HCV inhibits antigen processing and presentation and induces oxidative stress response in gastric mucosa

Productive hepatitis C virus (HCV) infection appears to be primarily confined to the liver. However, a wide variety of extrahepatic disease manifestations are associated with the infection and HCV RNA has been frequently detected in gastric mucosa. The present study aims to determine molecular alterations present in vivo in the stomach where HCV expression does not induce a carcinoma but a lymphoma, thus extending the knowledge of alterations in intracellular pathways consequent to HCV infection. We compared, by 2-D DIGE, the gastric protein expression profile from six HCV positive and six HCV negative samples lacking neoplastic or dysplastic conditions. In HCV positive tissue we observed a down regulation of proteins involved in MHC maturation and assembly, antigen processing and presentation and ER stress, in addition to an up regulation of proteins involved in cellular oxidative stress responses. Ubiquinol-cytochrome-C-reductase (UQCRFS1), part of the mitochondrial respiratory chain complex-III, was identified as the most up regulated protein. Data were confirmed by Western blot and immunohistochemistry. Our results demonstrate a HCV negative influence on the different pathways that determine antigen processing and presentation via MHC-I and the cellular attempts to counteract HCV induced oxidative stress. Both these processes facilitate immune escape and cell survival and probably contribute to HCV chronicization.     

An adaptive multilevel multigrid formulation for Cartesian hierarchical grid methods

A Cartesian grid method with adaptive mesh refinement and multigrid acceleration is presented for the compressible Navier-Stokes equations. Cut cells are used to represent boundaries on the Cartesian grid, while ghost cells are introduced to facilitate the implementation of boundary conditions. A cell-tree data structure is used to organize the grid cells in a hierarchical manner. Cells of all refinement levels are present in this data structure such that grid level changes as they are required in a multigrid context do not have to be carried out explicitly. Adaptive mesh refinement is introduced using phenomenon-based sensors. The application of the multilevel method in conjunction with the Cartesian cut-cell method to problems with curved boundaries is described in detail. A 5-step Runge-Kutta multigrid scheme with local time stepping is used for steady problems and also for the inner integration within a dual time-stepping method for unsteady problems. The inefficiency of customary multigrid methods on Cartesian grids with embedded boundaries requires a new multilevel concept for this application, which is introduced in this paper. This new concept is based on the following novelties: a formulation of a multigrid method for Cartesian hierarchical grid methods, the concept of averaged control volumes, and a mesh adaptation strategy allowing to directly control the number of refined and coarsened cells.     

High order compact scheme with multigrid local mesh refinement procedure for convection diffusion problems

We derive a new fourth order compact finite difference scheme which allows different meshsize in different coordinate directions for the two-dimensional convection diffusion equation. A multilevel local mesh refinement strategy is used to deal with the local singularity problem. A corresponding multilevel multigrid method is designed to solve the resulting sparse linear system. Numerical experiments are conducted to show that the local mesh refinement strategy works well with the high order compact discretization scheme to recover high order accuracy for the computed solution. Our solution method is also shown to be effective and robust with respect to the level of mesh refinement and the anisotropy of the problems.     

Analysis of the domain interactions between the protease and helicase of NS3 in dengue and hepatitis C virus

Flaviviridae non-structural 3 protein (NS3) is a multifunctional enzyme, composed by a protease domain (NS3pro) and an RNA helicase domain (NS3hel). The activities present in NS3 have proved to be critical for viral replication. The replicative cycle of Flaviviridae requires coordinated regulation of all the activities present in the full-length NS3 protein, however, the exact nature of these interactions remains unclear. The present work aimed to determine common structural features between NS3 of dengue and hepatitis C viruses and to characterize residues involved in the regulation of the interdomain motions between NS3pro and NS3hel. Analysis of the root mean square (RMS) variation shows that NS3pro increases the stability of subdomain 1 of the RNA helicase. Moreover, the dynamic behaviour of the carboxy terminus of NS3hel, supports the hypothesis that, upon release of the carboxy-terminus from NS3pro, the residues involved in this interaction are folded back into the last alpha-helix. Using normal mode analysis, we characterized slow collective motions of NS3, and observed that the two lowest-frequency normal modes are enough to describe reorientations of NS3pro relative to NS3hel. These movements induced an increment in the exposure of the active site of NS3pro that can be important during the proteolytic processing of the viral polyprotein. The third low-frequency normal mode was correlated to subdomain reorientations of NS3hel, similar to those proposed during NTP hydrolysis and dsRNA unwinding. Based on these data, we support a dynamic model, in which the domain movements between NS3pro and NS3hel result in the regulation of its activities.     

Characterization of virus replication

New viruses spread faster than ever and current signature based detection do not protect against these unknown viruses. Behavior based detection is the currently preferred defense against unknown viruses. The drawback of behavior based detection is the ability only to detect specific classes of viruses or have successful detection under certain conditions plus false positives. This paper presents a characterization of virus replication which is the only virus characteristic guaranteed to be consistently present in all viruses. Two detection models based on virus replication are developed, one using operation sequence matching and the other using frequency measures. Regression analysis was generated for both models. A safe list is used to minimize false positives. In our testing using operation sequence matching, over 250 viruses were detected with 43 subsequences. There were minimal false negatives. The replication sequence of just one virus detected 130 viruses, 45% of all tested viruses. Our testing using frequency measures detected all test viruses with no false negatives. The paper shows that virus replication can be identified and used to detect known and unknown viruses.     

Hepatitis C virus-induced oxidative stress and mitochondrial dysfunction: a focus on recent advances in proteomics

The natural history of chronic hepatitis C virus (HCV) infection presents two major aspects. On one side, the illness is by itself benign, whereas, on the other side, epidemiological evidence clearly identifies chronic HCV infection as the principal cause of cirrhosis, hepatocellular carcinoma, and extrahepatic diseases, such as autoimmune type II mixed cryoglobulinemia and some B cell non-Hodgkin's lymphomas. The mechanisms responsible for the progression of liver disease to severe liver injury are still poorly understood. Nonetheless, considerable biological data and studies from animal models suggest that oxidative stress contributes to steatohepatitis and that the increased generation of reactive oxygen and nitrogen species, together with the decreased antioxidant defense, promotes the development of hepatic and extrahepatic complications of HCV infection. The principal mechanisms causing oxidative stress in HCV-positive subjects have only been partially elucidated and have identified chronic inflammation, iron overload, ER stress, and a direct activity of HCV proteins in increasing mitochondrial ROS production, as key events. This review summarizes current knowledge regarding mechanisms of HCV-induced oxidative stress with its long-term effects in the context of HCV-related diseases, and includes a discussion of recent contributions from proteomics studies.     

A 15-point high-order compact scheme with multigrid computation for solving 3D convection diffusion equations

We propose a method with sixth-order accuracy to solve the three-dimensional (3D) convection diffusion equation. We first use a 15-point fourth-order compact discretization scheme to obtain fourth-order solutions on both fine and coarse grids using the multigrid method. Then an iterative mesh refinement technique combined with Richardson extrapolation is used to approximate the sixth-order accurate solution on the fine grid. Numerical results are presented for a variety of test cases to demonstrate the efficiency and accuracy of the proposed method, compared with the standard fourth-order compact scheme.     

Exploring the P2 and P3 ligand binding features for hepatitis C virus NS3 protease using some 3D QSAR techniques

Several three-dimensional quantitative structure-activity relationship (3D-QSAR) models have been constructed using the comparative molecular field analysis (CoMFA), comparative molecular similarity indices analysis (CoMSIA), and catalyst pharmacophore feature building programs for a series of 26 truncated ketoacid inhibitors designed particularly for exploring the P2 and P3 binding pockets of HCV NS3 protease. The structures of these inhibitors were built from a structure template extracted from the crystal structure of HCV NS3 protease. The structures were aligned through docking each inhibitor into the NS3 active site using program GOLD. The best CoMSIA model was identified from the stepwise analysis results and the corresponding pharmacophore features derived were used for constructing a pharmacophore hypothesis by the catalyst program. Pharmacophore features obtained by CoMFA and CoMSIA are found to be in accord with each other and are both mapped onto the molecular 5K surface of NS3 active site. These pharmacophore features were also compared with those obtained by the catalyst program and mapped onto the same NS3 molecular surface. The pharmacophore building process was also performed for 20 boronic acid based NS3 inhibitors characterized by a long hydrophobic side chain attached at position P2. This latter pharmacophore hypothesis built by the catalyst program was also mapped onto the molecular surface of NS3 active site to define a second hydrophobic feature at position P2. The possibility of using the pharmacophore features mapped P2 and P3 binding pocket to design more potent depeptidized NS3 inhibitors was discussed.     

Proteomics-based characterization of hemagglutinins in different strains of influenza virus

Infection with influenza A (subtypes H1N1 and H3N2) or B viruses results in over half a million deaths worldwide every year. Frequent antigenic changes (drift) in two major viral surface proteins hemagglutinin (HA) and neuraminidase lead to the constant emergence of antigenically distinct virus strains against which there is sub-optimal immunity in the population. Consequently the suitability of the viral strains included in the trivalent influenza vaccine (TIV) has to be re-evaluated annually. While virus seeds selected for vaccine manufacture are very well characterized, there is no assay in place to identify the source of HA in the formulated trivalent vaccine. Our study describes a proteomics-based method to identify the HA strain (not just subtype) and more fully characterize the final vaccine product. Unique and shared tryptic peptides of HAs were predicted by in silico tryptic digest of different influenza A and B virus strains. Recombinant HA and whole virus preparations of selected strains were then digested to identify the peptides detected by MS. Both subtype and strain-specific peptides were observed. The feasibility of this method to accurately identify HA strains in an inactivated TIV was tested using a 2006/2007 formulation. Each of the three HAs in the vaccine was identified in addition to a number of other viral and non-viral proteins. In summary, MS is a powerful method that is both specific and inclusive; in a single analysis, HAs of individual virus strains can be identified and the composition of the TIV fully characterized.     

Goal-Oriented Adaptivity and Multilevel Preconditioning for the Poisson-Boltzmann Equation

In this article, we develop goal-oriented error indicators to drive adaptive refinement algorithms for the Poisson-Boltzmann equation. Empirical results for the solvation free energy linear functional demonstrate that goal-oriented indicators are not sufficient on their own to lead to a superior refinement algorithm. To remedy this, we propose a problem-specific marking strategy using the solvation free energy computed from the solution of the linear regularized Poisson-Boltzmann equation. The convergence of the solvation free energy using this marking strategy, combined with goal-oriented refinement, compares favorably to adaptive methods using an energy-based error indicator. Due to the use of adaptive mesh refinement, it is critical to use multilevel preconditioning in order to maintain optimal computational complexity. We use variants of the classical multigrid method, which can be viewed as generalizations of the hierarchical basis multigrid and Bramble-Pasciak-Xu (BPX) preconditioners.     

Structure and dynamics of a predicted ferredoxin-like selenoprotein in Japanese encephalitis virus

Homologues of the selenoprotein glutathione peroxidase (GPx) have been previously identified in poxviruses and in RNA viruses including HIV-1 and hepatitis C virus (HCV). Sequence analysis of the NS4 region of Japanese encephalitis virus (JEV) suggests it may encode a structurally related but functionally distinct selenoprotein gene, more closely related to the iron-binding protein ferredoxin than to GPx, with three highly conserved UGA codons that align with essential Cys residues of ferredoxin. Comparison of the probe JEV sequence to an aligned family of ferredoxin sequences gave an overall 30.3% identity and 45.8% similarity, and was statistically significant at 4.9 S.D. (P < 10(-6)) above the average score computed for randomly shuffled sequences. A 3-dimensional model of the hypothetical JEV protein (JEV model) was constructed by homology modeling using SYBYL, based upon a high resolution X-ray structure of ferredoxin (PDB code: 1awd). The JEV model and the model from 1awd were subsequently subjected to molecular dynamics simulations in aqueous medium using AMBER 6. The solution structure of the JEV model indicates that it could fold into a tertiary structure globally similar to ferredoxin 1awd, with RMSD between the averaged structures of 1.8 A for the aligned regions. The modeling and MD simulations data also indicate that this structure for the JEV protein is energetically favorable, and that it could be quite stable at room temperature. This protein might play a role in JEV infection and replication via TNF and other cellular stimuli mediated via redox mechanisms.     

Array-based,parallel hierarchical mesh refinement algorithms for unstructured meshes

In this paper, we describe an array-based hierarchical mesh refinement capability through uniform refinement of unstructured meshes for efficient solution of PDE’s using finite element methods and multigrid solvers. A multi-degree, multi-dimensional and multi-level framework is designed to generate the nested hierarchies from an initial coarse mesh that can be used for a variety of purposes such as in multigrid solvers/preconditioners, to do solution convergence and verification studies and to improve overall parallel efficiency by decreasing I/O bandwidth requirements (by loading smaller meshes and in-memory refinement). We also describe a high-order boundary reconstruction capability that can be used to project the new points after refinement using high-order approximations instead of linear projection in order to minimize and provide more control on geometrical errors introduced by curved boundaries.The capability is developed under the parallel unstructured mesh framework “Mesh Oriented dAtaBase” (MOAB Tautges et al. (2004)). We describe the underlying data structures and algorithms to generate such hierarchies in parallel and present numerical results for computational efficiency and effect on mesh quality. We also present results to demonstrate the applicability of the developed capability to study convergence properties of different point projection schemes for various mesh hierarchies and to a multigrid finite-element solver for elliptic problems.     

Multigrid gradient vector flow computation on the GPU

Gradient vector flow (GVF) is a feature-preserving spatial diffusion of image gradients. It was introduced to overcome the limited capture range in traditional active contour segmentation. However, the original iterative solver for GVF, using Euler’s method, converges very slowly. Thus, many iterations are needed to achieve the desired capture range. Several groups have investigated the use of graphic processing units (GPUs) to accelerate the GVF computation. Still, this does not reduce the number of iterations needed. Multigrid methods, on the other hand, have been shown to provide a much better capture range using considerable less iterations. However, non-GPU implementations of the multigrid method are not as fast as the Euler method when executed on the GPU. In this paper, a novel GPU implementation of a multigrid solver for GVF written in OpenCL is presented. The results show that this implementation converges and provides a better capture range about 2–5 times faster than the conventional iterative GVF solver on the GPU.     

Extended recursion-based formalization of virus mutation

Computer viruses are programs that can replicate themselves by infecting other programs in a system. Bonfante, Kaczmarek and Marion have recently proposed a classification of viruses which relies on the recursion theory and its recursion theorems. We propose an extension of their formalism to consider in a more practical way the mutation of viruses. In particular, we are interested in modelling any depth of mutation, not just the first two levels. We show that this formalism still relies on recursion theorems, whatever the depth of mutation, even in the case of infinite depth. We also extend furthermore this formalism to model the viability of viral replication, which ensures that an infected program still can propagate the virus. An application of the proposed formalism to the class of combined viruses (multi-part viruses) is studied. Finally, given that metamorphic viruses can be modelled by grammars operating on grammars, we study a recursion-based approach of formal grammars and show that the recursion theorems of the recursion theory can be ported to the formal grammars theory.     

The combined impact of external computers and network topology on the spread of computer viruses

This paper aims to study the combined impact of external computers and network topology on the spread of computer viruses over the Internet. By assuming that the network underlying a recently proposed model capturing virus spreading behaviour under the influence of external computers follows a power-law degree distribution, a new virus epidemic model is proposed. A comprehensive study of the model shows the global stability of the virus-free equilibrium or the global attractivity of the viral equilibrium, depending on the basic reproduction number R₀. Next, the impacts of different model parameters on R₀ are analysed. In particular, it is found that (a) higher network heterogeneity benefits virus spreading, (b) higher-degree nodes are more susceptible to infections than lower-degree nodes, and (c) a lower rate at which external computers enter the Internet could restrain virus spreading. On this basis, some practical measures of inhibiting virus diffusion are suggested.     

基于复制行为的病毒检测

复制是所有病毒都具有的基本特征。给出一个通过检测病毒复制行为来检测病毒的方法。检测病毒复制行为的方法关注病毒复制时执行的读写操作,通过构造这些操作的关系树来检测病毒的复制行为。在实验中对每个病毒和程序调用的Win32 API的日志文件进行分析,检测是否出现了病毒复制行为,结果表明可以通过检测病毒的复制行为来检测病毒。     

An explicit Chebyshev pseudospectral multigrid method for incompressible Navier-Stokes equations

The two-dimensional steady incompressible Navier-Stokes equations in the form of primitive variables have been solved by Chebyshev pseudospectral method. The pressure and velocities are coupled by artificial compressibility method and the NS equations are solved by pseudotime method with an explicit four-step Runge-Kutta integrator. In order to reduce the computational time cost, we propose the spectral multigrid algorithm in full approximation storage (FAS) scheme and implement it through V-cycle multigrid and full multigrid (FMG) strategies. Four iterative methods are designed including the single grid method; the full single grid method; the V-cycle multigrid method and the FMG method. The accuracy and efficiency of the numerical methods are validated by three test problems: the modified one-dimensional Burgers equation; the Taylor vortices and the two-dimensional lid driven cavity flow. The computational results fit well with the exact or benchmark solutions. The spectral accuracy can be maintained by the single grid method as well as the multigrid ones, while the time cost is greatly reduced by the latter. For the lid driven cavity flow problem, the FMG is proved to be the most efficient one among the four iterative methods. A speedup of nearly two orders of magnitude can be achieved by the three-level multigrid method and at least one order of magnitude by the two-level multigrid method.     

Partial semi-coarsening multigrid method based on the HOC scheme on nonuniform grids for the convection–diffusion problems

A partial semi-coarsening multigrid method based on the high-order compact (HOC) difference scheme on nonuniform grids is developed to solve the 2D convection–diffusion problems with boundary or internal layers. The significance of this study is that the multigrid method allows different number of grid points along different coordinate directions on nonuniform grids. Numerical experiments on some convection–diffusion problems with boundary or internal layers are conducted. They demonstrate that the partial semi-coarsening multigrid method combined with the HOC scheme on nonuniform grids, without losing the high-order accuracy, is very efficient and effective to decrease the computational cost by reducing the number of grid points along the direction which does not contain boundary or internal layers.     

A finite element based level set method for two-phase incompressible flows

We present a method that has been developed for the efficient numerical simulation of two-phase incompressible flows. For capturing the interface between the phases the level set technique is applied. The continuous model consists of the incompressible Navier–Stokes equations coupled with an advection equation for the level set function. The effect of surface tension is modeled by a localized force term at the interface (so-called continuum surface force approach). For spatial discretization of velocity, pressure and the level set function conforming finite elements on a hierarchy of nested tetrahedral grids are used. In the finite element setting we can apply a special technique to the localized force term, which is based on a partial integration rule for the Laplace–Beltrami operator. Due to this approach the second order derivatives coming from the curvature can be eliminated. For the time discretization we apply a variant of the fractional step θ-scheme. The discrete saddle point problems that occur in each time step are solved using an inexact Uzawa method combined with multigrid techniques. For reparametrization of the level set function a new variant of the fast marching method is introduced. A special feature of the solver is that it combines the level set method with finite element discretization, Laplace–Beltrami partial integration, multilevel local refinement and multigrid solution techniques. All these components of the solver are described. Results of numerical experiments are presented.