bluuebunny/crossref_metadata_2025 huggingface dataset:
A novel assay for assessment of HIV‐specific cytotoxicity by multiparameter flow cytometry
Authors: Godoy‐Ramirez Karina , Mäkitalo Barbro , Thorstensson Rigmor , Sandström Eric , Biberfeld Gunnel , Gaines Hans
Published: October 2005

Background

Assessment of CD8+ T‐cell activity is of significant importance for the evaluation of cellular immune responses to viral infections, especially in HIV. We present a new assay for the assessment of HIV‐specific cytotoxicity by multiparameter flow cytometry.

Methods

Target cells, pulsed with peptide pools (Gag or Nef), were stained with 5‐ (and –6)‐carboxyfluorescein diacetate succinimidyl ester (CFSE), cultured with specific or nonspecific effector cells, and finally stained with propidium iodide (PI). Determination of cytolysis is based on the enumeration of viable target cells (CFSEhiPI−) in the test sample (target and specific effector cells) as compared with that of the viable target cells in the control sample (target and nonspecific effector cells). The 51Cr‐release assay and IFN‐γ ELISpot were performed by standard procedures.

Results

A comparison with the Cr‐release showed that the two assays were strongly correlated (r = 0.67; P < 0.001) but the sensitivity of the flow cytometric assay was significantly higher (P < 0.05), and the reproducibility good (CV, 7.7%). Good correlation was also found with the ELISpot assay (r = 0.66; P < 0.01).

Conclusion

This new assay provides both specific and sensitive results when employed for the detection of HIV‐specific CTL and can be a valuable tool for the evaluation of cytolytic activity in vaccine trials or in HIV‐infected subjects, especially if such responses are present at low levels. © 2005 Wiley‐Liss, Inc.
Automatic telomere length measurements in interphase nuclei by IQ‐FISH
Authors: Narath Rita , Lörch Thomas , Greulich‐Bode Karin M. , Boukamp Petra , Ambros Peter F.
Published: October 2005

To benefit from the fluorescence‐based automatic microscope (FLAME), we have adapted a PNA FISH technique to automatically determine telomere length in interphase nuclei. The method relies on the simultaneous acquisition of pan‐telomeric signals and reference probe signals. We compared the quantitative figures to those for existing methods, i.e. Southern blot analysis and quantitative FISH (Q‐FISH). Quantitative‐FISH on interphase nuclei (IQ‐FISH) allows the exact quantification of telomere length in interphase nuclei. Thus, this enables us to obtain not only exact information on the telomere length, but also morphological and topological details. The automatic measurement of large cell numbers allows the measurement of statistically relevant cell populations. © 2005 Wiley‐Liss, Inc.
Analysis of hypoxia‐inducible factor‐1α accumulation and cell cycle in geldanamycin‐treated human cervical carcinoma cells by laser scanning cytometry
Authors: Schwock Jörg , Geddie William R. , Hedley David W.
Published: October 2005

Background

Tumor hypoxia has been linked to increased disease aggressiveness and poorer treatment outcomes, and the transcription factor hypoxia‐inducible factor‐1 (HIF‐1) has been identified as the key molecule mediating the cellular response to hypoxic microenvironments. The α‐subunit of this factor is accumulated under hypoxia and rapidly degraded during re‐oxygenation, rendering the reliable measurement of HIF‐1α a difficult task. Heat shock protein 90 (Hsp90) is an essential protein that controls the activity, turnover, and trafficking of a variety of other proteins including HIF‐1α and cell cycle regulators. Hsp90 inhibitors like geldanamycin therefore have the potential to target tumor‐cell survival by at least two mechanisms, compromising the accumulation of HIF‐1α and cell proliferation.

Methods

We describe here the simultaneous measurement of HIF‐1α and cell cycle parameters by laser scanning cytometry (LSC) after exposure of two different human cervical carcinoma cell lines to hypoxia and geldanamycin.

Results

Our analysis demonstrates that the cell lines react to hypoxia and drug treatment in a distinct way, with SiHa being more affected by low oxygen concentrations than is ME180, which was more sensitive to geldanamycin treatment. Both cell lines respond to geldanamycin with a G2/M‐phase arrest and a decrease in HIF‐1α accumulation. Cell death due to geldanamycin occurs in association with mitosis, presumably through mitotic catastrophe.

Conclusion

Our results indicate that LSC can significantly contribute to the evaluation of in vitro drug effects particularly with respect to tumor hypoxia and the measurement of HIF‐1α. © 2005 Wiley‐Liss, Inc.
Controlling factors of gullying in the Maracujá Catchment, southeastern Brazil
Authors: de A. P. Bacellar L. , Netto A. L. Coelho , Lacerda W. A.
Published: October 2005

Hundreds of gullies (‘voçorocas’) of huge dimensions (up to 400–500 m long, 150 m wide and 50 m deep) are very common in the small Maracujá Catchment in southeastern Brazil. These erosional features, which occur with an uneven intensity throughout the area, started due to bad soil management practices at the beginning of European settlement, at the end of the 17th century, and nowadays are still evolving, but at a slower rate. As surface soils are usually very resistant to erosion, the outcrop of the more erodible basement saprolites seems to be an essential condition for their beginning. An analysis of well known erosion controlling factors was performed, aiming to explain the beginning and evolution of these gullies and to understand the reasons for their spatial distribution. Data shows that geology and, mainly, geomorphology are the main controlling factors, since gullies tend to be concentrated in basement rock areas with lower relief (domain 2) of Maracujá Catchment, mainly at the fringes of broad and flat interfluves. At the detailed scale (1:10 000), gullies are more common in amphitheatre‐like headwater hollows that frequently represent upper Quaternary gullies (paleogullies), which demonstrate the recurrence of channel erosion. So, gullies occur in areas of thicker saprolites (domain 2), in places with a natural concentration of surface and underground water (hollows). Saprolites of the preserved, non‐eroded hollows are usually pressurized (confined aquifer) due to a thick seal of Quaternary clay layer, in a similar configuration to the ones found in hollows of mass movement (mudflow) sites in southeastern Brazil. Therefore, the erosion of the resistant soils by human activities, such as road cuts and trenches (‘valos’), or their mobilization by mudflow movements, seem to be likely mechanisms of gullying initiation. Afterwards, gullies evolve by a combination of surface and underground processes, such as wash and tunnel erosion and falls and slumps of gully walls. Copyright © 2005 John Wiley & Sons, Ltd.
The effect of bed mobility on resistance to overland flow
Authors: Hu Shixiong , Abrahams Athol D.
Published: October 2005

When sediment grains are transported as bed load in overland flow, there is a net transfer of momentum from the flow to the grains. When these grains collide with other grains, whether on the bed or in the flow, streamwise flow velocity decreases and resistance to flow increases. Resistance to flow generated in this manner is termed bed‐load transport resistance. Resistance to flow f over a plane bed may be partitioned into grain resistance fg and bed‐load transport resistance fbt. We use the symbols fbtf and fbtm to denote fbt for flows over fixed beds and over mobile beds, respectively, and we compute the effect of bed mobility on flow resistance fmob by subtracting fbtf from fbtm.

The data for this study come from 54 flume experiments with fixed beds and 38 with mobile beds. On average fmob is approximately equal to half of fbtm, which is about one‐quarter of f. Hence, fmob is about one‐tenth of f. Predictive equations are developed for fbtf, fbtm and fmob using dimensional analysis to identify the relevant independent variables and regression analysis to evaluate the coefficients associated with these variables. Values of fmob are always positive which implies that mobile beds offer greater resistance to flow than do fixed beds. Evidently bed‐load grains colliding with mobile beds lose more momentum to the bed than do grains colliding with fixed beds. In other words, grain collisions with mobile beds are less elastic than those with fixed beds. Copyright © 2005 John Wiley & Sons, Ltd.
Symbolic computation of flow in a rotating pipe
Authors: Raszillier H. , Guiasu I. , Durst F.
Published: October 2005

A perturbation solution of the fully developed flow through a pipe of circular cross‐section, which rotates uniformly around an axis oriented perpendicularly to its own, is considered. The perturbation parameter is given by R = 2Ωa2/ν in terms of the angular velocity Ω, the pipe radius a and the kinematic viscosity ν of the fluid. The two coupled non‐linear equations for the axial velocity ω and the streamfunction ϕ of the transverse (secondary) flow lead to an infinite system of linear equations. This system allows first the computation of a given order ϕn, n ϕ 1, of the perturbation expansion ϕ = ∑ Rnϕn in terms of ωn‐1, the (n‐1)‐th order of the expansion ω = ∑ Rnωn, and of the lower orders ϕ1,…,ϕn − 1. Then it permits the computation of ωn from ω0,…,ωn − 1 and ϕ1,…,ϕ;n. The computation starts from the Hagen–Poiseuille flow ω0, i.e. the perturbation is around this flow.

The computations are performed analytically by computer, with the REDUCE and MAPLE systems. The essential elements for this are the appropriate co‐ordinates: in the complex co‐ordinates chosen the two‐dimensional harmonic (Laplace, Δ) and biharmonic (Δ2) operators are ideally suited for (symbolic) quadratures. Symmetry considerations as well as analysis of the equations for ωn, ϕn and of the boundary conditions lead to general (polynomial) formulae for these functions, with coeffcients to be determined. Their determination, order by order, implies, in complex co‐ordinates, only (symbolic) differentiation and quadratures. The coefficients themselves are polynomials in the Reynolds number c of the (unperturbed) Hagen–Poiseuille flow. They are tabulated in the paper for the orders n ⩽ 6 of the perturbation expansion.
Equilibrium and stability of tokamaks
Authors: Kerner Wolfgang
Published: October 2005

Axisymmetric, ideal MHD configurations with steady flow are computed by the finite‐element method. Rectangular elements with four to nine nodes are used. The equilibria are obtained in flux co‐ordinates by mesh rearrangement. The properties of the linearized motions around an equilibrium state are studied by a normal‐mode analysis. Dissipation is taken into account. Applying the Galerkin method leads to a large‐scale complex eigenvalue problem 𝒜x = λ ℬ︁x, which is solved by inverse iteration and by the Lanczos algorithm.
Global convergence of inexact Newton methods for transonic flow
Authors: Young David P. , Melvin Robin G. , Bieterman Michael B. , Johnson Forrester T. , Samant Satish S.
Published: October 2005

In computational fluid dynamics, non‐linear differential equations are essential to represent important effects such as shock waves in transonic flow. Discretized versions of these non‐linear equations are solved using iterative methods. In this paper an inexact Newton method using the GMRES algorithm of Saad and Schultz is examined in the context of the full potential equation of aerodynamics. In this setting, reliable and efficient convergence of Newton methods is difficult to achieve. A poor initial solution guess often leads to divergence or very slow convergence. This paper examines several possible solutions to these problems, including a standard local damping strategy for Newton's method and two continuation methods, one of which utilizes interpolation from a coarse grid solution to obtain the initial guess on a finer grid. It is shown that the continuation methods can be used to augment the local damping strategy to achieve convergence for difficult transonic flow problems. These include simple wings with shock waves as well as problems involving engine power effects. These latter cases are modelled using the assumption that each exhaust plume is isentropic but has a different total pressure and/or temperature than the freestream.
Data assimilation for non‐linear tidal models
Authors: Heemink A. W. , Kloosterhuis H.
Published: October 2005

A data assimilation procedure to incorporate measurements into a non‐linear tidal model by using Kalman‐filtering techniques is developed. The Kalman filter is based on the two‐dimensional shallow water equations. To account for the inaccuracies, these equations are embedded into a stochastic environment by introducing a coloured system noise process into the momentum equations. The continuity equation is assumed to be perfect. The deterministic part of the equations is discretized using an ADI method, the stochastic part using the Euler scheme. Assuming that the system noise is less spatially variable than the underlying water wave process, this stochastic part can be approximated on a coarser grid than the grid used to approximate the deterministic part. A Chandrasekhar‐type filter algorithm is employed to obtain the constant‐gain extended Kalman filter for weakly non‐linear systems. The capabilities of the filter are illustrated by applying it to the assimilation of water level measurements into a tidal model of the North Sea.
Modelling the initial motion of large cylindrical and spherical bubbles
Authors: Bugg J. D. , Rowe R. D.
Published: October 2005

A two‐dimensional, transient, finite difference technique based on a volume fraction specification of the free surface position and accounting for the effects of surface tension is shown to accurately predict the initial motion of large cylindrical and spherical bubbles. The predictions compare very favourably with the experimental data of Walters and Davidson. The initial acceleration of cylindrical and spherical bubbles is properly predicted as g and 2g respectively. The penetration of a tongue of liquid from below is the dominant process by which large deformations from the original shape take place and is well predicted by the model in both cases. For the spherical case the eventual transition into a toroidal bubble is demonstrated and the circulation associated with a rising toroidal bubble as a function of its volume upon release is shown to agree very well with experiments. Iterative linear equation‐solving techniques applicable to the special nature of the linear system resulting from such a free surface specification are surveyed and a simple Jacobi iteration based on red‐black ordering is found to perform well. The impact of the free surface on the relaxation of the linear system and the convergence criteria is also explored.
A coupled multigrid‐domain‐splitting technique for simulating incompressible flows in geometrically complex domains
Authors: Perng C. Y. , Street R. L.
Published: October 2005

This paper describes a domain decomposition numerical procedure for solving the Navier‐Stokes equations in regions with complex geometries. The numerical method includes a modified version of QUICK (quadratic upstream interpolation convective kinematics) for the formulation of convective terms and a central difference scheme for the diffusion terms. A second‐order‐accurate predictor‐corrector scheme is employed for the explicit time stepping. Although the momentum equations are solved independently on each subdomain, the pressure field is computed simultaneously on the entire flow field. A multigrid technique coupled with a Schwarz‐like iteration method is devised to solve the pressure equation over the composite domains. The success of this strategy depends crucially on appropriate methods for specifying intergrid pressure boundary conditions on subdomains. A proper method for exchanging information among subdomains during the Schwarz sweep is equally important to the success of the multigrid solution for the overall pressure field. These methods are described and subsequently applied to two forced convection flow problems involving complex geometries to demonstrate the power and versatility of the technique. The resulting pressure and velocity fields exhibit excellent global consistency. The ability to simulate complex flow fields with this method provides a powerful tool for analysis and prediction of mixing and transport phenomenon.
Investigation of use of reach‐back characteristics method for 2D dispersion equation
Authors: Yang Jinn‐Chuang , Chen Kun‐Nan , Lee Hong‐Yuan
Published: October 2005

The use of the Holly‐Preissmann two‐point scheme has been very popular for the calculation of the dispersion equation. The key to this scheme is to use the characteristics method incorporating the Hermite cubic interpolation technique to approximate the trajectory foot of the characteristics. This method can avoid the excessive numerical damping and oscillation associated with most finite difference schemes for advection computation. On the basis of the fundamental idea of the Holly‐Preissmann two‐point scheme, a new technique is introduced herein for the computation of the two‐dimensional dispersion equation. This new scheme allows the characteristics projecting back several time steps to fall on the spatial or temporal axis, while the characteristics foot is still solved by the Holly‐Preissmann two‐point method. The diffusion portion of the dispersion equation is solved by the commonly used Crank‐Nicholson method. The calculation for these two processes consisting of advection and diffusion is carried out separately but consecutively in one time step, a method known as the split operator algorithm. A hypothetical model was constructed to demonstrate the applicability of this new technique for the calculation of the pure advection and dispersion equation in two dimensions.
The two‐dimensional transmission and reflection of a solitary wave
Authors: Lu Q. Q.
Published: October 2005

In the present paper, limited to the discussion of weak non‐linear shallow water waves, the transmission and reflection of a planar soliton on a two‐dimensional structure are considered. The whole flow field is divided mainly into two subfields. One is in the vicinity of the structure, called the inner field; the other is far from the structure, called the outer field. In the outer field, according to its definition, the influence of the structure on the flow is negligible; to the order O(α, β) the governing equation for the flow is replaced by the Boussinesq equation. In the inner field the effect of the structure on the flow is significant, so the full Laplace equation is adopted as the governing equation for the flow field. Then the matched asymptotic expansion method is employed to connect smoothly the inner and outer solutions. Owing to the irregularity of the bottom of the structure, the boundary element method is incorporated. As an example, the case in which the incoming wave is a solitary wave is calculated and the time histories of transmitted and reflected waves are plotted.
Implementation of the Lagrange‐Galerkin method for the incompressible Navier‐Stokes equations
Authors: Buscaglia Gustavo C. , Dari Enzo A.
Published: October 2005

This paper is concerned with the implementation of Lagrange‐Galerkin finite element methods for the Navier‐Stokes equations. A scheme is developed to efficiently handle unstructed meshes with local refinement, using a quad‐tree‐based algorithm for the geometric search. Several difficulties that arise in the construction of the right‐hand side are discussed in detail and some useful tricks are proposed.

The resulting method is tested on the lid‐driven square cavity and the vortex shedding behind a rectangular cylinder and is found to give satisfactory agreement with previous works. A detailed analysis of the effect of time discretization is included.
Non‐Newtonian flow over a wedge with suction
Authors: Garg Vijay K.
Published: October 2005

A pseudo‐similarity solution is obtained for the flow of an incompressible fluid of second grade past a wedge with suction at the surface. The non‐linear differential equation is solved using quasi‐linearization and orthonormalization. The numerical method developed for this purpose enables computation of the flow characteristics for any values of the parameters K, a and b, where K is the dimensionless normal stress modulus of the fluid, a is related to the wedge angle and b is the suction parameter. A significant effect of suction on the wall shear stress is observed. The present results match exactly those from an earlier perturbation analysis for Kx2a ⩽ 0·01 but differ significantly as Kx2a increases.
An efficient pressure‐velocity procedure for gas‐droplet two‐phase flow calculations
Authors: Chen C. P. , Shang H. M. , Jiang Y.
Published: October 2005

This paper presents a non‐iterative numerical technique for computing time‐dependent gas‐droplet flows. The method is a fully interacting combination of Eulerian fluid and Lagrangian particle calculations. The interaction calculations between the two phases are formulated on a pressure‐velocity‐coupling procedure based on the operator‐splitting technique. This procedure eliminates the global iterations required in the conventional particle‐source‐in‐cell (PSIC) procedure. Turbulent dispersion calculations are treated by a stochastic procedure. Numerical calculations and comparisons with available experimental data as well as efficiency assessments are given for some sprays typical of spray combustion applications.
An ILU preconditioner with coupled node fill‐in for iterative solution of the mixed finite element formulation of the 2D and 3D Navier‐Stokes equations
Authors: Dahl O. , Wille S. Ø
Published: October 2005

In the present paper, preconditioning of iterative equation solvers for the Navier‐Stokes equations is investigated. The Navier‐Stokes equations are solved for the mixed finite element formulation. The linear equation solvers used are the orthomin and the Bi‐CGSTAB algorithms. The storage structure of the equation matrix is given special attention in order to avoid swapping and thereby increase the speed of the preconditioner. The preconditioners considered are Jacobian, SSOR and incomplete LU preconditioning of the matrix associated with the velocities. A new incomplete LU preconditioning with fill‐in for the pressure matrix at locations in the matrix where the corner nodes are coupled is designed. For all preconditioners, inner iterations are investigated for possible improvement of the preconditioning. Numerical experiments are executed both in two and three dimensions.
Drift forces on a pair of vertical cylinders
Authors: Rahman M. , Satish M. G. , Perrie W. , Zhu J.
Published: October 2005

An approximate method is presented here for estimating the hydrodynamic second‐order drift forces on a pair of bottom‐mounted, surface‐piercing circular cylinders in water of arbitrary uniform depth. The theoretical results are based upon the large‐spacing approximation. Results are presented to illustrate the influence of the various wave and structural parameters on the hydrodynamic forces on each of the cylinders.
Applications of boundary integral equation methods for two‐dimensional non‐linear water wave problems
Authors: Liu Philip L.‐F. , Hsu H.‐W. , Lean Meng H.
Published: October 2005

On the basis of the integral equation approach, numerical algorithms for solving non‐linear water wave problem are presented. The free surface flow is assumed to be irrotational. Two different Green functions are used in the integral equations. The non‐linear free‐surface boundary conditions are treated by a time‐stepping Lagrangian technique. Several numerical examples are given, including permanent periodic waves, overturning progressive waves, breaking standing waves and sloshing problems.
An improved approximation technique to obtain numerical solution of a class of two‐point boundary value similarity problems in fluid mechanics
Authors: Kafoussias N. G. , Williams E. W.
Published: October 2005

A simple and efficient approximate numerical technique is presented to obtain solutions to a wide class of two‐point boundary value similarity problems in fluid mechanics. This technique is based on the common finite difference method with central differencing, a tridiagonal matrix manipulation and an iterative procedure. The technique described in this paper has been successfully applied to three different representative similarity problems of fluid mechanics. Each one of these problems is described by a coupled, non‐linear system of three ordinary differential equations and has already been solved elsewhere using a different numerical method. So, the obtained numerical results, by our efficient numerical technique, permit a comparative study and show the accuracy and the effectiveness of this technique.
A frontal approach for internal node generation in Delaunay triangulations
Authors: Müller J.‐D. , Roe P. L. , Deconinck H.
Published: October 2005

The past decade has known an increasing interest in the solution of the Euler equations on unstructured grids due to the simplicity with which an unstructured grid can be tailored around very complex geometries and be adapted to the solution. It is desirable that the mesh can be generated with minimum input from the user, ideally, just specifying the boundary geometry and, perhaps, a function to prescribe some desired mesh size. The internal nodes should then be found automatically by the grid generation code. The approach we propose here combines the Delaunay triangulation with ideas from the advancing front method of Peraire et al. and Löhner et al. Both methods are briefly reviewed in Section 1. Our method uses a background grid to interpolate local mesh size parameters that is taken from the triangulation of the given boundary nodes. Geometric criteria are used to find a set of nodes in a frontal manner. This set is subsequently introduced into the existing mesh, thus providing an update Delaunay triangulation. The procedure is repeated until no more improvement of the grid can be achieved by inserting new nodes.
A least‐squares finite element method for time‐dependent incompressible flows with thermal convection
Authors: Tang Li Q. , Tsang Tate T. H.
Published: October 2005

The time‐dependent Navier–Stokes equations and the energy balance equation for an incompressible, constant property fluid in the Boussinesq approximation are solved by a least‐squares finite element method based on a velocity–pressure–vorticity–temperature–heat‐flux (u–P–ω–T–q) formulation discretized by backward finite differencing in time. The discretization scheme leads to the minimization of the residual in the l2‐norm for each time step. Isoparametric bilinear quadrilateral elements and reduced integration are employed. Three examples, thermally driven cavity flow at Rayleigh numbers up to 106, lid‐driven cavity flow at Reynolds numbers up to 104 and flow over a square obstacle at Reynolds number 200, are presented to validate the method.
A height–flux method for simulating free surface flows and interfaces
Authors: Mashayek F. , Ashgriz N.
Published: October 2005

A new technique for the numerical simulation of the free surface flows is developed. This technique is based on the finite element method with penalty formulation, and a flux method for surface advection. The advection part which is completely independent of the momentum solver is based on subdividing the fluid domain into small subvolumes along one of the co‐ordinate axis. The subvolumes are then used to find the height function which will later describe the free surface. The free surface of the fluid in each subvolume is approximated by a line segment and its slope is calculated using the volume of the fluid in the two neighbouring subvolumes. Later, the unidirectional volume flux from one subvolume to its neighbouring one is calculated using the conservation laws, and the new surface line segments are reconstructed. This technique, referred to as the Height–Flux Method (HFM) is implemented to simulate the temporal instability of a capillary jet. The results of the numerical simulation well predict the experimental data. It is also shown that the HFM is computationally more efficient than the techniques which use a kinematic boundary condition for the surface advection.
A proposed through‐flow inverse method for the design of mixed‐flow pumps
Authors: Borges João Eduardo
Published: October 2005

A through‐flow (hub‐to‐shroud) truly inverse method is proposed and described in this paper. It uses as a initial design specification, an imposition of mean swirl, i.e. radius times mean tangential velocity, given throughout the meridional section of the turbomachine. In the present implementation, it is assumed that the fluid is invsicid, incompressible and irrotational at inlet and the blades are supposed to have zero thickness. Only blade rows that impart to the fluid a constant work along the span will be considered.

An application of this procedure to design the rotor of a mixed‐flow pump will be described in detail. The strategy used to find a suitable mean swirl distribution and the other design inputs is also described. The final blade shape and pressure distributions on the blade surface are presented, showing that it is possible to obtain feasible designs using this technique. Another advantage of this technique is the fact that it does not require large amounts of CPU time.
Two‐phase flow modelling in gas‐stirred liquid vessels with SUPG‐stabilized equal‐order interpolations
Authors: Nigro N. , Storti M. , Idelsohn S.
Published: October 2005

The modelling of liquid flow in gas‐stirred vessels is described. A simple two‐phase model accounts for the buoyancy effect of bubbles. Friction between liquid and gas is modelled with the hypothesis of independent bubbles. The resulting PDE system is discretized with an original version of the SUPG‐FEM technique which stabilizes both the convection term and equal‐order interpolations for velocity and pressure, which are known to be unstable for incompressible flows. The resulting steady state discrete system is solved via pseudotemporal explicit iteration with a local time step and a preconditioning to homogenize the temporal scales for liquid and gas.
Simulation of three‐dimensional unsteady viscous free surface flow around a ship model
Authors: Alessandrini B. , Delhommeau G.
Published: October 2005

We present here a numerical method for solving the free surface flow around a ship at forward speed in calm water. The fluid is assumed to be Newtonian and the Reynolds‐averaged Navier‐Stokes equations are solved by a finite difference method. Modelization of turbulence is achieved by the algebraic model proposed by Baldwin and Lomax. Fully non‐linear free surface conditions are satisfied in the model and a method to avoid the incompatibility between free surface conditions and no‐slip conditions at the waterline is proposed. Numerical results obtained for a Wigley hull are compared with experimental results.
A new fully coupled solution of the Navier‐Stokes equations
Authors: Deng G. B. , Piquet J. , Queutey P. , Visonneau M.
Published: October 2005

A fully coupled method for the solution of incompressible Navier‐Stokes equations is investigated here. It uses a fully implicit time discretization of momentum equations, the standard linearization of convective terms, a cell‐centred colocated grid approach and a block‐nanodiagonal structure of the matrix of nodal unknowns. The Method is specific in the interpolation used for the flux reconstruction problem, in the basis iterative method for the fully coupled system and in the acceleration means that control the global efficiency of the procedure. The performance of the method is discussed using lid‐driven cavity problems, both for two and three‐dimensional geometries, for steady and unsteady flows.
Prediction of thermal stratification in a curved duct with 3D body‐fitted co‐ordinates
Authors: Ushijima S.
Published: October 2005

This paper concerns a numerical prediction method for buoyancy‐influenced flows using three‐dimensional non‐orthogonal curvilinear co‐ordinates. The numerical analysis of the transformed governing equations for thermal hydraulics is based on a Lagrangian method, in which advected physical values are evaluated by local cubic spline interpolations with third‐order accuracy in the three‐dimensional computational domain. In addition, the buoyancy and diffusion terms are discretized in the Lagrangian scheme so as to have second‐order accuracy with respect to time and space. The Neumann boundary conditions, which have been rather difficult for non‐orthogonal co‐ordinates to deal with, can be implemented by making use of normal vectors on the physical boundary surfaces and cubic spline interpolations. The developed numerical method is applied to the steady isothermal flow in a curved pipe and the unsteady stratified flow in a curved duct. Both of the predicted values are in good agreement with the experimental results and the validity of the prediction method is confirmed.
Fully discrete arbitrary‐order schemes for a model parabolic equation
Authors: Shi J.
Published: October 2005

A fully discrete methodology is investigated from which two‐level, explicit, arbitrary‐order, conservative numerical schemes for a model parabolic equation can be derived. To illustrate this, fully discrete three‐, five‐, seven‐ and nine‐point conservative numerical schemes are presented, revealing that a higher‐order scheme has a better stability condition. A method from which high‐order numerical schemes for a scalar advection‐diffusion equation can be developed is discussed. This method is based on high‐order schemes of both the advection and diffusion equations.
A simplified marker and cell method for unsteady flows on non‐staggered grids
Authors: Cheng Liang , Armfield Steven
Published: October 2005

The SMAC (simplified marker and cell) time‐advancing method for solving the unsteady incompressible Navier‐Stokes equations on non‐staggered grids is developed in generalized co‐ordinate systems. The primitive variable formulation uses Cartesian velocities and pressure, all defined at the centre of the control volume, as the dependent variables. A special elliptic flux correction at the faces of the finite volume is utilized in discretizing the continuity equation to suppress pressure oscillations. The test flows considered are a polar cavity flow starting from rest and the flow around a circular cylinder. The numerical results are compared with experimental results and results obtained by the well‐known SIMPLEC and PISO methods. The comparisons show that the elliptic flux correction technique works well in suppressing pressure oscillations and that the SMAC method is more efficient than the SIMPLEC and PISO methods for both steady and unsteady flows.
A numerical modelling study of the flow and salinity structure in the Godavari Estuary, east coast of India
Authors: Rao A. D.
Published: October 2005

The Godavari Estuary in Andhra Pradesh (a state bordering the east coast of India) communicates with the Bay of Bengal. Conditions in the estuary are characterized by a seasonally varying freshwater discharge and an intrusion of salt water from the bay dependent upon the flow associated with the semi‐diurnal component of the astronomical tide. A numerical model is applied to simulate the flow and salinity structures, which in the case of the Godavari Estuary have also been determined observationally and are documented in the literature. Observational data on the flow and salinity structure during two seasons are used in a comparison with theoretical results derived using a turbulent energy equation. Reasonable agreement is obtained between the model results and the observational data; in particular, streamlines are computed for the tidally averaged (or mean) component of the density‐controlled flow.
Mathematical modelling of the coupled reacting boundary layer equations
Authors: Villasenor R. , Chen J. Y.
Published: October 2005

A new numerical scheme for reacting axisymmetric jet flows formed between a fuel jet and co‐flowing air has been developed. The model is mathematically described by a set of non‐linear parabolic partial differential equations in two space dimensions, i.e. the boundary layer equations. The numerical scheme that the programme uses for solving the fully coupled conservation equations of mass, momentum, energy and species is a generaliztion of the discretization technique recently developed by Villasenor (J. Math. Comput. Simul., 36, 203–208 (1994)). Chemical production (and destruction) of the species is allowed to occur through N elementary reversible (or irreversible) reactions involving k species, although in the present model the reaction rates are evaluated with a simplified kinetic mechanism for a one‐step global reaction. Thermal radiation is considered assuming an optically thin limit and adopting the grey medium approximation. Allowances are made for natural convection effects and variable thermodynamic and molecular transport properties. The performance of the model in solving the coupled aerodynamic and finite rate chemistry effects is tested by comparing model predictions with experimental data of Mitchell et al. (Combust. Flame, 37, 227–244 (1980)) for a buoyant, laminar, diffusion axisymmetric methane‐air flame.
One‐dimensional, time‐dependent, homogeneous, two‐phase flow in volcanic conduits
Authors: Ramos J. I.
Published: October 2005

A one‐dimensional, time‐dependent, isothermal, homogeneous, two‐phase flow model was developed to study magma ascent in volcanic conduits. The physical modeling equations were numerically solved by means of a TVD (total variation diminishing) predictor‐corrector procedure and by means of a predictor‐corrector technique based on the method of characteristics. The results from the transient model were verified with an analytical solution for wave propagation in conduits without friction and gravitational effects. The numerical solutions were also compared with those of a steady‐state, homogeneous, two‐phase model for basaltic and rhyolitic magma ascents in the fissures and circular conduits of Vesuvius and Mt St. Helens. An application of the model to magma decompression in conduits indicates very short times for gas exsolution, fragmentation, and shock wave propagation, implying that the modelling of gas exsolution should involve non‐equilibrium kinetics effects. Future coupling of the transient magma ascent model with magma chamber and pyroclastic dispersion models should allow for more realistic simulations of the time‐dependent behavior of real volcanic eruptions.
Numerical studies on effect of check valve performance on pressure surges during pump trip in pumping systems with air entrainment
Authors: Lee T. S.
Published: October 2005

Recent numerical investigations on pressure surges during pump trip in pumping installations showed that by including an air entrainment variable wave speed model, reasonable predictions of transient pressure surges with proper phasing and attenuation of pressure peaks can be obtained. These calculated results are consistent with similar field measurements made with the pumps operating at low pump cut‐out levels, when air entrainment due to an attached surface vortex was observed. However, in the numerical calculation procedures it is assumed that the inertia of the moving elements of the check valve is small and that the check valve closes at zero reverse flow velocity. In practice, check valves seldom close precisely at zero reverse flow velocity. With the check valves not closing at zero reverse velocity, the present numerical computations show that the air content in a fluid system can adversely affect the check valve performance. With the fluid system operating within a critical range of air entrainment values, the present analysis showed that there is a possibility of ‘check valve slamming’ when the check valves are selected based only on the analysis of an air‐free system. This phenomenon is confirmed through field observations.
Atheroma development in apolipoprotein E‐null mice is not regulated by phosphorylation of p27Kip1 on threonine 187
Authors: Sanz‐González Silvia M. , Melero‐Fernández de Mera Raquel , Malek Nisar P. , Andrés Vicente
Published: October 2005

Excessive cellular proliferation is thought to contribute to neointimal lesion development during atherosclerosis and restenosis after angioplasty. Inhibition of cyclin‐dependent kinase (CDK) activity by p27 inhibits mammalian cell growth. Mounting evidence indicates that p27 negatively regulates neointimal thickening in animal models of restenosis and atherosclerosis, and its expression in human neointimal lesions is consistent with such a protective role. Cell cycle progression is facilitated by cyclinE/CDK2‐dependent phosphorylation of p27 on threonine 187 (T187) during late G1. The purpose of this study was to assess whether this phosphorylation event plays a role during atherosclerosis. To this end, we generated apolipoprotein E‐null mice with both p27 alleles replaced by a mutated form non‐phosphorylatable at T187 (apoE−/−p27T187A mice) and investigated the kinetics of atheroma development in these animals compared to apoE−/− controls with an intact p27 gene. Fat feeding resulted in comparable level of hypercholesterolemia in both groups of mice. Surprisingly, aortic p27 expression was not increased in fat‐fed apoE−/−p27T187A mice compared with apoE−/− controls. Moreover, atheroma size, lesion cellularity, proliferation, and apoptotic rates were undistinguishable in both groups of fat‐fed mice. Thus, in contrast to previous studies that highlight the importance of p27 phosphorylation at T187 on the control of p27 expression and function in different tissues and pathophysiological scenarios, our findings demonstrate that this phosphorylation event is not implicated in the control of aortic p27 expression and atheroma progression in hypercholesterolemic mice. J. Cell. Biochem. 97: 735–743, 2006. © 2005 Wiley‐Liss, Inc.
Expansion of mesenchymal stem cells isolated from pediatric and adult donor bone marrow
Authors: Mareschi Katia , Ferrero Ivana , Rustichelli Deborah , Aschero Simona , Gammaitoni Loretta , Aglietta Massimo , Madon Enrico , Fagioli Franca
Published: October 2005

The enormous plasticity of mesenchymal stem cells (MSCs) suggests an improvement of a standard protocol of isolation and ex vivo expansion for experimental and clinical use. We isolated and expanded MSCs from bone marrow (BM) of pediatric and young adult donors, to analyze the growth kinetic, immunophenotype, telomere length, karyotype during ex vivo expansion. Seventeen BM samples were collected from young adult donors and 8 from pediatric donors. MSCs isolated from two groups showed no morphological differences while their cell growth was strictly related to the donor's age. The MSCs isolated from pediatric donors reached a cumulative PD almost twice as high as MSCs isolated from young adult donors after 112 days (10.2 ± 1.9 versus 5.5 ± 3.7). Furthermore, we analyzed the modulation of antigen expression in the MSCs isolated from two groups until 10th passage (77 days) and there was no significant difference between the modulation of antigen expression. In particular, at the first passage, MSCs showed a low contamination of hemopoietic cells which became insignificant in the following passages. There was a high expression of CD90, CD29, CD44 and CD105 and variable and moderate expression of CD166 and CD106 at the start of MSC culture and at each passage during expansion. No chromosomal alteration or evidence of cellular senescence were observed in all analyzed samples. All these data suggest that MSCs can be isolated and expanded from most healthy donors, providing for an autologous source of stem cells. J. Cell. Biochem. 97: 744–754, 2006. © 2005 Wiley‐Liss, Inc.
Differentiation‐specific transcriptional regulation of the ESE‐2 gene by a novel keratinocyte‐restricted factor
Authors: Tummala Ramakumar , Sinha Satrajit
Published: October 2005

Epithelium specific Ets‐2 (ESE‐2), an epithelium‐specific ETS‐domain transcription factor, is highly expressed in differentiated keratinocytes. To understand the molecular mechanisms that govern the cell‐type and differentiation‐specific expression of ESE‐2 in keratinocytes, we have focused our studies on the identification and characterization of its cis‐regulatory elements. We first performed DNase I hypersensitive site mapping and demonstrated that the promoter region of ESE‐2 is in open chromatin conformation in differentiated keratinocytes. Next, we performed transient transfection assays with several 5′ serially deleted constructs containing segments of the ESE‐2 promoter. These experiments have led to the identification of a short fragment that shows remarkable sequence conservation between several species and harbors most of the transcriptional activity. Interestingly, a high level of transcriptional activity was only observed when the transfected keratinocytes were induced to differentiate by increasing the calcium concentration in the cell‐culture medium. To identify the factors that mediate the transcriptional activity, we analyzed this segment by mutational and electrophoretic mobility shift assays (EMSA) experiments. Our studies have identified a critical stretch of nucleotides that is important for both basal as well as calcium responsive reporter activity and that binds to a nuclear factor, keratinocyte restricted factor (KRF). KRF is a novel transcription factor that is restricted to nuclear extracts isolated from keratinocytes and that binds to unique DNA sequences, which do not resemble any known consensus binding motif for transcription factors. Our preliminary experiments shed light on the biochemical nature of KRF and set the stage for future studies in identification of KRF and testing its role in governing ESE‐2 gene expression in vivo. J. Cell. Biochem. 97: 766–781, 2006. © 2005 Wiley‐Liss, Inc.
Micro‐Raman spectroscopy used to identify and grade human skin pilomatrixoma
Authors: Cheng Wen‐Ting , Liu Ming‐Tzen , Liu Han‐Nan , Lin Shan‐Yang
Published: October 2005

Raman microspectroscopy was applied to analyze the changes in structural conformation and chemical composition of the mass of human skin pilomatrixoma (PMX). The normal skin dermis, collagen type I, and hydroxyapatite (HA) were used as control. The excised specimens from two patients diagnosed as a typical PMX were detected, in which one specimen was a soft mass, but the other was a hard mass with somewhat calcified deposits via histopathological examination. The Raman spectrum of normal skin dermis was found to be similar to the Raman spectrum of collagen type I, confirming that the collagen type I was a predominant component in normal skin dermis. The differences of Raman peak intensity between normal skin dermis and soft or hard PMX mass were obvious at 1,622–1,558, 1,400–1,230, 1,128, 1,000–850, 749, and 509 cm−1. In particular, the peak at 1,665 cm−1 assigned to amide I band shifted to 1,655 cm−1 and the peak at 1,246 cm−1 corresponding to amide III band was reduced in its intensity in hard PMX mass. The significant changes in collagen content and its structural conformation, the higher content of tryptophan, and disulfide formation in PMX masses were markedly evidenced. In addition, the shoulder and weak peak at 960 cm−1 assigned to the stretching vibration of PO of HA also appeared respectively in the Raman spectra of soft and hard PMX masses, suggesting the occurrence of calcification of HA in the PMX tissue, particularly in the hard PMX mass. The result indicates that the micro‐Raman spectroscopy may provide a highly sensitive and specific method for identifying normal skin dermis and how it differs in chemical composition from different PMX tissues. Microsc. Res. Tech. 68:75–79, 2005. © 2005 Wiley‐Liss, Inc.