root only) and a crush-avulsion group (the L4 lumbar nerve root was crushed 1 week prior to the avulsion). Immunofluorescent staining revealed that the survival rate of motor neurons was significantly greater in the crush-avulsion group than in the avulsion-only group, and this difference remained for at least 5 weeks after avulsion. The higher neuronal survival rate may be explained by the upregulation of heat shock protein 27 expression in motor neurons in the crush-avulsion group. Furthermore, preconditioning crush greatly attenuated the expression of nitric oxide synthase in the motor neurons. Our findings indicate that the neuroprotective action of preconditioning crush is mediated through the upregulation of heat shock protein 27 expression and the attenuation of neuronal nitric oxide synthase upregulation following avulsion. PMID:25206852

Emittance of TD-NiCr after simulated reentry

NASA Technical Reports Server (NTRS)

Clark, R. K.; Dicus, D. L.; Lisagor, W. B.

1978-01-01

The effects of simulated reentry heating on the emittance of TD-NiCr were investigated. Groups of specimens with three different preconditioning treatments were exposed to 6, 24, and 30 half-hour simulated reentry exposure cycles in a supersonic arc tunnel at each of three conditions intended to produce surface temperatures of 1255, 1365, and 1475 K. Emittance was determined at 1300 K on specimens which were preconditioned only and specimens after completion of reentry simulation exposure. Oxide morphology and chemistry were studied by scanning electron microscopy and X-ray diffraction analysis. A consistent relationship was established between oxide morphology and total normal emittance. Specimens with coarser textured oxides tended to have lower emittances than specimens with finer textured oxides.

Exercise training improves free testosterone in lifelong sedentary aging men.

PubMed

Hayes, Lawrence D; Herbert, Peter; Sculthorpe, Nicholas F; Grace, Fergal M

2017-07-01

As the impact of high-intensity interval training (HIIT) on systemic hormones in aging men is unstudied to date, we investigated whether total testosterone (TT), sex hormone-binding globulin (SHBG), free testosterone (free-T) and cortisol (all in serum) were altered following HIIT in a cohort of 22 lifelong sedentary (62 ± 2 years) older men. As HIIT requires preconditioning exercise in sedentary cohorts, participants were tested at three phases, each separated by six-week training; baseline (phase A), following conditioning exercise (phase B) and post-HIIT (phase C). Each measurement phase used identical methods. TT was significantly increased following HIIT (~17%; P  < 0.001) with most increase occurring during preconditioning (~10%; P  = 0.007). Free-T was unaffected by conditioning exercise ( P  = 0.102) but was significantly higher following HIIT compared to baseline (~4.5%; P  = 0.023). Cortisol remained unchanged from A to C ( P  = 0.138). The present data indicate a combination of preconditioning, and HIIT increases TT and SHBG in sedentary older males, with the HIIT stimulus accounting for a small but statistically significant increase in free-T. Further study is required to determine the biological importance of small improvements in free-T in aging men. © 2017 The authors.

Co-Leadership – A Management Solution for Integrated Health and Social Care

PubMed Central

Hansson, Johan; Hasson, Henna; Sachs, Magna Andreen

2016-01-01

Introduction: Co-leadership has been identified as one approach to meet the managerial challenges of integrated services, but research on the topic is limited. In the present study, co-leadership, practised by pairs of managers – each manager representing one of the two principal organizations in integrated health and social care services – was explored. Aim: To investigate co-leadership in integrated health and social care, identify essential preconditions in fulfilling the management assignment, its operationalization and impact on provision of sustainable integration of health and social care. Method: Interviews with eight managers exercising co-leadership were analysed using directed content analysis. Respondent validation was conducted through additional interviews with the same managers. Results: Key contextual preconditions were an organization-wide model supporting co-leadership and co-location of services. Perception of the management role as a collective activity, continuous communication and lack of prestige were essential personal and interpersonal preconditions. In daily practice, office sharing, being able to give and take and support each other contributed to provision of sustainable integration of health and social care. Conclusion and discussion: Co-leadership promoted robust management by providing broader competence, continuous learning and joint responsibility for services. Integrated health and social care services should consider employing co-leadership as a managerial solution to achieve sustainability. PMID:27616963

No influence of ischemic preconditioning on running economy.

PubMed

Kaur, Gungeet; Binger, Megan; Evans, Claire; Trachte, Tiffany; Van Guilder, Gary P

2017-02-01

Many of the potential performance-enhancing properties of ischemic preconditioning suggest that the oxygen cost for a given endurance exercise workload will be reduced, thereby improving the economy of locomotion. The aim of this study was to identify whether ischemic preconditioning improves exercise economy in recreational runners. A randomized sham-controlled crossover study was employed in which 18 adults (age 27 ± 7 years; BMI 24.6 ± 3 kg/m 2 ) completed two, incremental submaximal (65-85% VO 2max ) treadmill running protocols (3 × 5 min stages from 7.2-14.5 km/h) coupled with indirect calorimetry to assess running economy following ischemic preconditioning (3 × 5 min bilateral upper thigh ischemia) and sham control. Running economy was expressed as mlO 2 /kg/km and as the energy in kilocalories required to cover 1 km of horizontal distance (kcal/kg/km). Ischemic preconditioning did not influence steady-state heart rate, oxygen consumption, minute ventilation, respiratory exchange ratio, energy expenditure, and blood lactate. Likewise, running economy was similar (P = 0.647) between the sham (from 201.6 ± 17.7 to 204.0 ± 16.1 mlO 2 /kg/km) and ischemic preconditioning trials (from 202.8 ± 16.2 to 203.1 ± 15.6 mlO 2 /kg/km). There was no influence (P = 0.21) of ischemic preconditioning on running economy expressed as the caloric unit cost (from 0.96 ± 0.12 to 1.01 ± 0.11 kcal/kg/km) compared with sham (from 1.00 ± 0.10 to 1.00 ± 0.08 kcal/kg/km). The properties of ischemic preconditioning thought to affect exercise performance at vigorous to severe exercise intensities, which generate more extensive physiological challenge, are ineffective at submaximal workloads and, therefore, do not change running economy.

Preconditioning of bone marrow-derived mesenchymal stromal cells by tetramethylpyrazine enhances cell migration and improves functional recovery after focal cerebral ischemia in rats.

PubMed

Li, Lin; Chu, Lisheng; Fang, Yan; Yang, Yan; Qu, Tiebing; Zhang, Jianping; Yin, Yuanjun; Gu, Jingjing

2017-05-12

Transplantation of bone marrow-derived mesenchymal stem cells (BMSCs) is one of the new therapeutic strategies for treating ischemic stroke. However, the relatively poor migratory capacity of BMSCs toward infarcted regions limited the therapeutic potential of this approach. Pharmacological preconditioning can increase the expression of CXC chemokine receptor 4 (CXCR4) in BMSCs and enhance cell migration toward the injury site. In the present study, we investigated whether tetramethylpyrazine (TMP) preconditioning could enhance BMSCs migration to the ischemic brain and improve functional recovery through upregulating CXCR4 expression. BMSCs were identified by flow cytometry analysis. BMSCs migration was evaluated in vitro by transwell migration assay, and CXCR4 expression was measured by quantitative reverse transcription-polymerase chain reaction and western blot analysis. In rats with focal cerebral ischemia, the neurological function was evaluated by the modified neurological severity score, the adhesive removal test and the corner test. The homing BMSCs and angiogenesis were detected by immunofluorescence, and expression of stromal cell-derived factor-1 (SDF-1) and CXCR4 was measured by western blot analysis. Flow cytometry analysis demonstrated that BMSCs expressed CD29 and CD90, but not CD34 and CD45. TMP pretreatment dose-dependently induced BMSCs migration and CXCR4 expression in vitro, which was significantly inhibited by AMD3100, a CXCR4 antagonist. In rat stroke models, we found more TMP-preconditioned BMSCs homing toward the infarcted regions than nonpreconditioned cells, leading to improved neurological performance and enhanced angiogenesis. Moreover, TMP-preconditioned BMSCs significantly upregulated the protein expression of SDF-1 and CXCR4 in the ischemic boundary regions. These beneficial effects of TMP preconditioning were blocked by AMD3100. TMP preconditioning enhances the migration and homing ability of BMSCs, increases CXCR4 expression, promotes angiogenesis, and improves neurological performance. Therefore, TMP preconditioning may be an effective strategy to improve the therapeutic potency of BMSCs for ischemic stroke due to enhanced BMSCs migration to ischemic regions.

Preconditioning of adipose tissue-derived mesenchymal stem cells with deferoxamine increases the production of pro-angiogenic, neuroprotective and anti-inflammatory factors: Potential application in the treatment of diabetic neuropathy.

PubMed

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 evaluated in an in vitro model of DN. Altogether, our findings suggest that DFX preconditioning of AD-MSCs improves their therapeutic potential and should be considered as a potential strategy for the generation of new alternatives for DN treatment.

Preconditioning of adipose tissue-derived mesenchymal stem cells with deferoxamine increases the production of pro-angiogenic, neuroprotective and anti-inflammatory factors: Potential application in the treatment of diabetic neuropathy

PubMed Central

Oses, Carolina; Olivares, Belén; Ezquer, Marcelo; Acosta, Cristian; Bosch, Paul; Donoso, Macarena; Léniz, Patricio

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 evaluated in an in vitro model of DN. Altogether, our findings suggest that DFX preconditioning of AD-MSCs improves their therapeutic potential and should be considered as a potential strategy for the generation of new alternatives for DN treatment. PMID:28542352

Methods for ensuring compliance in an international greenhouse gas trading system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hargrave, T.; Helme, E.A.

1998-12-31

At the third Conference of the Parties to the UN Framework Convention on Climate Change held in December, 1997, the international community established binding greenhouse gas (GHG) emissions obligations for industrialized countries. The Parties to the new Kyoto Protocol also agreed on the use of a number of market-based mechanisms, including international GHG emissions trading. These market mechanisms were of critical to the importance because they have the potential to significantly reduce the costs of treaty compliance. In principle, an international cap-and-trade system appears to be one of the most cost-effective means of reducing GHG emissions. Maintaining the integrity ofmore » the trading system is of primary importance in ensuring that trading helps countries to meet their GHG commitments. This paper explores methods for ensuring compliance in an international greenhouse gas trading system, starting with a discussion of preconditions for participation in trading and then moving to features of an international compliance system. Achieving maximum compliance with international requirements may best be accomplished by limiting participation in trading to Annex I countries that maintain strong domestic compliance systems. Prior to the climate negotiations in Kyoto in December 1997, the US Administration proposed a number of preconditions for participation in trading, including the adoption of international measurement standards and the establishment of domestic compliance and enforcement programs. This paper explores these and other preconditions, including the establishment of tough domestic financial penalties on companies that exceed allowed emissions and seller responsibility for the delivery of real reductions. The paper also discusses several necessary features of the international compliance system.« less

Linking microbial community structure and product spectrum of rice straw fermentation with undefined mixed culture

NASA Astrophysics Data System (ADS)

Ai, Binling; Chi, Xue; Meng, Jia; Sheng, Zhanwu; Zheng, Lili; Zheng, Xiaoyan; Li, Jianzheng

2017-12-01

Undefined mixed culture-based fermentation is an alternative strategy for biofuels and bioproducts production from lignocellulosic biomass without supplementary cellulolytic enzymes. Mixed culture produces mixed carboxylates. To estimate the relationship between microbial community structure and product spectrum, carboxylate production was initiated by mixed cultures with different microbial community structure. All the inoculum cultures were derived from the same enrichment culture from the combination of cattle manure, pig manure compost, corn field soil and rotten wood. Due to the differences in the preparation method and culture time, the inoculum cultures for batch fermentation had high similarity in microbial community structure, while the community structure of each inoculum culture for repeated batch fermentation differed from that of another. The inoculum cultures with similar community structure led to a similar product spectrum. In batch fermentation, the selectivity of main product butyric acid stabilized around 76%. The inoculum cultures with different community structures resulted in different product spectra. In repeated batch fermentation, the butyric acid content gradually decreased to 27%, and the by-product acetic acid content steadily increased to 56%. The other by-products including propionic, valeric and caproic acids were also increased. It is deduced that keeping the microbial community structure stable makes the basic and key precondition for steady production of specific carboxylic acid with undefined mixed culture.

Suzuki-Trotter Formula for Real-Time Dependent LDA I: Electron Dynamics

NASA Astrophysics Data System (ADS)

Sugino, Osamu; Miyamoto, Yoshiyuki

1998-03-01

To investigate various physical and chemical processes where electron dynamics play a role (e.g. collisions or photochemical reactions), solving the real-time Schrödinger equation is essentially important. ihbar fracpartialφpartial t=H φ Trial of solving eqn. (1) from first principles has begun very recently(K. Yabana and G. F. Bertch, Phys. Rev. B54) 4484 (1996)., and it is now in the stage of establishing efficient, stable, and accurate method for numerical calculation. In this talk, we present several improvements in the method of solving eqn. (1) within the density functional theory: (A) higher order Suzuki-Trotter formula(M. Suzuki, Phys. Lett. A146) 319 (1990). to integrate eqn. (1) keeping the orthonormality of the wavefunctions, (B) special interpolation scheme for the self-consistent potential to reduce the drift in the total-energy, and (C) the preconditioning techniques to increase the time step for the simulation. We will demonstrate numerical stability and efficiency using several cluster calculations, and will address the accuracy by comparing the computed cross sections for atom-electron collisions with experiment.

Augmentation of aerobic respiration and mitochondrial biogenesis in skeletal muscle by hypoxia preconditioning with cobalt chloride

DOE Office of Scientific and Technical Information (OSTI.GOV)

Saxena, Saurabh; Shukla, Dhananjay; Bansal, Anju, E-mail: anjubansaldipas@gmail.com

High altitude/hypoxia training is known to improve physical performance in athletes. Hypoxia induces hypoxia inducible factor-1 (HIF-1) and its downstream genes that facilitate hypoxia adaptation in muscle to increase physical performance. Cobalt chloride (CoCl{sub 2}), a hypoxia mimetic, stabilizes HIF-1, which otherwise is degraded in normoxic conditions. We studied the effects of hypoxia preconditioning by CoCl{sub 2} supplementation on physical performance, glucose metabolism, and mitochondrial biogenesis using rodent model. The results showed significant increase in physical performance in cobalt supplemented rats without (two times) or with training (3.3 times) as compared to control animals. CoCl{sub 2} supplementation in rats augmentedmore » the biological activities of enzymes of TCA cycle, glycolysis and cytochrome c oxidase (COX); and increased the expression of glucose transporter-1 (Glut-1) in muscle showing increased glucose metabolism by aerobic respiration. There was also an increase in mitochondrial biogenesis in skeletal muscle observed by increased mRNA expressions of mitochondrial biogenesis markers which was further confirmed by electron microscopy. Moreover, nitric oxide production increased in skeletal muscle in cobalt supplemented rats, which seems to be the major reason for peroxisome proliferator activated receptor-gamma coactivator-1α (PGC-1α) induction and mitochondrial biogenesis. Thus, in conclusion, we state that hypoxia preconditioning by CoCl{sub 2} supplementation in rats increases mitochondrial biogenesis, glucose uptake and metabolism by aerobic respiration in skeletal muscle, which leads to increased physical performance. The significance of this study lies in understanding the molecular mechanism of hypoxia adaptation and improvement of work performance in normal as well as extreme conditions like hypoxia via hypoxia preconditioning. -- Highlights: ► We supplemented rats with CoCl{sub 2} for 15 days along with training. ► CoCl{sub 2} supplementation augmented endurance performance and aerobic respiration. ► It increased glucose uptake and metabolism in muscle. ► It enhanced mitochondrial biogenesis in red gastrocnemius muscle.« less

Numerical Aspects of Nonhydrostatic Implementations Applied to a Parallel Finite Element Tsunami Model

NASA Astrophysics Data System (ADS)

Fuchs, A.; Androsov, A.; Harig, S.; Hiller, W.; Rakowsky, N.

2012-04-01

Based on the jeopardy of devastating tsunamis and the unpredictability of such events, tsunami modelling as part of warning systems is still a contemporary topic. The tsunami group of Alfred Wegener Institute developed the simulation tool TsunAWI as contribution to the Early Warning System in Indonesia. Although the precomputed scenarios for this purpose qualify for satisfying deliverables, the study of further improvements continues. While TsunAWI is governed by the Shallow Water Equations, an extension of the model is based on a nonhydrostatic approach. At the arrival of a tsunami wave in coastal regions with rough bathymetry, the term containing the nonhydrostatic part of pressure, that is neglected in the original hydrostatic model, gains in importance. In consideration of this term, a better approximation of the wave is expected. Differences of hydrostatic and nonhydrostatic model results are contrasted in the standard benchmark problem of a solitary wave runup on a plane beach. The observation data provided by Titov and Synolakis (1995) serves as reference. The nonhydrostatic approach implies a set of equations that are similar to the Shallow Water Equations, so the variation of the code can be implemented on top. However, this additional routines cause a lot of issues you have to cope with. So far the computations of the model were purely explicit. In the nonhydrostatic version the determination of an additional unknown and the solution of a large sparse system of linear equations is necessary. The latter constitutes the lion's share of computing time and memory requirement. Since the corresponding matrix is only symmetric in structure and not in values, an iterative Krylov Subspace Method is used, in particular the restarted Generalized Minimal Residual Algorithm GMRES(m). With regard to optimization, we present a comparison of several combinations of sequential and parallel preconditioning techniques respective number of iterations and setup/application time. Since the used software package pARMS 3.2, that provides solving and preconditioning techniques, works via MPI parallelism, in an auxiliary branch we adapted TsunAWI and switched from OpenMP to MPI with attached importance to internal partition management.

Antidepressant-like effects of mild hypoxia preconditioning in the learned helplessness model in rats.

PubMed

Rybnikova, Elena; Mironova, Vera; Pivina, Svetlana; Tulkova, Ekaterina; Ordyan, Natalia; Vataeva, Ludmila; Vershinina, Elena; Abritalin, Eugeny; Kolchev, Alexandr; Nalivaeva, Natalia; Turner, Anthony J; Samoilov, Michail

2007-05-07

The effects of preconditioning using mild repetitive hypobaric hypoxia (360 Torr for 2 h each of 3 days) have been studied in the learned helplessness model of depression in rats. Male Wistar rats displayed persistent depressive symptoms (depressive-like behaviour in open field, increased anxiety levels in elevated plus maze, ahedonia, elevated plasma glucocorticoids and impaired dexamethasone test) following the exposure to unpredictable and inescapable footshock in the learned helplessness paradigm. Antidepressant treatment (ludiomil, 5 mg/kg i.p.) augmented the development of the depressive state. The hypoxic preconditioning had a clear antidepressive action returning the behavioural and hormonal parameters to the control values and was equally effective in terms of our study as the antidepressant. The findings suggest hypoxic preconditioning as an effective tool for the prophylaxis of post-stress affective pathologies in humans.

Preceptors' reflections on their educational role before and after a preceptor preparation course: A prospective qualitative study.

PubMed

Mårtensson, Gunilla; Löfmark, Anna; Mamhidir, Anna-Greta; Skytt, Bernice

2016-07-01

During clinical practice, preceptors play an important educational role in helping nursing students become secure and effective practitioners. For this educational role they need adequate preparation. The aim of the present prospective study was to describe preceptors' experiences of their educational role before and after attending a university preceptor preparation course. This 7.5-credit, Master's level course is offered on a part-time basis and covers one semester. The theoretical approach was self-directed and reflective learning. Twentyseven preceptors participated in group interviews before and after the course, and data were analyzed using qualitative content analysis. The findings revealed a shift in preceptors' perceptions. Their view of the educational role changed from being characterized by individual experiences and notions to being guided by personal and formal demands. Before the course, the lack of sufficient preconditions for preceptorship predominated, whereas after the course participants described ways of creating such preconditions. Before the course, the supervisory process was described as teaching, whereas after the course it was described as a learning process for students. Using reflective learning in a preceptor preparation course can develop and strengthen preceptors' view of their educational role and help them manage and create the preconditions for preceptorship. Copyright © 2016 Elsevier Ltd. All rights reserved.

Preconditioning With Tauroursodeoxycholic Acid Protects Against Contrast-Induced HK-2 Cell Apoptosis by Inhibiting Endoplasmic Reticulum Stress.

PubMed

Peng, Pingan; Ma, Qian; Wang, Le; Zhang, Ou; Han, Hongya; Liu, Xiaoli; Zhou, Yujie; Zhao, Yingxin

2015-11-01

To investigate whether tauroursodeoxycholic acid (TUDCA) could attenuate contrast media (CM)-induced renal tubular cell apoptosis by inhibiting endoplasmic reticulum stress (ERS), we exposed HK-2 cells to increasing doses of meglumine diatrizoate (20, 40, and 80 mg I/mL) for 2 to 16 hours, with/without TUDCA preconditioning for 24 hours. Cell viability test, Hoechst 33258 staining, and flow cytometry were used to detect meglumine diatrizoate-induced cell apoptosis, while real-time polymerase chain reaction and Western blot analysis were used to measure the expressions of ERS markers of glucose-regulated protein 78 (GRP78), activating transcription factor 4 (ATF4), and the apoptosis-related marker of caspase 12. Cell apoptosis and messenger RNA (mRNA) expression of GRP78 (P = .005), ATF4 (P = .01), and caspase 12 (P = .001) were significantly higher in the CM 4 hours group than the control as well as the protein expressions. The TUDCA preconditioning reduced the mRNA expression of GRP78, ATF4, and caspase 12 in the CM 4 hours groups (P = .009, .019, and .003, respectively) as well as the protein expression. In conclusion, TUDCA could protect renal tubular cells from meglumine diatrizoate-induced apoptosis by inhibiting ERS. © The Author(s) 2015.

[The complex plague--reconsiderations of an epidemic from the past].

PubMed

Moseng, Ole Georg

2007-12-13

Speculations have arisen about the black plague in recent years - was it a disease caused by YERSINIA PESTIS: or something else? Extensive outbreaks in India in the 1890s have formed the basis for descriptions of the plague, both for those who believe that the medieval plagues and modern plague were different diseases and for those who claim that the plague has been one and the same disease throughout history. The plague was more or less defined as a disease in the 1890s, and the understanding of its clinical course and dissemination at the time has uncritically been understood as the general model for spreading of the plague. But plague is a many-faceted disease. It has spread to five continents in modern times, through an array of ecosystems and under widely different climatic conditions. It can also be passed on to man, and from one individual to another, in different ways. The biological conditions that prevailed in India have not been relevant for medieval Norway. The preconditions for spreading of plague epidemics of the past in a Nordic climate must therefore have been different. It can only be expected that contemporary descriptions of historic epidemics are different from those in modern times.

Suppression of pyritic sulphur during flotation tests using the bacterium Thiobacillus ferrooxidans.

PubMed

Townsley, C C; Atkins, A S; Davis, A J

1987-07-01

Environmental concern about sulphur dioxide emissions has led to the examination of the possibility of removing pyritic sulphur from coal prior to combustion during froth flotation, a routine method for coal cleaning at the pit-head. The bacterium Thiobacillus ferrooxidans was effective in leaching 80% and 63% -53 mum pyrite at 2% and 6% pulp density in shake flasks in 240 and 340 h, respectively.The natural floatability of pyrite was significantly reduced in the Hallimond tube following 2.5 min of conditioning in membrane-filtered bacterial liquor prior to flotation. The suppression effect was greatly enhanced in the presence of Thiobacillus ferrooxidans. A bacterial suspension in pH 2.0 distilled water showed 85% suppression, whereas in spent growth liquor this value was 95%. The optimum bacterial density was 3.25 x 10(10) cells/g pyrite in 230-ml distilled water (2% pulp density) in the Hallimond tube. The degree of suppression by the cells was related to particle size but not to pH or temperature. The sulphur content of a synthetic coal/pyrite mixture was reduced from 10.9 to 2.1% by flotation after bacterial preconditioning. It is postulated that pyrite removal in coals which are cleaned by froth flotation could be significantly reduced using a bacterial preconditioning stage with a short residence time of 2.5 min.

PIXIE3D: A Parallel, Implicit, eXtended MHD 3D Code

NASA Astrophysics Data System (ADS)

Chacon, Luis

2006-10-01

We report on the development of PIXIE3D, a 3D parallel, fully implicit Newton-Krylov extended MHD code in general curvilinear geometry. PIXIE3D employs a second-order, finite-volume-based spatial discretization that satisfies remarkable properties such as being conservative, solenoidal in the magnetic field to machine precision, non-dissipative, and linearly and nonlinearly stable in the absence of physical dissipation. PIXIE3D employs fully-implicit Newton-Krylov methods for the time advance. Currently, second-order implicit schemes such as Crank-Nicolson and BDF2 (2^nd order backward differentiation formula) are available. PIXIE3D is fully parallel (employs PETSc for parallelism), and exhibits excellent parallel scalability. A parallel, scalable, MG preconditioning strategy, based on physics-based preconditioning ideas, has been developed for resistive MHD, and is currently being extended to Hall MHD. In this poster, we will report on progress in the algorithmic formulation for extended MHD, as well as the the serial and parallel performance of PIXIE3D in a variety of problems and geometries. L. Chac'on, Comput. Phys. Comm., 163 (3), 143-171 (2004) L. Chac'on et al., J. Comput. Phys. 178 (1), 15- 36 (2002); J. Comput. Phys., 188 (2), 573-592 (2003) L. Chac'on, 32nd EPS Conf. Plasma Physics, Tarragona, Spain, 2005 L. Chac'on et al., 33rd EPS Conf. Plasma Physics, Rome, Italy, 2006

Insurance in clinical research

PubMed Central

Ghooi, Ravindra B.; Divekar, Deepa

2014-01-01

Aims and Objectives: Sponsors need to pay for management of all serious adverse events suffered by subjects in a clinical trial and to compensate for injuries or deaths related to the trial. This study examines if insurance policies of trials, cover all contingencies that require reimbursement or compensation. Materials and Methods: Insurance policies of trials submitted to Sahyadri Hospitals between January 2013 and December 2013 were studied, with respect to the policy period, the limit of liability, deductibles, and preconditions if any. Results: All the policies studied had some deficiencies, in one respect or the other and none had a provision to pay full compensation if required. Some insurers have put in preconditions that could jeopardize the payment of compensation to subjects. Conclusions: Insurances are complicated documents, and need to be critically examined by the ethics committee before approval of the study documents. PMID:25276622

Acidic preconditioning of endothelial colony-forming cells (ECFC) promote vasculogenesis under proinflammatory and high glucose conditions in vitro and in vivo.

PubMed

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 signs of inflammation in the animals receiving preconditioned ECFC. Acidic preconditioning improved ECFC survival and angiogenic activity in the presence of proinflammatory and damage signals present in the ischemic milieu, even under high glucose conditions, and increased their therapeutic potential for postischemia tissue regeneration in a murine model of type 2 diabetes. Collectively, our data suggest that acidic preconditioning of ECFC is a simple and inexpensive strategy to improve the effectiveness of cell transplantation in diabetes, where tissue repair is highly compromised.

Modelling wildfire activity in Iberia with different Atmospheric Circulation WTs

NASA Astrophysics Data System (ADS)

Sousa, P. M.; Trigo, R.; Pereira, M. G.; Rasilla, D.; Gouveia, C.

2012-04-01

This work focuses on the spatial and temporal variability of burnt area (BA) for the entire Iberian Peninsula (IP) and on the construction of statistical models to reproduce the inter-annual variability, based on Weather Types Classification (WTC). A common BA dataset was assembled for the first time for the entire Iberian Peninsula, by merging BA records for the 66 administrative regions of Portugal and Spain. A normalization procedure was then applied to the various size regions before performing a k-means cluster analysis to identify large areas characterized by similar fire regimes. The most compelling results were obtained for 4 clusters (Northwestern, Northern, Southwestern and Eastern) whose spatial patterns and seasonal fire regimes are shown to be related with constraining factors such as topography, vegetation cover and climate conditions. The response of fire burnt surface at monthly time scales to both long-term climatic pre-conditions and short-term synoptic forcing was assessed through correlation and regression analysis using: (i) temperature and precipitation from 2 to 7 months in advance to fire peak season; (ii) synoptic weather patterns derived from 11 distinct classifications derived under the COSTaction-733. Different responses were obtained for each of the considered regions: (i) a relevant link between BA and short-term synoptic forcing (represented by monthly frequencies of WTC) was identified for all clusters; (ii) long-term climatic preconditioning was relevant for all but one cluster (Northern). Taking into account these links, we developed stepwise regression models with the aim of reproducing the observed BA series (i.e. in hindcast mode). These models were based on the best climatic and synoptic circulation predictors identified previously. All models were cross-validated and their performance varies between clusters, though models exclusively based on WTCs tend to better reproduce annual BA time series than those only based on pre-conditioning climatic information. Nevertheless, the best results are attained when both synoptic and climatic predictors are used simultaneously as predictors, in particular for the two western clusters, where correlation coefficient values are higher than 0.7. Finally, we have used WTC composite maps to characterize the typical synoptic configurations that favor high values of BA. These patterns correspond to dry and warm fluxes, associated with anticyclonic regimes, which foster fire ignition (Pereira et al., 2005). Pereira, M.G., Trigo, R.M., DaCamara, C.C., Pereira, J.M.C., Leite, S.M., 2005: "Synoptic patterns associated with large summer forest fires in Portugal". Agricultural and Forest Meteorology. 129, 11-25. COST733, 2011: "COST 733 Wiki - Harmonisation and Applications of Weather Type Classifications for European regions or COST733 spatial domains for Europe". Available at http://geo21.geo.uni-augsburg.de/cost733wiki/Cost733_Wiki_Main [accessed 1 September 2011].

TRPV1 Agonist, Capsaicin, Induces Axon Outgrowth after Injury via Ca2+/PKA Signaling.

PubMed

Frey, Erin; Karney-Grobe, Scott; Krolak, Trevor; Milbrandt, Jeff; DiAntonio, Aaron

2018-01-01

Preconditioning nerve injuries activate a pro-regenerative program that enhances axon regeneration for most classes of sensory neurons. However, nociceptive sensory neurons and central nervous system neurons regenerate poorly. In hopes of identifying novel mechanisms that promote regeneration, we screened for drugs that mimicked the preconditioning response and identified a nociceptive ligand that activates a preconditioning-like response to promote axon outgrowth. We show that activating the ion channel TRPV1 with capsaicin induces axon outgrowth of cultured dorsal root ganglion (DRG) sensory neurons, and that this effect is blocked in TRPV1 knockout neurons. Regeneration occurs only in NF200-negative nociceptive neurons, consistent with a cell-autonomous mechanism. Moreover, we identify a signaling pathway in which TRPV1 activation leads to calcium influx and protein kinase A (PKA) activation to induce a preconditioning-like response. Finally, capsaicin administration to the mouse sciatic nerve activates a similar preconditioning-like response and induces enhanced axonal outgrowth, indicating that this pathway can be induced in vivo . These findings highlight the use of local ligands to induce regeneration and suggest that it may be possible to target selective neuronal populations for repair, including cell types that often fail to regenerate.

Involvement of adenosine and standardization of aqueous extract of garlic (Allium sativum Linn.) on cardioprotective and cardiodepressant properties in ischemic preconditioning and myocardial ischemia-reperfusion induced cardiac injury

PubMed Central

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

Ischemic Preconditioning Increases the Tolerance of Fatty Liver to Hepatic Ischemia-Reperfusion Injury in the Rat

PubMed Central

Serafín, Anna; Roselló-Catafau, Joan; Prats, Neus; Xaus, Carme; Gelpí, Emilio; Peralta, Carmen

2002-01-01

Hepatic steatosis is a major risk factor in ischemia-reperfusion. The present study evaluates whether preconditioning, demonstrated to be effective in normal livers, could also confer protection in the presence of steatosis and investigates the potential underlying protective mechanisms. Fatty rats had increased hepatic injury and decreased survival after 60 minutes of ischemia compared with lean rats. Fatty livers showed a degree of neutrophil accumulation and microcirculatory alterations similar to that of normal livers. However, in presence of steatosis, an increased lipid peroxidation that could be reduced with glutathione-ester pretreatment was observed after hepatic reperfusion. Ischemic preconditioning reduced hepatic injury and increased animal survival. Both in normal and fatty livers, this endogenous protective mechanism was found to control lipid peroxidation, hepatic microcirculation failure, and neutrophil accumulation, reducing the subsequent hepatic injury. These beneficial effects could be mediated by nitric oxide, because the inhibition of nitric oxide synthesis and nitric oxide donor pretreatment abolished and simulated, respectively, the benefits of preconditioning. Thus, ischemic preconditioning could be an effective surgical strategy to reduce the hepatic ischemia-reperfusion injury in normal and fatty livers under normothermic conditions, including hepatic resections, and liver transplantation. PMID:12163383

Improved Flux Formulations for Unsteady Low Mach Number Flows

DTIC Science & Technology

2012-06-01

it requires the resolution of disparate time scales. Unsteady effects may arise from a combination of hydrodynamic effects in which pressure...including rotorcraft flows, jets and shear layers include a combination of both acoustic and hydrodynamic effects. Furthermore these effects may be...preconditioning parameter used for time scaling also affects the dissipation for the spatial flux, hydrodynamic unsteady effects (such as vortex propagation

Perceptual Contrast Enhancement with Dynamic Range Adjustment

PubMed Central

Zhang, Hong; Li, Yuecheng; Chen, Hao; Yuan, Ding; Sun, Mingui

2013-01-01

Recent years, although great efforts have been made to improve its performance, few Histogram equalization (HE) methods take human visual perception (HVP) into account explicitly. The human visual system (HVS) is more sensitive to edges than brightness. This paper proposes to take use of this nature intuitively and develops a perceptual contrast enhancement approach with dynamic range adjustment through histogram modification. The use of perceptual contrast connects the image enhancement problem with the HVS. To pre-condition the input image before the HE procedure is implemented, a perceptual contrast map (PCM) is constructed based on the modified Difference of Gaussian (DOG) algorithm. As a result, the contrast of the image is sharpened and high frequency noise is suppressed. A modified Clipped Histogram Equalization (CHE) is also developed which improves visual quality by automatically detecting the dynamic range of the image with improved perceptual contrast. Experimental results show that the new HE algorithm outperforms several state-of-the-art algorithms in improving perceptual contrast and enhancing details. In addition, the new algorithm is simple to implement, making it suitable for real-time applications. PMID:24339452

Multilevel Iterative Methods in Nonlinear Computational Plasma Physics

NASA Astrophysics Data System (ADS)

Knoll, D. A.; Finn, J. M.

1997-11-01

Many applications in computational plasma physics involve the implicit numerical solution of coupled systems of nonlinear partial differential equations or integro-differential equations. Such problems arise in MHD, systems of Vlasov-Fokker-Planck equations, edge plasma fluid equations. We have been developing matrix-free Newton-Krylov algorithms for such problems and have applied these algorithms to the edge plasma fluid equations [1,2] and to the Vlasov-Fokker-Planck equation [3]. Recently we have found that with increasing grid refinement, the number of Krylov iterations required per Newton iteration has grown unmanageable [4]. This has led us to the study of multigrid methods as a means of preconditioning matrix-free Newton-Krylov methods. In this poster we will give details of the general multigrid preconditioned Newton-Krylov algorithm, as well as algorithm performance details on problems of interest in the areas of magnetohydrodynamics and edge plasma physics. Work supported by US DoE 1. Knoll and McHugh, J. Comput. Phys., 116, pg. 281 (1995) 2. Knoll and McHugh, Comput. Phys. Comm., 88, pg. 141 (1995) 3. Mousseau and Knoll, J. Comput. Phys. (1997) (to appear) 4. Knoll and McHugh, SIAM J. Sci. Comput. 19, (1998) (to appear)

Improving multi-objective reservoir operation optimization with sensitivity-informed problem decomposition

NASA Astrophysics Data System (ADS)

Chu, J. G.; Zhang, C.; Fu, G. T.; Li, Y.; Zhou, H. C.

2015-04-01

This study investigates the effectiveness of a sensitivity-informed method for multi-objective operation of reservoir systems, which uses global sensitivity analysis as a screening tool to reduce the computational demands. Sobol's method is used to screen insensitive decision variables and guide the formulation of the optimization problems with a significantly reduced number of decision variables. This sensitivity-informed problem decomposition dramatically reduces the computational demands required for attaining high quality approximations of optimal tradeoff relationships between conflicting design objectives. The search results obtained from the reduced complexity multi-objective reservoir operation problems are then used to pre-condition the full search of the original optimization problem. In two case studies, the Dahuofang reservoir and the inter-basin multi-reservoir system in Liaoning province, China, sensitivity analysis results show that reservoir performance is strongly controlled by a small proportion of decision variables. Sensitivity-informed problem decomposition and pre-conditioning are evaluated in their ability to improve the efficiency and effectiveness of multi-objective evolutionary optimization. Overall, this study illustrates the efficiency and effectiveness of the sensitivity-informed method and the use of global sensitivity analysis to inform problem decomposition when solving the complex multi-objective reservoir operation problems.

Thin-film microextraction coupled to LC-ESI-MS/MS for determination of quaternary ammonium compounds in water samples.

PubMed

Boyacı, Ezel; Sparham, Chris; Pawliszyn, Janusz

2014-01-01

The dual nature of the quaternary ammonium compounds, having permanently charged hydrophilic quaternary ammonium heads and long-chain hydrophobic tails, makes the sample preparation step and analysis of these compounds challenging. A high-throughput method based on thin-film solid-phase microextraction (SPME) and liquid chromatography mass spectrometry was developed for simultaneous quantitative analysis of nine benzylic and aliphatic quaternary ammonium compounds. Chromatographic separation and detection of analytes were obtained in reverse-phase mode in 8 min using a triple quadrupole mass spectrometer. Hydrophilic lipophilic balance particle-coated blades were found to be the most suitable among the different coatings tested in terms of recoveries and carryover on the blades. For desorption solvents, 70/30, v/v (A/B) with 0.1 % formic acid (where A is 10 mM ammonium acetate in acetonitrile/water (95/5 , v/v) and B is 0.1 %  (v/v) formic acid in isopropyl alcohol) was shown to be the most efficient solvent for the desorption of the analytes from the SPME sorbent. The SPME method was optimised in terms of extraction, pH, and preconditioning, as well as extraction and desorption times. Optimum conditions were 45 min of extraction time and 15 min of desorption time, all with agitation. The extraction was found to be optimum in a range of pH 6.0 to 8.0, which is consistent with the natural pH of water samples. Wide linear dynamic ranges with the developed method were obtained for each compound, enabling the application of the method for a wide range of concentrations. The developed method was validated according to the Food and Drug Administration criteria. The proposed method is the first SPME-based approach describing the applicability of the high-throughput thin-film SPME in a 96-well system for analysis of such challenging compounds.

Fourier analysis of finite element preconditioned collocation schemes

NASA Technical Reports Server (NTRS)

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.

A Higher Order Iterative Method for Computing the Drazin Inverse

PubMed Central

Soleymani, F.; Stanimirović, Predrag S.

2013-01-01

A method with high convergence rate for finding approximate inverses of nonsingular matrices is suggested and established analytically. An extension of the introduced computational scheme to general square matrices is defined. The extended method could be used for finding the Drazin inverse. The application of the scheme on large sparse test matrices alongside the use in preconditioning of linear system of equations will be presented to clarify the contribution of the paper. PMID:24222747