bluuebunny/crossref_metadata_2025 huggingface dataset:
Equivalence of u–p and ζ–ψ formulations of the time‐dependent Navier–Stokes equations
Authors: Guermond J.‐L. , Quartapelle L.
Published: August 2005

This paper deals with the non‐stationary incompressible Navier‐‐Stokes equations for two‐dimensional flows expressed in terms of the velocity and pressure and of the vorticity and streamfunction. The equivalence of the two formulations is demonstrated, both formally and rigorously, by virtue of a condition of compatibility between the boundary and initial values of the normal component of velocity. This condition is shown to be the only compatibility condition necessary to allow for solutions of a minimal regularity, namely H1 for the velocity, as in most current numerical schemes relying on spatial discretizations of local type.
Multigrid pressure correction techniques for the computation of quasi‐incompressible internal flows
Authors: Luchini P. , D'Alascio A.
Published: August 2005

A study is reported on the possibility of improving the speed of convergence of existing numerical programmes for the simulation of flow in combustion chambers by applying the multigrid method to the pressure correction phase only. A version of the multigrid algorithm is introduced for this purpose which achieves a 1:10 residual reduction in a single V(1, 1) cycle. The overall decrease in computation time with respect to an industry‐standard SIMPLE algorithm with single‐grid pressure correction ranges from four to five times for SIMPLE itself and several other well‐known algorithms to six times for a newly developed pressure correction strategy we call difference operator triangularization (DOT).
On the Riemann problem for liquid or gas‐liquid media
Authors: Chen Tze‐Jang , Cooke Charlie H.
Published: August 2005

Self‐similar solutions to the Riemann problem for water with the modified Tait equation of state are presented. The methods of Smoller for gas dynamics are employed to reduce the problem to the solution of a single non‐linear equation. The same methods are used for solving the Riemann problem at a gas‐water interface. In both cases the method of interval bisections affords a solution technique free of problems with convergence.
Chebyshev collocation method and multidomain decomposition for the incompressible Navier‐Stokes equations
Authors: Pinelli A. , Vacca A.
Published: August 2005

The two‐dimensional incompressible Navier‐Stokes equations in primitive variables have been solved by a pseudospectral Chebyshev method using a semi‐implicit fractional step scheme. The latter has been adapted to the particular features of spectral collocation methods to develop the monodomain algorithm. In particular, pressure and velocity collocated on the same nodes are sought in a polynomial space of the same order; the cascade of scalar elliptic problems arising after the spatial collocation is solved using finite difference preconditioning. With the present procedure spurious pressure modes do not pollute the pressure field.

As a natural development of the present work a multidomain extent was devised and tested. The original domain is divided into a union of patching sub‐rectangles. Each scalar problem obtained after spatial collocation is solved by iterating by subdomains. For steady problems a C1 solution is recovered at the interfaces upon convergence, ensuring a spectrally accurate solution.

A number of test cases have been solved to validate the algorithm in both its single‐block and multidomain configurations.

The preliminary results achieved indicate that collocation methods in multidomain configurations might become a viable alternative to the spectral element technique for accurate flow prediction.
Multigrid solution of compressible turbulent flow on unstructured meshes using a two‐equation model
Authors: Mavriplis D. J. , Martinelli L.
Published: August 2005

The steady state solution of the system of equations consisting of the full Navier‐Stokes equations and two turbulence equations has been obtained using a multigrid strategy on unstructured meshes. The flow equations and turbulence equations are solved in a loosely coupled manner. The flow equations are advanced in time using a multistage Runge‐Kutta time‐stepping scheme with a stability‐bound local time step, while the turbulence equations are advanced in a point‐implicit scheme with a time step which guarantees stability and positivity. Low‐Reynolds‐number modifications to the original two‐equation model are incorporated in a manner which results in well‐behaved equations for arbitrarily small wall distances. A variety of aerodynamic flows are solved, initializing all quantities with uniform freestream values. Rapid and uniform convergence rates for the flow and turbulence equations are observed.
Boundary element method solution of MHD flow in a rectangular duct
Authors: Tezer‐Sezgin Munevver
Published: August 2005

The magnetohydrodynamic (MHD) flow of an incompressible, viscous, electrically conducting fluid in a rectangular duct with an external magnetic field applied transverse to the flow has been investigated. The walls parallel to the applied magnetic field are conducting while the other two walls which are perpendicular to the field are insulators. The boundary element method (BEM) with constant elements has been used to cast the problem into the form of an integral equation over the boundary and to obtain a system of algebraic equations for the boundary unknown values only. The solution of this integral equation presents no problem as encountered in the solution of the singular integral equations for interior methods. Computations have been carried out for several values of the Hartmann number (1 ⩽ M ⩽ 10). It is found that as M increases, boundary layers are formed close to the insulated boundaries for both the velocity and the induced magnetic field and in the central part their behaviours are uniform. Selected graphs are given showing the behaviours of the velocity and the induced magnetic field.
Résumé and remarks on the open boundary condition minisymposium
Authors: Sani R. L. , Gresho P. M.
Published: August 2005

The incompressible Navier‐Stokes equations—and their thermal convection and stratified flow analogue, the Boussinesq equations—possess solutions in bounded domains only when appropriate/legitimate boundary conditions (BCs) are appended at all points on the domain boundary. When the boundary—or, more commonly, a portion of it—is not endowed with a Dirichlet BC, we are faced with selecting what are called open boundary conditions (OBCs), because the fluid may presumably enter or leave the domain through such boundaries. The two minisymposia on OBCs that are summarized in this paper had the objective of finding the best OBCs for a small subset of two‐dimensional test problems. This objective, which of course is not really well‐defined, was not met (we believe), but the contributions obtained probably raised many more questions/issues than were resolved—notable among them being the advent of a new class of OBCs that we call FBCs (fuzzy boundary conditions).
Finite element implementation of boundary conditions for the pressure Poisson equation of incompressible flow
Authors: Hassanzadeh Siamak , Sonnad Vijay , Foresti Stefano
Published: August 2005

In this paper we address the problem of the implementation of boundary conditions for the derived pressure Poisson equation of incompressible flow. It is shown that the direct Galerkin finite element formulation of the pressure Poisson equation automatically satisfies the inhomogeneous Neumann boundary conditions, thus avoiding the difficulty in specifying boundary conditions for pressure. This ensures that only physically meaningful pressure boundary conditions consistent with the Navier‐Stokes equations are imposed. Since second derivatives appear in this formulation, the conforming finite element method requires C1 continuity. However, for many problems of practical interest (i.e. high Reynolds numbers) the second derivatives need not be included, thus allowing the use of more conventional C0 elements. Numerical results using this approach for a wall‐driven contained flow within a square cavity verify the validity of the approach. Although the results were obtained for a two‐dimensional problem using the p‐version of the finite element method, the approach presented here is general and remains valid for the conventional h‐version as well as three‐dimensional problems.
The influence of normal flow boundary conditions on spurious modes in finite element solutions to the shallow water equations
Authors: Westerink J. J. , Luettich R. A. , Wu J. K. , Kolar R. L.
Published: August 2005

Finite element solutions of the primitive equation (PE) form of the shallow water equations are notorious for the severe spurious 2Δx modes which appear. Wave equation (WE) solutions do not exhibit these numerical modes. In this paper we show that the severe spurious modes in PE solutions are strongly influenced by essential normal flow boundary conditions in the coupled continuity‐momentum system of equations. This is demonstrated through numerical examples that avoid the use of essential normal flow boundary conditions either by specifying elevation values over the entire boundary or by implementing natural flow boundary conditions in the weak weighted residual form of the continuity equation. Results from a series of convergence tests show that PE solutions are of nearly the same quality as WE solutions when spurious modes are suppressed by alternative specification of the boundary conditions. Network intercomparisons indicate that varying nodal support does not excite spurious modes in a solution, although it does enhance the spurious modes introduced when an essential normal flow boundary condition is used.

Dispersion analysis of discrete equations for interior and boundary nodes offers an explanation of the observed solution behaviour. For certain PE algorithms a mixed situation can arise where the boundary nodes exhibit a monotonic (noise‐free) dispersion relationship and the interior nodes exhibit a folded (noisy) dispersion relationship. We have found that the mixed situation occurs when all boundary nodes are specified elevation nodes (which are enforced as essential conditions in the continuity equation) or when specified flow boundary nodes are treated as natural boundary conditions in the continuity equation. In either case the effect is to generate a solution that is essentially free of noise. Apparently, the monotonic dispersion behaviour at the boundaries suppresses the otherwise noisy behaviour caused by the folded dispersion relation on the interior.
Transport of radionuclides in isolated fractures in crystalline rocks
Authors: Grandi G. M. , Ferreri J. C.
Published: August 2005

This paper presents a generalization of a computational method for the prediction of solute dispersion in fractured porous media. This method is specially useful for the prediction of subsurface flows in crystalline rocks. The model now includes a linear kinetics mechanism to represent the effects of sorption of radionuclides in the rock matrix. The method is improved in its accuracy and provides results useful for the assessment of radionuclide migration in high‐level, radioactive waste repositories. Results including verification (analytical) and physical test simulations are given. These results provide a partial validation of the numerical model.
A semi‐implicit lagrangian scheme for 3D shallow water flow with a two‐layer turbulence model
Authors: Stansby Peter K. , Lloyd Peter M.
Published: August 2005

A semi‐implicit Lagrangian finite difference scheme for 3D shallow water flow has been developed to include an eddy viscosity model for turbulent mixing in the vertical direction. The α‐co‐ordinate system for the vertical direction has been introduced to give accurate definition of bed and surface boundary conditions. The simple two‐layer mixing length model for rough surfaces is used with the standard assumption that the shear stress across the wall region at a given horizontal location is constant. The bed condition is thus defined only by its roughness height (avoiding the need for a friction formula relating to depth‐averaged flow, e.g. Chezy, used previously). The method is shown to be efficient and stable with an explicit Lagrangian formulation for convective terms and terms for surface elevation and vertical mixing handled implicitly. The method is applied to current flow around a circular island with gently sloping sides which produce periodic recirculation zones (vortex shedding). Comparisons are made with experimental measurements of velocity using laser Doppler anemometry (time histories at specific points) and surface particle‐tracking velocimetry.
Why you should not use ‘Hybrid’, ‘Power‐Law’ or related exponential schemes for convective modelling—there are much better alternatives
Authors: Leonard B. P. , Drummond J. E.
Published: August 2005

In many areas of computational fluid dynamics, especially numerical convective heat and mass transfer, the ‘Hybrid’ and ‘Power‐Law’ schemes have been widely used for many years. The popularity of these methods for steady‐state computations is based on a combination of algorithmic simplicity, fast convergence, and plausible looking results. By contrast, classical (second‐order central) methods often involve convergence problems and may lead to obviously unphysical solutions exhibiting spurious numerical oscillations. Hybrid, Power‐Law, and the exponential‐difference scheme on which they are based give reasonably accurate solutions for steady, quasi‐one‐dimensional flow (when the grid is aligned with the main flow direction). However, they are often also used, out of context, for flows oblique or skew to the grid, in which case, inherent artificial viscosity (or diffusivity) seriously degrades the solution. This is particularly trouble‐some in the case of recirculating flows, sometimes leading to qualitatively incorrect results—since the effective artificial numerical Reynolds (or Péclet) number may then be orders of magnitude less than the correct physical value. This is demonstrated in the case of thermally driven flow in tall cavities, where experimentally observed recirculation cells are not predicted by the exponential‐based schemes. Higher‐order methods correctly predict the onset of recirculation cells. In the past, higher‐order methods have not been popular because of convergence difficulties and a tendency to generate unphysical overshoots near (what should be) sharp, monotonic transitions. However, recent developments using robust deferred‐correction solution methods and simple flux‐limiter techniques have eliminated all of these difficulties. Highly accurate, physically correct solutions can now be obtained aptimum computational efficiency.
Recent advances towards an effective virtual‐pulse (VIP) explicit time integral methodology for general multidimensional thermal analysis
Authors: Tamma Kumar K. , Mei Y. , Chen X. , Sha D.
Published: August 2005

Recent advances and progress towards the development of an effective Virtual‐Pulse (VIP) explicit time integral methodology of computation for applicability to general multidimensional non‐linear transient thermal analysis of structures and materials is overviewed. The computational methodology is derived from new and different perspectives and the theoretical basis as well as the practical applicability to multidimensional thermal analysis situations are detailed. The VIP methodology inherits improved accuracy and superior stability characteristics in comparison to the traditional approaches customarily employed by thermal analysts. With the notion of providing techniques for high‐speed computing environments and parallel architectures, the present approach is developed for such computations and also ideally suited for personal workstation computing environments. Results of the numerical test models for multidimensional problems validate the overall concepts for general applicability to thermal analysis situations.
Modelling of single shot induction heating by inverse finite element method
Authors: Maizza G. , Calì M.
Published: August 2005

The induction heating model described herein couples the standard heat conduction equation with electro‐magnetic proximity‐skin equations. An Inverse Finite Element procedure, which is based on prior deterministic and probabilistic concepts, has been designed to solve the inherent inverse equation model with respect to the unknown coil current parameter. Simulated experiments using different noises in the input data have been performed in order to determine their influence on the estimated parameter. The IFEM has shown its capability to predict the optimal location for the temperature sensors, together with their numbers, consistently with a pre‐specified estimate accuracy. Specifically, only one temperature sensor, located in the middle of the two turns of the coil, results to be sufficient to estimate the unknown parameter to a satisfactory accuracy degree. This, may significantly help to design optimal experiments.
Melting of a PCM inside a vertical cylindrical capsule
Authors: Wu Yong Ke , Lacroix Marcel
Published: August 2005

A numerical study of natural convection melting of a phase change material within an isothermal vertical cylinder was conducted. The governing conservation equations are formulated in terms of a stream function, vorticity and temperature. Body‐fitted co‐ordinates are employed for tracking the irregular shape of the timewise changing solid–liquid phase front. Results show that the convective flow patterns and time evolution of the phase front, resulting from simultaneous bottom, side and top heating, are far more complicated than those for the melting from a single isothermal boundary. The heat transfer rate at the top surface is found to decrease monotonically to zero as convection is fully developed in the melt. The highest heat transfer rates are observed at the bottom surface where Bénard convective cells develop. Due to the convective motion of the melt along the vertical heated wall, the onset of Bénard convection occurs at a much earlier time than that for the case of melting within a cylinder heated from below.
Multidimensional upwinding: Its relation to finite elements
Authors: Carette J.‐C. , Deconinck H. , Paillere H. , Roe P. L.
Published: August 2005

Vertex‐based multidimensional upwind schemes for scalar advection are compared with shock‐capturing SUPG finite element methods based on linear triangular elements. Both methods share the same compact stencil and are formulated as cell‐wise residual distribution methods. The distribution for the finite element method is 1/3, supplemented with a Lax‐Wendrov‐type dissipation term, while the distribution for the upwind schemes is limited to the downstream nodes of the element. The multidimensional upwind schemes use positivity as the monotonicity criterion, while the finite element method includes a residual‐based non‐linear dissipation.

For hyperbolic systems such as the compressible Euler equations the upwind method relies on a multidimensional wave model to decompose the residual into scalar contributions. From this observation a new SUPG formulation for systems is proposed in which the scalar SUPG method is applied to each of the decomposed residuals obtained from the wave model, thereby providing a better‐founded definition of the τ dissipation matrix and shock‐capturing term in the SUPG methods.
GMRES acceleration of iterative implicit finite element solvers for compressible Euler and Navier‐Stokes equations
Authors: Choquet Rémi , Leyland Pénélope , Tefy Tiana
Published: August 2005

Implicit iterative schemes based on linearized and non‐linear Newton methods are discussed, with resolution of a matrix subsystem or a matrix‐free method by preconditioned GMRES algorithms. The defaults of convergence due to the locality of Newton algorithms can be partially overcome by using stabilizing descent techniques, restarting and global strategies such as line search backtracking procedures, or by tuning the iterations once the approximate Jacobians are closer to the exact ones. Comparison with a more conventional relaxation method and their implementation on parallel architectures are discussed.
Coupled heat, water and gas flow in deformable porous media
Authors: Gawin Dariusz , Baggio Paolo , Schrefler Bernhard A.
Published: August 2005

A fully coupled numerical model to simulate the slow transient phenomena involving heat and mass transfer in deforming porous media is developed. It makes use of the modified effective stress concept together with the capillary pressure relationship. The heat transfer through conduction and convection as well as the latent heat transfer (evaporation and/or condensation) is taken into account.

The governing equations in terms of displacements, temperature, capillary pressure and gas pressure are coupled non‐linear differential equatiosn and are solved by the finite element method.

The model is validated with respect to a documented experiment on semisaturated soil behaviour. Two other examples involving subsidence due to pumping from a phreatic aquifer and thermoelastic consolidation of saturated and semisaturated media are also presented.
Stability analysis of mixed finite element formulations with special mention of equal‐order interpolations
Authors: Idelsohn S. , Storti M. , Nigro N.
Published: August 2005

We present a method to assess the stability of pairs of interpolation spaces for mixed formulations. The method is based on a straightforward calculation of the eigenvalues of the discrete matrices through Fourier decomposition in plane waves and is intended to give, via straightforward numerical computations, a sharper determination of stability than the well‐known ‘patch test’ of Zienkiewicz et al. Special attention is devoted to the study of stability and accuracy of equal‐order interpolations.
Adaptive hybrid prismatic/tetrahedral grids
Authors: Kallinderis Y.
Published: August 2005

Employment of hybrid prismatic/tetrahedral grids is a relatively new approach for viscous flow computations with 3D complex geometries. The body surface is covered with triangles, which provides geometric flexibility, while the structure of the mesh in the direction normal to the surface provides thin prismatic elements suitable for the viscous region. The outermost layer of the prismatic grid is then used as the inner boundary surface for a tetrahedral grid which covers the rest of the computational domain. The hybrid grid is employed for performing Navier‐Stokes calculations in the prismatic region near the body and Euler calculations in the tetrahedral regions away from the body.

The generation method of hybrid prismatic/tetrahedral grids marches a triangulated surface mesh away from the body to form a semi‐unstructured prismatic grid. Tetrahedra are then constructed which are linked directly to the nodes of the outermost prismatic layer. The hybrid grid is locally refined over both the prismatic and tetrahedral regions. Directional embedding of the prisms preserves the structure of the mesh in the normal‐to‐surface direction.
Investigation of generalized flux vector splitting for compressible flows on triangular meshes
Authors: Stoufflet Bruno
Published: August 2005

The paper presents some investigations in developing schemes based on a splitting of the Euler equations into a pure convective part and an acoustic part (pressure term) combined with a multidimensional treatment on unstructured triangular meshes. Two decompositions are considered and are compared with classical approaches on two‐dimensional inviscid flow simulations.
Integral transform solution of developing laminar duct flow in Navier‐Stokes formulation
Authors: Guerrero J. S. Perez , Cotta R. M.
Published: August 2005

The generalized integral transform technique is employed in the hybrid numerical‐analytical solution of the Navier‐Stokes equations in streamfunction‐only formulation, which govern the incompressible laminar flow of a Newtonian fluid within a parallel plate channel. Owing to the analytic nature of this approach, the outflow boundary condition for an infinite duct is handled exactly, and the error involved in considering finite duct lengths is investigated. The present error‐controlled solutions are used to inspect the relative accuracy of previously reported purely numerical schemes and to compare Navier‐Stokes and boundary layer formulations for various combinations of inlet conditions and Reynolds number.
Translation of a sphere in a rotating viscous fluid: A numerical study
Authors: Rao C. V. Raghava , Sekhar T. V. S.
Published: August 2005

The translation of a sphere moving along the axis of a rotating viscous fluid is studied by the finite difference method at moderate Reynolds (up to R = 500) and Taylor (up to T = 100) numbers. Suppression of the separation is observed with increasing rotation parameter T. The drag coefficient is also presented. It is observed that the drag coefficient is less than that with no rotation in the range 0<N<0·7, where N = 2T/R is the inverse Rossby number. The same phenomenon was observed experimentally by Maxworthy in the range 0<N<0·75±0·03.
Introduction of turbulent model in a mixed finite volume/finite element method
Authors: Le Ribault C. , Buffat M. , Jeandel D.
Published: August 2005

The aim of this work is to present a new numerical method to compute turbulent flows in complex configurations. With this in view, a k‐ϵ model with wall functions has been introduced in a mixed finite volume/finite element method. The numerical method has been developed to deal with compressible flows but is also able to compute nearly incompressible flows. The physical model and the numerical method are first described, then validation results for an incompressible flow over a backward‐facing step and for a supersonic flow over a compression ramp are presented. Comparisons are performed with experimental data and with other numerical results. These simulations show the ability of the present method to predict turbulent flows, and this method will be applied to simulate complex industrial flows (flow inside the combustion chamber of gas turbine engines). The main goal of this paper is not to test turbulence models, but to show that this numerical method is a solid base to introduce more sophisticated turbulence model.
Fluid dynamics of slender, thin, annular liquid jets
Authors: Ramos J. I.
Published: August 2005

Perturbation methods are used to obtain the one‐dimensional, asymptotic equations that govern the fluid dynamics of slender, thin, inviscid, incompressible, axisymmetric, irrotational, annular liquid jets from the Euler equations. It is shown that, depending on the magnitude of the Weber number, two flow regimes are possible: an inertia‐dominated one corresponding to large Weber numbers, and a capillary regime for Weber numbers of the order of unity. The steady equations governing these two regimes have analytical solutions for the liquid's axial velocity component and require a numerical integration to determine the jet's mean radius for inertia‐dominated jets. The one‐dimensional equations derived in this paper are shown to be particular cases of a hydraulic model for annular liquid jets, and this model is used to determine the effects of gravity modulation on the unsteady fluid dynamics of annular liquid jets in the absence of mass injection into the volume enclosed by the jet and mass absorption. It is shown that both the convergence length and the pressure coefficient are periodic functions of time which have the same period as that of the gravity modulation, but undergo large variations as the amplitude, frequency and width of gravitational pulses is varied.
The instability of jets of arbitrary exit geometry
Authors: Baty Roy S. , Morris Philip J.
Published: August 2005

This paper describes a calculation technique to determine the linear instability characteristics of jets of arbitrary exit geometry. In particular, elliptic and rectangular jets are considered. The numerical procedure involves both a conformal transformation between the computational domain and the physical plane and a solution of the transformed stability equation in the computational domain. Modern, efficient, conformal mappings are used for both simply and doubly connected domains. The numerical solution is based on a hybrid finite difference/pseudospectral discretization of the stability equation. The technique is validated by comparison with previous stability calculations for circular and elliptic jets. Calculations are performed for the stability characteristics of elliptic and rectangular jets of aspect ratio 2:1. Growth rates, phase velocities, and pressure eigenfunctions are presented.
Ventral–striatal/nucleus–accumbens sensitivity to prediction errors during classification learning
Authors: Rodriguez P. F. , Aron A.R. , Poldrack R.A.
Published: August 2005

A prominent theory in neuroscience suggests reward learning is driven by the discrepancy between a subject's expectation of an outcome and the actual outcome itself. Furthermore, it is postulated that midbrain dopamine neurons relay this mismatch to target regions including the ventral striatum. Using functional MRI (fMRI), we tested striatal responses to prediction errors for probabilistic classification learning with purely cognitive feedback. We used a version of the Rescorla‐Wagner model to generate prediction errors for each subject and then entered these in a parametric analysis of fMRI activity. Activation in ventral striatum/nucleus‐accumbens (Nacc) increased parametrically with prediction error for negative feedback. This result extends recent neuroimaging findings in reward learning by showing that learning with cognitive feedback also depends on the same circuitry and dopaminergic signaling mechanisms. Hum Brain Mapp, 2005. © 2005 Wiley‐Liss, Inc.
A preliminary in vitro and in vivo study of the effects of new anthraquinones on neutrophils and bone remodeling
Authors: Savarino L. , Benetti D. , Baldini N. , Tarabusi C. , Greco M. , Aloisi R. , Frascarelli S. , Fantozzi R. , Dianzani C. , Mian M.
Published: August 2005

Osteolysis, that is, progressive periprosthetic bone loss, is responsible for approximately 70% of aseptic loosening and implant failure. Usually, it is due to a granulomatous reaction wear‐induced, leading to macrophage and osteoclast‐mediated bone resorption. At present, there is no established prophylaxis or treatment for this process. For this purpose, as a preliminary investigation, we aimed to study the effects in two directions, inhibition of proinflammatory signals, and bone remodeling activity, of two newly synthesized anthraquinone molecules [N,N′‐Diethylamino‐2,6‐anthraquinone‐disulfonamide (GR375) and N,N′‐(p‐ethoxyphenyl)‐2,6‐anthraquinone‐disulfon amide (GR377)]. Among the pro‐inflammatory signals, the ability of the two anthraquinones to interfere with the production of superoxide anion (O2−), which was assumed as a marker of reactive oxygen species (ROS), was evaluated in an in vitro cell model by testing phagocytes, such as human neutrophils, challenged by the chemotactic agent N‐formylmethionyl‐leucyl‐phenylalanine (FMLP). Both compounds inhibited O2− production, in a dose‐dependent way, without exerting scavenger effects. An in vivo model was applied to investigate their effect on bone remodeling. Fifty‐four female Wistar rats were divided into eight groups of six animals each, and a 4‐week treatment was applied in two phases. A 25 mg/kg/os dose in the first phase and 12.5–6.25mg/kg/os doses in the second one were employed. The tibia trabecular bone at the secondary spongiosa level was analyzed, and trabecular bone volume (%TBV), trabecular thickness (TbTh), and apatite lattice parameters were measured. At the highest doses of GR375 and GR377 the %TBV and the TbTh increased by 33.2, 34.6%, and 3.6 and 9.1%, respectively, whereas crystallographic parameters were not significantly different from the untreated group. Our results suggest a simultaneous antiinflammatory and antiosteoclastic activity of both drugs that encourages to perform further research. If it will be confirmed, they could be proposed in a variety of bone diseases, in particular, when acute inflammation is associated to osteolytic processes and, eventually, in the prevention and treatment of periprosthetic osteolysis. © 2005 Wiley Periodicals, Inc. J Biomed Mater Res, 2005
The effects of calcium phosphate deposition upon corrosion of CoCr alloys and the potential for implant failure
Authors: Lewis A. C. , Heard P. J.
Published: August 2005

Physical wear of orthopedic implants is inevitable. CoCr metal samples, typically used in joint reconstruction, corrode rapidly after removal of the protective oxide layer. The behavior of CoCr pellets immersed in human serum, fetal bovine serum (FBS), synovial fluid, and water were studied using time‐of‐flight secondary ion mass spectroscopy (ToF‐SIMS). The differences in the corrosive nature of human serum, FBS, synovial fluid, and water after 5 days immersion were highlighted by the oxide/hydroxide layer, which was, respectively, 25, 10, 1.5, and 3–3.5 nm thick. The thickness of calcium phosphate deposit from human serum, FBS, and synovial fluid was, respectively, 30, 20, and 2 nm. Co and Cr ions migrated from the bulk metal surface and were trapped in the serum deposits, where chromium existed as oxides, hydroxides, and phosphates, whereas the cobalt chemistry was dominated only by phosphates and hydroxides. This may account for the composition of wear debris from CoCr orthopedic implants, which are predominantly hydroxyphosphate compounds. From the literature, proteoglycans, pyrophosphates, phospholipids, lubricin, and superficial zone protein (SZP) have been identified as possible causes for the insignificant deposit of calcium phosphate from synovial fluid. Circulation of these compounds around the whole implant may inhibit calcium phosphate deposition and therefore contribute to osteolysis. © 2005 Wiley Periodicals, Inc. J Biomed Mater Res, 2005
PTEN enters the nucleus by diffusion
Authors: Liu Fenghua , Wagner Stefan , Campbell Robert B. , Nickerson Jeffrey A. , Schiffer Celia A. , Ross Alonzo H.
Published: August 2005

Despite much evidence for phosphatidylinositol phosphate (PIP)‐triggered signaling pathways in the nucleus, there is little understanding of how the levels and activities of these proteins are regulated. As a first step to elucidating this problem, we determined whether phosphatase and tensin homolog deleted on chromosome 10 (PTEN) enters the nucleus by passive diffusion or active transport. We expressed various PTEN fusion proteins in tsBN2, HeLa, LNCaP, and U87MG cells and determined that the largest PTEN fusion proteins showed little or no nuclear localization. Because diffusion through nuclear pores is limited to proteins of 60,000 Da or less, this suggests that nuclear translocation of PTEN occurs via diffusion. We examined PTEN mutants, seeking to identify a nuclear localization signal (NLS) for PTEN. Mutation of K13 and R14 decreased nuclear localization, but these amino acids do not appear to be part of an NLS. We used fluorescence recovery after photobleaching (FRAP) to demonstrate that GFP‐PTEN can passively pass through nuclear pores. Diffusion in the cytoplasm is retarded for the PTEN mutants that show reduced nuclear localization. We conclude that PTEN enters the nucleus by diffusion. In addition, sequestration of PTEN in the cytoplasm likely limits PTEN nuclear translocation. © 2005 Wiley‐Liss, Inc.
Low pH and Helicobacter pylori increase nuclear factor kappa B binding in gastric epithelial cells: A common pathway for epithelial cell injury?
Authors: O'Toole Dermot , Abdel‐Latif Mohamed M.M. , Long Aideen , Windle Henry J. , Murphy Anne M. , Bowie Andrew , O'Neill Luke A.J. , Weir Donald G. , Kelleher Dermot
Published: August 2005

Helicobacter pylori infection results in peptic ulceration and chronic gastritis through mechanisms which are not fully elucidated. Live H. pylori activate the pro‐inflammatory transcription factor NF‐κB in gastric epithelial cells. Patients may have peptic ulcer disease in the absence of H. pylori infection; therefore other factors contribute to the inflammatory process. Maximal acid output in patients with H. pylori infection and duodenal ulceration is significantly increased indicating a role for acid in the pathogenesis of mucosal ulceration. The effect of low pH on NF‐κB activation in gastric epithelial cells has not been studied. Human gastric epithelial cells (AGS) were exposed to a range of pH changes in the presence or absence of H. pylori. NF‐κB DNA‐binding and cytosolic IκB‐α were measured using electrophoretic mobility shift assay and Western blotting. NF‐κB DNA‐binding in gastric epithelial cells dramatically increased when the pH of the culture medium decreased. Increases in NF‐κB nuclear binding were paralleled by decreasing amounts of cytosolic IκB‐α. These findings were similar but less potent than those observed when cells were exposed to H. pylori. Low pH resulted in enhancement of H. pylori‐induced NF‐κB nuclear binding. DNA binding of NF‐κB activation secondary to low pH was attenuated by PD98059 but not by SB203580. Similar to H. pylori, low pH potently and independently augments NF‐κB nuclear binding in AGS cells and such activation appears to be mediated through MEK1‐dependant signaling pathways. © 2005 Wiley‐Liss, Inc.
Malaria‐suppressible expression of the anti‐apoptotic triple GTPase mGIMAP8
Authors: Krücken Jürgen , Epe Markus , Benten W. Peter M. , Falkenroth Nina , Wunderlich Frank
Published: August 2005

The IMAP/IAN family of AIG1‐like GTPases is conserved among vertebrates and angiosperm plants and has been postulated to regulate apoptosis, particularly in context with diseases such as cancer, diabetes, and infections. The human genes were recently renamed as gimap for GTPase of the immunity associated protein (GIMAP) family. Here we extend this new nomenclature to the murine gimap gene family. All gimap genes of the mouse are clustered on chromosome 6B with eight functional members and one pseudogene. The mGIMAP proteins contain one GTP‐binding site and display molecular masses between 33 and 38 kDa except for the very unusual 77 kDa mGIMAP8 protein, which is the first characterized protein containing three GTP‐binding domains. Northern blot analysis revealed expression of mgimap8 predominantly in the thymus. The low expression level observed in the spleen was further suppressed by Plasmodium chabaudi malaria. Confocal laser scanning microscopy demonstrated localization of mGIMAP8 at ER, Golgi, and mitochondria. Overexpression of mGIMAP8 could significantly impair anisomycin‐induced activation of caspase 3. Our data support the view that mGIMAP8 exerts an anti‐apoptotic effect in the immune system and is involved in responses to infections. © 2005 Wiley‐Liss, Inc.
Isolation and identification of 1α‐hydroxy‐3‐epi‐vitamin D3, a potent suppressor of parathyroid hormone secretion
Authors: Brown Alex J. , Ritter Cynthia S. , Weiskopf A.S. , Vouros P. , Sasso Gino J. , Uskokovic Milan R. , Wang Guochun , Reddy G. Satyanarayana
Published: August 2005

Since our original demonstration of the metabolism of 1α,25(OH)2D3 into 1α,25(OH)2‐3‐epi‐D3 in human keratinocytes, there have been several reports indicating that epimerization of the 3 hydroxyl group of vitamin D compounds is a common metabolic process. Recent studies reported the metabolism of 25OHD3 and 24(R),25(OH)2D3 into their respective C‐3 epimers, indicating that the presence of 1α hydroxyl group is not necessary for the 3‐epimerization of vitamin D compounds. To determine whether the presence of a 25 hydroxyl group is required for 3‐epimerization of vitamin D compounds, we investigated the metabolism of 1αOHD3, a non‐25 hydroxylated vitamin D compound, in rat osteosarcoma cells (ROS 17/2.8). We noted metabolism of 1αOHD3 into a less polar metabolite which was unequivocally identified as 1αOH‐3‐epi‐D3 using the techniques of HPLC, GC/MS, and 1H‐NMR analysis. We also identified 1αOH‐3‐epi‐D3 as a circulating metabolite in rats treated with pharmacological concentrations of 1αOHD3. Thus, these results indicated that the presence of a 25 hydroxyl group is not required for 3‐epimerization of vitamin D compounds. Furthermore, the results from the same studies also provided evidence to indicate that 1αOH‐3‐epi‐D3, like 1αOHD3, is hydroxylated at C‐25. We then evaluated the biological activities of 1αOH‐3‐epi‐D3. Treatment of normal rats every other day for 7 days with 2.5 nmol/kg of 1αOH‐3‐epi‐D3 did not raise serum calcium, while the same dose of 1αOHD3 increased serum calcium by 3.39 ± 0.52 mg/dl. Interestingly, in the same rats which received 1αOH‐3‐epi‐D3 we also noted a reduction in circulating PTH levels by 65 ± 7%. This ability of 1αOH‐3‐epi‐D3 to suppress PTH levels in normal rats without altering serum calcium was further tested in rats with reduced renal function. The results indicated that the ED50 of 1αOH‐3‐epi‐D3 for suppression of PTH was only slightly higher than that of 1α,25(OH)2D3, but that the threshold dose of the development of hypercalcemia (total serum Ca > 10.5 mg/dl) was nearly 80 times higher. These findings indicate that 1αOH‐3‐epi‐D3 is a highly selective vitamin D analog with tremendous potential for treatment of secondary hyperparathyroidism in chronic renal failure patients. © 2005 Wiley‐Liss, Inc.
Interactions between the rabbit CSN1 gene and the nuclear matrix of stably transfected HC11 mammary epithelial cells vary with its level of expression
Authors: Poussin Karine , Hayes Hélène , Pauloin Alain , Chanat Eric , Fontaine Marie‐Louise , Aujean Etienne , Sun Jian‐Sheng , Debey Pascale , Devinoy Eve
Published: August 2005

The expression of casein genes is specific to the mammary gland and maximal during lactation. However, among the numerous mammary cell lines described so far, only a few express some casein genes. The regulatory regions of casein genes have been largely described but the mechanisms explaining the mammary specific expression of these genes, and their silencing in most mammary cell lines, have not yet been fully elucidated. To test the hypothesis that the nuclear location of the casein genes may affect their expression, we transfected HC11 mouse mammary cell line with a 100 kb DNA fragment surrounding the rabbit alpha S1 casein gene. We derived stable clones which express or not the transfected rabbit casein gene, in the same cellular context, independently of the number of transgene copies. Metaphase spreads were prepared from the different clones and the transfected genes were localized. Unexpectedly, we observed that in the original HC11 cell line the number of chromosomes per metaphase spread is close to 80, suggesting that HC11 cells have undergone a duplication event, since the mouse karyotype is 2n = 40. In alpha S1 casein expressing cells, the expression level does not clearly correlate with a localization of the transfected DNA proximal to the centromeres or the telomeres. Analysis of the localization of the transfected DNA in nuclear halos allows us to conclude that when expressed, transfected DNA is more closely linked to the nuclear matrix. The next step will be to study the attachment of the endogenous casein gene in mammary nuclei during lactation. © 2005 Wiley‐Liss, Inc.
A microtubule associated protein (hNUDC) binds to the extracellular domain of thrombopoietin receptor (Mpl)
Authors: Pan Rui‐Min , Yang Yan , Wei Ming‐Xu , Yu Xiao‐Bin , Ge Yi‐Chen , Xu Peilin
Published: August 2005

Human NUDC (hNUDC) was initially characterized as a nuclear migration protein based on the similarity of its C‐terminus to that of fungal NUDC from Aspergillus nidulans. However, hNUDC is a 331 amino acid protein whereas fungal NUDC is 198 amino acids in length. The extra N‐terminal portion of hNUDC has no known function or homology to other proteins. In this study, we report the binding of hNUDC to the extracellular domain of the thrombopoietin receptor (Mpl) as detected by the yeast two‐hybrid system, GST pull‐down, and co‐immunoprecipitation. Our deletion analysis demonstrated that amino acids between positions 100 and 238 as the critical domain mediating the hNUDC and Mpl interactions as detected by the two‐hybrid system and GST pull‐down assay. Immunofluorescence staining of human megakaryocyte cells indicated that hNUDC and Mpl colocalized at all stages of megakaryocyte development. Substantial colocalization of hNUDC with microtubules was also detected around nuclei and elongated microtubular structures, especially in proplatelet extensions. © 2005 Wiley‐Liss, Inc.
Cyclic AMP‐dependent modification of gonad‐selective TAFII105 in a human ovarian granulosa cell line
Authors: Wu Yimin , Lu Yunzhe , Hu Yanfen , Li Rong
Published: August 2005

In response to gonadotropins, the elevated level of intracellular‐cyclic AMP (cAMP) in ovarian granulosa cells triggers an ordered activation of multiple ovarian genes, which in turn promotes various ovarian functions including folliculogenesis and steroidogenesis. Identification and characterization of transcription factors that control ovarian gene expression are pivotal to the understanding of the molecular basis of the tissue‐specific gene regulation programs. The recent discovery of the mouse TATA binding protein (TBP)‐associated factor 105 (TAFII105) as a gonad‐selective transcriptional co‐activator strongly suggests that general transcription factors such as TFIID may play a key role in regulating tissue‐specific gene expression. Here we show that the human TAFII105 protein is preferentially expressed in ovarian granulosa cells. We also identified a novel TAFII105 mRNA isoform that results from alternative exon inclusion and is predicted to encode a dominant negative mutant of TAFII105. Following stimulation by the adenylyl cyclase activator forskolin, TAFII105 in granulosa cells undergoes rapid and transient phosphorylation that is dependent upon protein kinase A (PKA). Thus, our work suggests that pre‐mRNA processing and post‐translational modification represent two important regulatory steps for the gonad‐specific functions of human TAFII105. © 2005 Wiley‐Liss, Inc.
During male pronuclei formation chromatin remodeling is uncoupled from nucleus decondensation
Authors: Monardes Antonia , Iribarren Claudio , Morin Violeta , Bustos Paula , Puchi Marcia , Imschenetzky María
Published: August 2005

Male pronucleus formation involves sperm nucleus decondensation and sperm chromatin remodeling. In sea urchins, male pronucleus decondensation was shown to be modulated by protein kinase C and a cdc2‐like kinase sensitive to olomoucine in vitro assays. It was further demonstrated that olomoucine blocks SpH2B and SpH1 phosphorylation. These phosphorylations were postulated to participate in the initial steps of male chromatin remodeling during male pronucleus formation. At final steps of male chromatin remodeling, all sperm histones (SpH) disappear from male chromatin and are subsequently degraded by a cysteine protease. As a result of this remodeling, the SpH are replaced by maternal histone variants (CS). To define if sperm nucleus decondensation is coupled with sperm chromatin remodeling, we have followed the loss of SpH in zygotes treated with olomoucine. SpH degradation was followed with anti‐SpH antibodies that had no cross‐reactivity with CS histone variants. We found that olomoucine blocks SpH1 and SpH2B phosphorylation and inhibits male pronucleus decondensation in vivo. Interestingly, the normal schedule of SpH degradation remains unaltered in the presence of olomoucine. Taken together these results, it was concluded that male nucleus decondensation is uncoupled from the degradation of SpH associated to male chromatin remodeling. From these results, it also emerges that the phosphorylation of SpH2B and SpH1 is not required for the degradation of the SpH that is concurrent to male chromatin remodeling. © 2005 Wiley‐Liss, Inc.