bluuebunny/crossref_metadata_2025 huggingface dataset:
Four improved statistics for contrasting means by correcting skewness and kurtosis
Authors: Yanagihara Hirokazu , Yuan Ke‐Hai
Published: November 2005

This paper is concerned with removing the influence of non‐normality in the classicalt‐statistic for contrasting means. Using higher‐order expansion to quantify the effect of non‐normality, four corrected statistics are provided. Two aim to correct the mean bias and two to correct the overall distribution. The classicalt‐statistic is also robust against non‐normality when the observed variables satisfy certain structures. A special case is when the marginal distributions of the contrast are independent and identically distributed.
Independent component analysis as a rotation method: A very different solution to Thurstone's box problem
Authors: Jennrich Robert I. , Trendafilov Nickolay T.
Published: November 2005

In this paper we consider the well‐known Thurstone box problem in exploratory factor analysis. Initial loadings and components are extracted using principal component analysis. Rotating the components towards independence rather than rotating the loadings towards simplicity allows one to accurately recover the dimensions of each box and also produce simple loadings. It is shown how this may be done using an appropriate rotation criterion and a general rotation algorithm. Methods from independent component analysis are used, and this paper may be viewed as an introduction to independent component analysis from the perspective of factor analysis.
Book Reviews
Authors: Lovie Sandy
Published: November 2005

Measurement theory and practice: The world through quantification

By Hand D. J.

London: Arnold 2004, Cased £45, ISBN 034067783X
Influence curves for factor loadings
Authors: Kwan C.W. , Fung W. K.
Published: November 2005

Influence curves for the initial and rotated loadings are derived for the maximum likelihood factor analysis (MLFA) model. Cook's distances based on the empirical influence curves of factor loadings are proposed for the identification of influential observations. The distances are shown to be invariant under scale transformation and factor rotation. We find that an observation with a very large Cook's distance based on the sample influence curve may not necessarily exert an excessive influence on the factor loadings pattern but may change the ordering of the factors. The issue of the switching of factors is also studied by means of the empirical influence curve and factor scores.
Genetic Basis of Drought Resistance at Reproductive Stage in Rice: Separation of Drought Tolerance From Drought Avoidance
Authors: Yue Bing , Xue Weiya , Xiong Lizhong , Yu Xinqiao , Luo Lijun , Cui Kehui , Jin Deming , Xing Yongzhong , Zhang Qifa
Published: November 2005

Drought tolerance (DT) and drought avoidance (DA) are two major mechanisms in drought resistance of higher plants. In this study, the genetic bases of DT and DA at reproductive stage in rice were analyzed using a recombinant inbred line population from a cross between an indica lowland and a tropical japonica upland cultivar. The plants were grown individually in PVC pipes and two cycles of drought stress were applied to individual plants with unstressed plants as the control. A total of 21 traits measuring fitness, yield, and the root system were investigated. Little correlation of relative yield traits with potential yield, plant size, and root traits was detected, suggesting that DT and DA were well separated in the experiment. A genetic linkage map consisting of 245 SSR markers was constructed for mapping QTL for these traits. A total of 27 QTL were resolved for 7 traits of relative performance of fitness and yield, 36 QTL for 5 root traits under control, and 38 for 7 root traits under drought stress conditions, suggesting the complexity of the genetic bases of both DT and DA. Only a small portion of QTL for fitness- and yield-related traits overlapped with QTL for root traits, indicating that DT and DA had distinct genetic bases.
Acis-regulatory Sequence Within theyellowLocus ofDrosophila melanogasterRequired for Normal Male Mating Success
Authors: Drapeau Mark David , Cyran Shawn A , Viering Michaela M , Geyer Pamela K , Long Anthony D
Published: November 2005

Drosophila melanogaster males perform a courtship ritual consisting of a series of dependent fixed-action patterns. The yellow (y) gene is required for normal male courtship behavior and subsequent mating success. To better characterize the requirement for y in the manifestation of innate male sexual behavior, we measured the male mating success (MMS) of 12 hypomorphic y mutants and matched-outbred-background controls using a y+ rescue element on a freely segregating minichromosome. We found that 4 hypomorphs significantly reduced MMS to varying degrees. Reduced MMS was largely independent of adult pigmentation patterns. These mutations defined a 300-bp regulatory region upstream of the transcription start, the mating-success regulatory sequence (MRS), whose function is required for normal MMS. Visualization of gene action via GFP and a Yellow antibody suggests that the MRS directs y transcription in a small number of cells in the third instar CNS, the developmental stage previously implicated in the role of y with regard to male courtship behavior. The presence of Yellow protein in these cells positively correlates with MMS in a subset of mutants. The MRS contains a regulatory sequence controlling larval pigmentation and a 35-bp sequence that is highly conserved within the genus Drosophila and is predicted to bind known transcription factors.
Fixation of the Human-Specific CMP-N-Acetylneuraminic Acid Hydroxylase Pseudogene and Implications of Haplotype Diversity for Human Evolution
Authors: Hayakawa Toshiyuki , Aki Ikuko , Varki Ajit , Satta Yoko , Takahata Naoyuki
Published: November 2005

The human CMP-N-acetylneuraminic acid hydroxylase gene (CMAH) suffered deletion of an exon that encodes an active center for the enzyme ∼3.2 million years ago (MYA). We analyzed a 7.3-kb intronic region of 132 CMAH genes to explore the fixation process of this pseudogene and the demographic implication of its haplotype diversity. Fifty-six variable sites were sorted into 18 different haplotypes with significant linkage disequilibrium. Despite the rather low nucleotide diversity, the most recent common ancestor at CMAH dates to 2.9 MYA. This deep genealogy follows shortly after the original exon deletion, indicating that the deletion has fixed in the population, although whether this fixation was facilitated by natural selection remains to be resolved. Remarkable features are exceptionally long persistence of two lineages and the confinement of one lineage in Africa, implying that some African local populations were in relative isolation while others were directly involved in multiple African exoduses of the genus Homo. Importantly, haplotypes found in Eurasia suggest interbreeding between then-contemporaneous human species. Although population structure within Africa complicates the interpretation of phylogeographic information of haplotypes, the data support a single origin of modern humans, but not with complete replacement of archaic inhabitants by modern humans.
A Logistic Regression Mixture Model for Interval Mapping of Genetic Trait Loci Affecting Binary Phenotypes
Authors: Deng Weiping , Chen Hanfeng , Li Zhaohai
Published: November 2005

Often in genetic research, presence or absence of a disease is affected by not only the trait locus genotypes but also some covariates. The finite logistic regression mixture models and the methods under the models are developed for detection of a binary trait locus (BTL) through an interval-mapping procedure. The maximum-likelihood estimates (MLEs) of the logistic regression parameters are asymptotically unbiased. The null asymptotic distributions of the likelihood-ratio test (LRT) statistics for detection of a BTL are found to be given by the supremum of a χ2-process. The limiting null distributions are free of the null model parameters and are determined explicitly through only four (backcross case) or nine (intercross case) independent standard normal random variables. Therefore a threshold for detecting a BTL in a flanking marker interval can be approximated easily by using a Monte Carlo method. It is pointed out that use of a threshold incorrectly determined by reading off a χ2-probability table can result in an excessive false BTL detection rate much more severely than many researchers might anticipate. Simulation results show that the BTL detection procedures based on the thresholds determined by the limiting distributions perform quite well when the sample sizes are moderately large.
Nucleotide Polymorphism and Linkage Disequilibrium in Wild Populations of the Partial Selfer Caenorhabditis elegans
Authors: Cutter Asher D
Published: November 2005

An understanding of the relative contributions of different evolutionary forces on an organism's genome requires an accurate description of the patterns of genetic variation within and between natural populations. To this end, I report a survey of nucleotide polymorphism in six loci from 118 strains of the nematode Caenorhabditis elegans. These strains derive from wild populations of several regions within France, Germany, and new localities in Scotland, in addition to stock center isolates. Overall levels of silent-site diversity are low within and between populations of this self-fertile species, averaging 0.2% in European samples and 0.3% worldwide. Population structure is present despite a lack of association of sequences with geography, and migration appears to occur at all geographic scales. Linkage disequilibrium is extensive in the C. elegans genome, extending even between chromosomes. Nevertheless, recombination is clearly present in the pattern of polymorphisms, indicating that outcrossing is an infrequent, but important, feature in this species ancestry. The range of outcrossing rates consistent with the data is inferred from linkage disequilibrium, using “scattered” samples representing the collecting phase of the coalescent process in a subdivided population. I propose that genetic variation in this species is shaped largely by population subdivision due to self-fertilization coupled with long- and short-range migration between subpopulations.
Dormancy Genes From Weedy Rice Respond Divergently to Seed Development Environments
Authors: Gu Xing-You , Kianian Shahryar F , Foley Michael E
Published: November 2005

Genes interacting with seed developmental environments control primary dormancy. To understand how a multigenic system evolved to adapt to the changing environments in weedy rice, we evaluated genetic components of three dormancy QTL in a synchronized nondormant genetic background. Two genetically identical populations segregating for qSD1, qSD7-1, and qSD12 were grown under greenhouse and natural conditions differing in temperature, relative humidity, and light intensity during seed development. Low temperatures tended to enhance dormancy in both conditions. However, genotypes responded to the environments divergently so that two populations displayed similar distributions for germination. Additive and/or dominance effects of the three loci explained ∼90% of genetic variances and their epistases accounted for the remainder in each environment. The qSD1 and qSD7-1 main effects were increased, while the qSD12 additive effect was decreased by relatively low temperatures. Both gene main and epistatic effects were involved in G × E interactions, which in magnitude were greater than environmental main effect. The divergent responses of dormancy genes observed in this simple multigenic system presumably have selective advantages in natural populations adapted to changing environments and hence represent a genetic mechanism stabilizing the dormancy level of weedy rice ripened in different seasons or temperature regimes.
Genetic Interactions Between Nhp6 and Gcn5 With Mot1 and the Ccr4–Not Complex That Regulate Binding of TATA-Binding Protein in Saccharomyces cerevisiae
Authors: Biswas Debabrata , Yu Yaxin , Mitra Doyel , Stillman David J
Published: November 2005

Our previous work suggests that the Nhp6 HMGB protein stimulates RNA polymerase II transcription via the TATA-binding protein TBP and that Nhp6 functions in the same functional pathway as the Gcn5 histone acetyltransferase. In this report we examine the genetic relationship between Nhp6 and Gcn5 with the Mot1 and Ccr4–Not complexes, both of which have been implicated in regulating DNA binding by TBP. We find that combining either a nhp6ab or a gcn5 mutation with mot1, ccr4, not4, or not5 mutations results in lethality. Combining spt15 point mutations (in TBP) with either mot1 or ccr4 also results in either a growth defect or lethality. Several of these synthetic lethalities can be suppressed by overexpression of TFIIA, TBP, or Nhp6, suggesting that these genes facilitate formation of the TBP–TFIIA–DNA complex. The growth defect of a not5 mutant can be suppressed by a mot1 mutant. HO gene expression is reduced by nhp6ab, gcn5, or mot1 mutations, and the additive decreases in HO mRNA levels in nhp6ab mot1 and gcn5 mot1 strains suggest different modes of action. Chromatin immunoprecipitation experiments show decreased binding of TBP to promoters in mot1 mutants and a further decrease when combined with either nhp6ab or gcn5 mutations.
Analyses of SUM1-1-Mediated Long-Range Repression
Authors: Valenzuela Lourdes , Gangadharan Sunil , Kamakaka Rohinton T
Published: November 2005

In Saccharomyces cerevisiae, local repression is promoter specific and localized to a small region on the DNA, while silencing is promoter nonspecific, encompasses large domains of chromatin, and is stably inherited for multiple generations. Sum1p is a local repressor protein that mediates repression of meiosis-specific genes in mitotic cells while the Sir proteins are long-range repressors that stably silence genes at HML, HMR, and telomeres. The SUM1-1 mutation is a dominant neomorphic mutation that enables the mutant protein to be recruited to the HMR locus and repress genes, even in the absence of the Sir proteins. In this study we show that the mutation in Sum1-1p enabled it to spread, and the native HMR barrier blocked it from spreading. Thus, like the Sir proteins, Sum1-1p was a long-range repressor, but unlike the Sir proteins, Sum1-1p-mediated repression was more promoter specific, repressing certain genes better than others. Furthermore, repression mediated by Sum1-1p was not stably maintained or inherited and we therefore propose that Sum1-1p-mediated long-range repression is related but distinct from silencing.
Diverse Mitotic and Interphase Functions of Condensins in Drosophila
Authors: Cobbe Neville , Savvidou Ellada , Heck Margarete M S
Published: November 2005

The condensin complex has been implicated in the higher-order organization of mitotic chromosomes in a host of model eukaryotes from yeasts to flies and vertebrates. Although chromosomes paradoxically appear to condense in condensin mutants, chromatids are not properly resolved, resulting in chromosome segregation defects during anaphase. We have examined the role of different condensin complex components in interphase chromatin function by examining the effects of various condensin mutations on position-effect variegation in Drosophila melanogaster. Surprisingly, most mutations affecting condensin proteins were often found to result in strong enhancement of variegation in contrast to what might be expected for proteins believed to compact the genome. This suggests either that the role of condensin proteins in interphase differs from their expected role in mitosis or that the way we envision condensin's activity needs to be modified to accommodate alternative possibilities.
A novel DFNA9 mutation in the vWFA2 domain of COCH alters a conserved cysteine residue and intrachain disulfide bond formation resulting in progressive hearing loss and site‐specific vestibular and central oculomotor dysfunction
Authors: Street Valerie A. , Kallman Jeremy C. , Robertson Nahid G. , Kuo Sharon F. , Morton Cynthia C. , Phillips James O.
Published: November 2005

Mutations within the COCH gene (encoding the cochlin protein) lead to auditory and vestibular impairment in the DFNA9 disorder. In this study, we describe the genetic mapping of progressive autosomal dominant sensorineural hearing loss first affecting high‐frequency auditory thresholds within a human pedigree to the long arm of chromosome 14 in band q12. A maximal pairwise LOD score of 7.08 was obtained with marker D14S1021. We identified a c.1625G > T mutation in exon 12 of COCH that co‐segregates with auditory dysfunction in the pedigree. The mutation results in a predicted p.C542F substitution at an evolutionarily conserved cysteine residue in the C‐terminus of cochlin. The c.1625G > T transversion in COCH exon 12 represents the first reported mutation outside of the LCCL domain which is encoded by exons 4 and 5. The 542F mutant cochlin is translated and secreted by transfected mammalian cells. Western blot analysis under non‐reducing and reducing conditions suggests that the 542F mutation alters intramolecular cochlin disulfide bond formation. In the vestibular system, a progressive horizontal canal hypofunction and a probable saccular otolith challenge were detected in family members with the c.1625G > T COCH alteration. Abnormal central oculomotor test results in family members with the c.1625G > T COCH alteration imply a possible central nervous system change not previously noted in DFNA9 pedigrees harboring mutations within the LCCL domain. © 2005 Wiley‐Liss, Inc.
Oriented Schwann cell growth on microgrooved surfaces
Authors: Hsu Shan‐hui , Chen Chun‐Yu , Lu Po Seng , Lai Chao‐Sung , Chen Chun‐Jung
Published: November 2005

Silicon wafers bearing microgrooved surfaces with various groove width, spacing, and depth were fabricated using microlithography. The orientation of rat Schwann cells along the direction of the grooves was measured at 24 h after seeding the cells. When the width/spacing of the grooves was fixed at 10/10 µm, the mean percentage of aligned cells was 12% for grooves of 0.5 µm depth, 15% for those of 1 µm depth, and 26% for those of 1.5 µm depth (P < 0.05). When the depth of grooves was fixed at 1.5 µm, the mean percentage of aligned cells increased from 26% for width/spacing 10/10 µm, to 33% for 10/20 µm or 20/10 µm, and up to 41% for 20/20 µm (P < 0.05). On the surface with grooves of width/spacing/depth = 20/20/1.5 µm and modified by laminin, the alignment at 24 h approached 60%, versus 51% for collagen‐coated surface and 41% for uncoated surface (P < 0.05). At 48 h after seeding, about 66% of the cells were aligned on the above laminin‐modified surface. The groove depth influenced orientation of Schwann cells significantly. The cell alignment on 20/20/3 µm microgrooved poly(D,L‐lactide‐co‐glycolide) 90:10 (PLGA) surfaces transferred from silicon reached 72% at 48 h and 92% at 72 h (P < 0.05). Coating this surface with laminin enhanced cell alignment only in short term (67% vs. 62% at 24 h, P < 0.05). The cell alignment guided by surface microgrooves was time dependent. © 2005 Wiley Periodicals, Inc.
A new interpretation of ASM2d for modeling of SBR performance for enhanced biological phosphorus removal under different P/HAc ratios
Authors: Yagci Nevin , Insel Guclu , Tasli Ruya , Artan Nazik , Randall Clifford W. , Orhon Derin
Published: November 2005

This study evaluated the prediction capability of Activated Sludge Model No. 2d (ASM2d), for the enhanced biological phosphorus removal (EBPR) performance of a sequencing batch reactor (SBR) receiving variable influent phosphate load. For this purpose, a laboratory‐scale SBR was operated with a synthetic feed containing acetate as the sole carbon source. The experiments were conducted in four different Runs to ensure a range of different phosphate/acetate ratios in the influent. Model evaluations were carried out using concentration profiles measured throughout a representative cycle at steady state. An iterative calibration methodology was developed based on sensitivity analysis and applied to four different sets of experimental data on relevant model parameters reflecting SBR performance. ASM2d was able to predict the steady state behavior of the SBR system receiving variable influent phosphate loads only with the recalibrated parameter set. The regular changing pattern of the coefficients could be interpreted with the ability of the SBR system to sustain glycogen accumulating microorganisms, GAOs, which can store substrate under anaerobic conditions without polyphosphate energy, but deriving energy from the degradation of glycogen. Thus they are capable of prevailing at lower P/Ac ratios. The results indicate the need to include glycogen and GAOs as model components for processes involving both phosphate accumulating organisms, (PAOs) and GAOs, in order to obtain a better prediction of XPHA and oxygen uptake rate (OUR) profiles in the system. © 2005 Wiley Periodicals, Inc.
Spurious, zeroth‐order entropy generation along a kinked wall
Authors: van der Maarel Eric , Koren Barry
Published: November 2005

Numerical entropy generation is studied in the case of steady, subsonic Euler flow along a kinked solid wall. For a standard upwind finite volume discretization the numerical entropy error, a component of the global discretization error, appears to be zeroth‐order in mesh size. Two possible causes of the zeroth‐order entropy error are studied. First an investigation is made of the local truncation error on a kinked grid. Although this error also appears to be zeroth‐order in the neighbourhood of the kink, it probably does not cause the zeroth‐order entropy error. Next a study is made of the existence of a singularity in the exact solution. Probably, the Euler flow solution is singular at the kink in the wall. The form of this likely singularity is unknown. Therefore the construction of a computational method which uses a priori knowledge about the singularity is not possible. Finally it is shown by numerical experiments that the subsonic Euler flow along a kinked wall still can be computed with vanishing entropy errors by using an appropriate sequence of continuously curved walls which converge to the kinked wall in the limit of zero mesh width.
A numerical study of the turbulent flow around the stern of ship models
Authors: Tzabiras G. D.
Published: November 2005

The present work is concerned with the numerical calculation of the turbulent flow field around the stern of ship models. The finite volume approximation is employed to solve the Reynolds equations in the physical domain using a body‐fitted, locally orthogonal curvilinear co‐ordinate system. The Reynolds stresses are modelled according to the standard k‐ε turbulence model. Various numerical schemes (i.e. hybrid, skew upwind and central differencing) are examined and grid dependence tests have been performed to compare calculated with experimental results. Moreover, a direct solution of the momentum equations within the near‐wall region is tried to avoid the disadvantages of the wall function approach. Comparisons between calculations and measurements are made for two ship models, i.e. the SSPA and HSVA model.
Effect of river discharge on the circulation in the western Bay of Bengal
Authors: Dube S. K. , Sinha P. C. , Rao G. S. , Rao A. D.
Published: November 2005

A three‐dimensional numerical model has been applied to study the impact of freshwater discharge from a river on the coastal circulation in the western Bay of Bengal. The basic dynamical framework of the model follows closely that described by Johns et al.1 for the simulation of coastal upwelling off the east coast of India. Using this model, experiments have been performed to investigate the impact of the freshwater discharge at the location of Godavari river along the east coast of India. A comparison of the model results, with and without the inclusion of river discharge, shows that the river discharge into the western Bay of Bengal suppresses the upwelling near the river mouth. Though there are no detailed observations on the flow structure near the mouth of the Godavari river, the computed results are in qualitative agreement with the observations documented by Rao and Jayaraman2 and Rao,3 who have shown that during monsoon period the upwelling off Godavari estuary is suppressed.
Generalization of physical component boundary fitted co‐ordinate (PCBFC) method for the analysis of free‐surface flow
Authors: Takizawa Akihiko , Koshizuka Seiichi , Kondo Shunsuke
Published: November 2005

This paper presents a systematic and theoretically consistent approach for the analysis of free‐surface flow, making use of a number of established ideas such as physical component, boundary‐fitted co‐ordinate (BFC) and Lagrangian front tracking. The approach extends, theoretically as well as numerically, the use of physical component to general non‐orthogonal moving grids and provides a numerically stable BFC method with little labour of free‐surface positioning, grid generation and grid renewal. The approach conserves mass even at the free surface and allows time step of the order of the Coulant number. The main body of the present paper starts with the definition of analytical space and Riemannian geometry intrinsic to the physical component by applying to it the theorems of differential geometry and manifold theory. Then the governing equations of flow and free surface for the physical component are defined in the general 3D form with the notation of the new Riemannian geometry. Numerical procedures and the fully discrete equations are also presented for the benefit of potential users. Finally, several 2D examples demonstrate the basic performance of the present method by showing the computability of complex free‐surface motion.
Buoyancy‐driven instability in a vertical cylinder: Binary fluids with Soret effect. Part II: Weakly non‐linear solutions
Authors: Hardin G. R. , Sani R. L.
Published: November 2005

The buoyancy‐driven instability of a monocomponent or binary fluid that is completely contained in a vertical circular cylinder is investigated, including the influence of the Soret effect for the binary mixture. The Boussinesq approximation is used, and weakly‐non‐linear solutions are generated via Galerkin's technique using an expansion in the eigensolutions of the associated linear stability problem. Various types of fluid mixtures and cylindrical domains are considered. Flow structure and associated heat transfer are computed and experimental observations are cited when possible.
Newton's method for solving heat transfer, fluid flow and interface shapes in a floating molten zone
Authors: Lan C. W.
Published: November 2005

Newton's method is applied to the finite volume approximation for the steady state heat transfer, fluid flow and unknown interfaces in a floating molten zone. The streamfunction/vorticity and temperature formulation of the Navier–Stokes and energy equations and their associated boundary conditions are written in generalized curvilinear co‐ordinates and conservative law form with the Boussinesq approximation. During Newton iteration the ILU(0) preconditioned GMRES matrix solver is applied for solving the linear system, where the sparse Jacobian matrix is estimated by finite differences. Nearly quadratic convergence of the method is observed. Sample calculations are reported for sodium nitrate, a high‐Prandtl‐number material (Pr = 9.12). Both natural convection and thermocapillary flow as well as an overall mass balance constraint in the molten zone are considered. The effects of convection and heat input on the flow patterns, zone position and interface shapes are illustrated. After the lens effect due to the molten zone is considered, the calculated flow patterns and interface shapes are compared with the observed ones and are found to be in good agreement.
A partially implicit method for simulating viscous aerofoil flows
Authors: Badcock K. J.
Published: November 2005

A partially implicit method for the unsteady compressible Navier‐Stokes equations is developed. The method is based on an explicit treatment of streamwise fluxes and an implicit treatment of normal fluxes. This leads to a linear system which is generated by an efficient finite difference procedure and which is block pentadiagonal. The method is tested on a shock‐induced oscillatory flow over an aerofoil. Parallel implementations of an explicit, fully implicit and partially implicit method are investigated.
A numerical method for accelerating the rate of convergence of the SIMPLE‐like algorithm for flow through a thin filter
Authors: Wen X. , Ingham D. B.
Published: November 2005

The control volume, finite difference method and the k‐ϵ tubulence model are employed in a numerical simulation of the turbulent fluid flow both outside and inside a blunt cylindrical sampler which houses a paper filter in its chamber. The presence of a paper filter, which has a very large resistance, results in a large pressure drop across the filter and this causes difficulties in making the SIMPLE or the SIMPLEC scheme converge. In order to improve the rate of convergence of the SIMPLE‐like algorithm when the resistance of the filter is very large, an average pressure correction formula is proposed. Based on global mass conservation, a line average pressure correction for the paper filter is derived using a modified Darcy law for a porous medium. A combination of this formula and the SIMPLE‐like algorithm can rapidly build up the pressure drop across the filter and hence dramatically improve the rate of convergence of the iterative scheme. Comparisons of the convergence histories and the numerical results for the fluid flow when using SIMPLE and SIMPLEC with the average pressure correction method show that the average pressure correction method for dealing with the paper filter significantly accelerates the rate of convergence of the iterative scheme.
Development of projection and artificial compressibility methodologies using the approximate factorization technique
Authors: Pentaris A. , Nikolados K. , Tsangaris S.
Published: November 2005

Predictions for two‐dimensional, steady, incompressible flows under both laminar and turbulent conditions are presented. The standard k‐ϵ turbulence model is used for the turbulent flows. The computational method is based on the approximate factorization technique. The coupled approach is used to link the equations of motion and the turbulence model equations. Mass conservation is enforced by either the pseudocompressibility method or the pressure correction method. Comparison of the two methods shows a superiority of the pressure correction method. Second‐ and fourth‐order artifical dissipation terms are used in order to achieve good convergence and to handle the turbulence model equations efficiently. Several internal and external test cases are investigated, including attached and separated flows.
Finite element calculations and experimental verification of the unsteady potential flow in a centrifugal volute pump
Authors: Badie R. , Jonker J. B. , van den Braembussche R. A.
Published: November 2005

In this paper we present a finite‐element‐based methode for the calculation of the unsteady potential flow in rotor/stator configurations. A numerical algorithm was developed to calculate the two‐dimensional flow through a centrifugal volute pump, taking into account the width variation of the volute in the axial direction and the vortex wakes downstream of the impeller blades by a linearized vortex distribution. The pressure field was obtained from the unsteady Bernoulli equation, with the entire configuration of the pump being included in the calculations. For that purpose the computational domain was split into a region containing the rotor and one containing the stationary parts, each region being treated in a different co‐ordinate system. The corresponding finite element grids qare matched by an interface consisting of connect elements which move with time. The method is applied to a laboratory centrifugal pump set up at the Von Karman Institute for Fluid Dynamics, which made an experimental validation possible. The total head of the pump and the velocity and pressure fields were computed and analysed for various mass flows. The agreement with the experimental data was satisfactory. The deviation was largest at low mass flow, the maximum deviation in the velocity around the impeller being 10 per cent. The overall behaviour of the pump could be well predicted.
Calculation of Reynolds stresses in turbulent supersonic flows
Authors: Ladeinde Foluso , Intile John C.
Published: November 2005

The baseline numerical procedure of interest in this study combines flux vector splitting, flux difference splitting and an explicit treatment of the diffusion terms of the flow equations. The viscous terms are treated explicitly to preserve the wave propagation properties of the Euler fluxes and permit splitting. The experience with this scheme has been limited to laminar or, at best, ‘eddy viscosity’ flows. In this paper the applicability of the scheme is extended to include the calculation of turbulent Reynolds stresses in supersonic flows. The schemes and our implementation are discussed. Both laminar and turbulence subsets of the Reynolds/Favre‐averaged equations are tested, with a discussion of relative performance. The test problem for turbulence consists of a zero‐pressure‐gradient supersonic boundary layer as well as a supersonic boundary layer experiencing the combined effects of adverse pressure gradient, bulk compression and a concave streamline curvature. Excellent agreement with experimental measurements is observed for most of the quantities compared, which suggests that the numerical procedures presented in this paper are potentially very useful.
A finite element simulation of the cross‐effects of viscoelasticity and inertia in an agitated vessel
Authors: Anne‐Archard D. , Boisson H. C.
Published: November 2005

Numerical simulation by a finite element method is used to examine the problem of the rotating flow of a viscoelastic fluid in a cylindrical vessel agitated with a paddle impeller. The mathematical model consists of a viscoelastic constitutive equation of Oldroyd B type coupled to the hydrodynamic equations expressed in a rotating frame. This system is solved by using an unsteady approach for velocity, pressure and stress fields. For Reynolds numbers in the range 0.1–10, viscoelastic effects are taken into account up to a Deborah number De of 1.33 and viscoelasticity and inertia cross‐effects are studied. Examining the velocity and stress fields as well as the power consumption, it is found that their evolutions are significantly different for low and moderate inertia. These results confirm the trends of experimental studies and show the specific contribution of elasticity without interference of the pseudoplastic character found in actual fluids.
A comparison of integration and interpolation Eulerian‐Lagrangian methods
Authors: Oliveira Anabela , Baptista António M.
Published: November 2005

Selected finite element Eulerian‐Lagrangian methods for the solution of the transport equation are compared systematically in the relatively simple context of 1D, constant coefficient, conservative problems. A combination of formal analysis and numerical experimentation is used to characterize the stability and accuracy that results from alternative treatments of the concentrations at the feet of the characteristic lines. Within the methods analyzed, those that approach such treatment with the perspective of ‘integration’ rather than ‘interpolation’ tend to have superior accuracy. Exact integration leads to unconditional stability and excellent accuracy. Quadrature integration leads only to conditional stability, but newly derived criteria show that stability restrictions are relatively mild and should not preclude the usefulness of quadrature integration methods in a range of practical applications. While conclusions cannot be extended directly to multiple dimensions and complex flows and geometries, results should provide useful insight to the development and behaviour of specific Eulerian‐Lagrangian transport models.
Numerical simulation of axisymmetric unsteady incompressible flow by a vorticity‐velocity method
Authors: Li Yuan , Dexun Fu , Yanwen Ma
Published: November 2005

A new numerical method for solving the axisymmetric unsteady incompressible Navier‐Stokes equations using vorticity‐velocity variables and a staggered grid is presented. The solution is advanced in time with an explicit two‐stage Runge‐Kutta method. At each stage a vector Poisson equation for velocity is solved. Some important aspects of staggering of the variable location, divergence‐free correction to the velocity field by means of a suitably chosen scalar potential and numerical treatment of the vorticity boundary condition are examined. The axisymmetric spherical Couette flow between two concentric differentially rotating spheres is computed as an initial value problem. Comparison of the computational results using a staggered grid with those using a non‐staggered grid shows that the staggered grid is superior to the non‐staggered grid. The computed scenario of the transition from zero‐vortex to two‐vortex flow at moderate Reynolds number agrees with that simulated using a pseudospectral method, thus validating the temporal accuracy of our method.
Solutions of magnetohydrodynamic problems based on a conventional computational fluid dynamics code
Authors: Sazhin S. S. , Makhlouf M. , Ishii T.
Published: November 2005

It is pointed out that there exists a hidden analogy between magnetohydrodynamic (MHD) and conventional computational fluid dynamic (CFD) equations. This allows the generalization of any conventional CFD code so that the effects of MHD can be accounted for. This generalization is actually made for the FLUENT CFD code. Although this generalized FLUENT code can easily be adjusted to any MHD environment, it has been specifically designed for metallurgical applications. Predictions of the code are validated against the analytical solutions for the Poiseuille‐Hartmann flow and for the shielding of magnetic field oscillations by a conducting medium (skin effect).
A control‐volume based finite element method for three‐dimensional incompressible turbulent fluid flow, heat transfer, and related phenomena
Authors: Costa V. A. F. , Oliveira L. A. , Figueiredo A. R.
Published: November 2005

A control‐volume based finite element method of equal‐order type for three‐dimensional incompressible turbulent fluid flow, heat transfer, and related phenomena is presented. The discretization equations are based mainly on the physics of the phenomena under consideration, more than on mathematical arguments. Special emphasis is devoted to the discretization of the convective terms and the continuity equation, and to the treatment of the boundary conditions imposed by the use of a high Reynolds k‐ϵ, type turbulence model. The pressure‐velocity coupling in the fluid flow calculation is made from a derivative of the original SIMPLER method, without pressure correction. The discretized equations are solved in a sequential, rather than a coupled, form with significant advantage in the required computer time and storage. The method is an extension of a former version proposed by us for two‐dimensional, laminar problems, and is here successfully applied to the following situations: three‐dimensional deflected turbulent jet, and flows in 90° and 45° junctions of ducts with rectangular cross sections. The calculated results are in very good agreement with the experimental and numerical (obtained with the well established finite difference method) data available in the literature.
Assessment of some iterative methods for non‐symmetric linear systems arising in computational fluid dynamics
Authors: Soria Antonio , Ruel François
Published: November 2005

Various tests have been carried out in order to compare the performances of several methods used to solve the non‐symmetric linear systems of equations arising from implicit discretizations of CFD problems, namely the scalar advection‐diffusion equation and the compressible Euler equations. The iterative schemes under consideration belong to three families of algorithms: relaxation (Jacobi and Gauss‐Seidel), gradient and Newton methods. Two gradient methods have been selected: a Krylov subspace iteration method (GMRES) and a non‐symmetric extension of the conjugate gradient method (CGS). Finally, a quasi‐Newton method has also been considered (Broyden). The aim of this paper is to provide indications of which appears to be the most adequate method according to the particular circumstances as well as to discuss the implementation aspects of each scheme.
Multicomponent variance estimation for binary traits in family‐based studies
Authors: Noh M. , Yip B. , Lee Y. , Pawitan Y.
Published: November 2005

In biometrical genetic analyses of binary traits, the use of family data overcomes some limitations of twin studies, particularly in terms of sample size and types of genetic or environmental factors that can be estimated. However, because of computational problems, recent methods in the application of generalized linear mixed models for family data structure have limited the ability to handle large data sets with general covariates. In this paper, we investigate the use of the hierarchical likelihood approach to the analysis of binary traits from family data. In a simulation study, the method is shown to be highly accurate for the estimation of both the variance components and fixed regression parameters, even for small family sizes. For illustration, we analyze a real data set of familial aggregation of preeclampsia, a pregnancy‐induced hypertension. When possible, the analysis is compared with the exact maximum likelihood approach.Genet. Epidemiol.2005. © 2005 Wiley‐Liss, Inc.
His36Pro point‐mutated proteolipid protein retained in the endoplasmic reticulum of oligodendrocytes in the Shaking pup
Authors: Song Jonathan , Goetz Brian D. , Duncan Ian D.
Published: November 2005

The shaking pup (shp) is a canine mutation that affects the myelin protein proteolipid protein (PLP) and its smaller and less abundant isoform, DM20, with proline replacing histidine36, resulting in a severe myelin deficiency in the central nervous system. We present evidence that the mutation leads to disrupted trafficking of the shp PLP/DM20 within oligodendrocytes. Immunohistochemical studies revealed significantly reduced levels of PLP/DM20 and other major myelin components such as myelin basic protein (MBP), myelin associated glycoprotein (MAG), and 2′,3′‐cyclic nucleotide 3′‐phosphodiesterase (CNP) in shp myelin. The distribution of shp PLP/DM20 proteins were altered and mostly retained in perinuclear cytoplasm and proximal processes, which co‐localized with distended rough endoplasmic reticulum (RER) within oligodendrocytes. No abnormal accumulation of MAG, MBP, or CNP in the cell body was found. These results suggest that mutated PLP/DM20 in the shp could be selectively retained in RER, causing disruption of their translocation to the periphery to myelinate axons. © 2005 Wiley‐Liss, Inc.
Oligodendrocyte precursor cells generate pituicytes in vivo during neurohypophysis development
Authors: Virard Isabelle , Coquillat Delphine , Bancila Mircea , Kaing Sovann , Durbec Pascale
Published: November 2005

In the vertebrate brain, much remains to be understood concerning the origin of glial cell diversity and the potential lineage relationships between the various types of glia. Besides astrocytes and myelin‐forming oligodendrocytes, other macroglial cell populations are found in discrete areas of the central nervous system (CNS). They share functional features with astrocytes and oligodendrocytes but also display specific characteristics. Such specialized cells, called pituicytes, are located in the neurohypophysis (NH). Our work focuses on the lineage of the pituicytes during rodent development. First, we show that cells identified with a combination of oligodendrocyte precursor cell (OPC) markers are present in the developing rat NH. In culture, neonatal NH progenitors also share major functional characteristics with OPCs, being both migratory and bipotential, i.e. able to give rise to type 2 astrocytes and oligodendrocytes. We then observe that, either in vitro or after transplantation into myelin‐deficient Shiverer brain, pieces of NH generate myelinating oligodendrocytes, confirming the oligodendrogenic potentiality of NH cells. However, no mature oligodendrocyte can be found in the NH. This led us to hypothesize that the OPCs present in the developing NH might be generating other glial cells, especially the pituicytes. Consistent with this hypothesis, the OPCs appear during NH development before pituicytes differentiate. Finally, we establish a lineage relationship between olig1+ cells, most likely OPCs, and the pituicytes by fate‐mapping experiments using genetically engineered mice. This constitutes the first demonstration that OPCs generate glial cells other than oligodendrocytes in vivo. © 2005 Wiley‐Liss, Inc.
Role of intracellular S100A4 for migration of rat astrocytes
Authors: Takenaga Keizo , Kozlova Elena N.
Published: November 2005

S100A4 is a member of the EF‐hand family of calcium‐binding proteins, first identified in tumor cells, and implicated in tumor invasion and metastasis. Intracellular upregulation of S100A4 is associated with increased motility of tumor cells. Extracellular application of S100A4 increases the motility of glioma cells in vitro. We showed previously that astrocytes in spinal cord and brain white matter also express S100A4. This expression is markedly increased in reactive white matter astrocytes after injury. Here, we have explored how changes in intracellular S100A4 affect migration of astrocytes. We produced cultures of white matter, S100A4 expressing astrocytes, and developed a small interfering (si) RNA approach to specifically eliminate S100A4 expression in these cells, and compared the migration of astrocytes expressing S100A4 with astrocytes transfected with S100A4 siRNA. As a “positive control” we used S100A4 expressing C6 glioma cells. In contrast to malignant cells, S100A4 expressing astrocytes increased their migration capacity after S100A4 siRNA treatment. At the same time, and in parallel with increased migration, white matter astrocytes increased their expression of metalloproteinases MMP‐9 and MT1‐MMP. The addition of MMP‐2/MMP‐9 inhibitor resulted in a significant inhibition of migration in S100A4 siRNA‐treated astrocytes. These findings indicate that S100A4 has a stabilizing function in reactive white matter astrocytes, a function that may contribute to the development of a rigid, growth‐inhibitory glial scar. © 2005 Wiley‐Liss, Inc.