bluuebunny/crossref_metadata_2025_split huggingface dataset:
A staggered spectral element model with application to the oceanic shallow water equations
Authors: Iskandarani Mohamed , Haidvogel Dale B. , Boyd John P. 
Published: August 2005

AbstractA staggered spectral element model for the solution of the oceanic shallow water equations is presented. We introduce and compare both an implicit and an explicit time integration scheme. The former splits the equations with the operator‐integration factor method and solves the resulting algebraic system with generalized minimum residual (GMRES) iterations. Comparison of the two schemes shows the performance of the implicit scheme to lag that of the explicit scheme because of the unpreconditioned implementation of GMRES. The explicit code is successfully applied to various geophysical flows in idealized and realistic basins, notably to the wind‐driven circulation in the North Atlantic Ocean. The last experiment reveals the geometric versatility of the spectral element method and the effectiveness of the staggering in eliminating sprious pressure modes when the flow is nearly non‐divergent.
Modelling of the turbulent thermal boundary layer implemented in CFD code N3S and application to flows in heated and cooled rooms
Authors: Delenne B. , Manzoni D. , Pot G. 
Published: August 2005

AbstractThis paper presents an efficient finite element method for solving the unsteady Navier–Stokes equations for turbulent incompressible flow coupled with thermal problems. This method has been implemented in the N3S code, developed at Electricité de France. The time discretization is first described. We precise then the Chorin and the ‘projected Uzawa’ algorithms used for the Stokes problem. Recent improvements concerning the optimization of finite element calculations are also detailed. The second part deals with the modelling of the thermal boundary layer used to simulate walls with fixed temperature in turbulent flows. The differences with other modelling suggested in the literature are discussed. The last part presents some applications. EDF is involved in the conception of heating or cooling systems and numerical methods constitute a very useful tool to study the movements of air in habitations. The calculations are validated by comparisons with measurements.
Numerical study of radiative ignition of pyrolysing solid fuels
Authors: Durbetaki P. , Phuoc T. X. , Mathur M. P. , Ekmann J. M. 
Published: August 2005

AbstractA numerical model of radiative ignition of pyrolysing solid fuels is developed. The model is one‐dimensional and transient. The following mechanisms are simultaneously accounted for: (i) the surface heat and mass transport, (ii) the surface oxidation chemical reaction, (iii) the in‐depth pyrolysis, (iv) the gas‐phase heating by absorption of the radiation and by heat conduction/convection from the solid surface, and (v) the gas‐phase chemical reaction. The solutions are obtained numerically with the method of lines. Using lignite and bituminous coal for the simulations, the results confirm that the pyrolysis products absorb a significant amount of the external radiation. Predictions of the ignition times show that both the surface ignition time and the gas‐phase ignition time decrease rapidly with increasing radiation intensities. A good agreement between predictions and experiments is obtained.A sensitivity analysis is also carried out with the key kinetic parameters. This analysis establishes an upper limit for surface and pyrolysis activation energies and a lower limit for gas‐phase activation energy. Within these limits, the radiative ignition of coals appears as an integration of two consecutive ignition modes: the surface ignition occurs first, which is then followed by the gas‐phase ignition. Beyond these limits, the single gas‐phase ignition mode is the only ignition mode to prevail.
Numerical modelling of confined flow past a cylinder of square cross‐section at various orientations
Authors: Li Guoping , Humphrey Joseph A. C. 
Published: August 2005

AbstractResults are presented for the unsteady, two‐dimensional flow and heat transfer due to a square obstruction of diameter d located asymmetrically between the parallel sliding walls of a channel with length‐to‐height ratio W/H = 6·44. Analysis is based on the numerical solution of spatially and temporally second‐order accurate finite difference approximations of the transport equations expressed in curvilinear co‐ordinates. Laminar, constant property flow is assumed for obstruction configurations in which the blockage ratio is d/H = 0·192, the nearest‐wall distances are g/d = 0·2, 0·5 and 1, the orientation angles are α=0°, 10° and 20° and the Reynolds numbers are Re=100, 500, and 1000. Preparatory testing of the numerical procedure was performed for a variety of documented flows to verify its physiconumerical accuracy and obtain estimates of the residual grid‐dependent uncertainties in the variables calculated. Heat transfer, drag and lift coefficients and Strouhal numbers for the present flow were finally calculated to within 4%–7% of their grid‐dependent values using non‐uniformly spaced grids consisting of (x=99, y=55) nodes. Above a critical value of the Reynolds number, which depends on the geometrical parameters, the flow is characterized by alternate vortex shedding from the obstruction top and bottom surfaces. Streamline, vorticity and particle streakline plots provide qualitative impressions of the unsteady vortical flow. Especially noteworthy are the extremes in the lift coefficient which ranges from large positive values for an obstruction with g/d=0·2 and α=10° to negative values for one with g/d=0·5 and α=0°. Both the drag and lift coefficients as well as the Strouhal number exhibit non‐monotonic variations with respect to the parameters explored. Asymmetries in the obstruction location and orientation account for relatively large vortex‐induced periodic variations in heat transfer, especially along the wall nearest the obstruction. Notable differences are also predicted for the heat transfer coefficients of the individual obstruction surfaces as a function of the orientation angle.
Numerical solution of coupled burgers equations in inhomogeneous form
Authors: Shankar Rama , Singh T. V. , Bassaif Anwar A. 
Published: August 2005

AbstractA finite difference scheme based on the operator‐splitting technique with cubic spline functions is derived for solving the two‐dimensional Burgers equations in ‘inhomogeneous’ form. The scheme is of first‐order accuracy in time and second‐order accuracy in space direction and is unconditionally stable. The numerical results are obtained with severe/moderate gradients in the initial and boundary conditions and the steady state solutions are plotted for different values of the parameters. It is concluded that the resulting scheme works very well even in the case of very severe gradient in the solution. Also, the general nature of the scheme provides a wider application in the solution of non‐linear problems.
Fractional step method for solution of incompressible Navier‐Stokes equations on unstructured triangular meshes
Authors: Despotis G. K. , Tsangaris S. 
Published: August 2005

AbstractIn this paper an implicit fractional step method for the solution of the two‐dimensional, time‐dependent, incompressible Navier‐Stokes equations is presented. The current method was developed for use on an unstructured grid made up of triangles. The basic principles of this method are that the evaluation of the time evolution is split into intermediate steps and that for the spatial discretization of the flow equations a finite volume discretization on an unstructured triangular mesh is used. The present approach has been used to simulate viscous, laminar flows for various Reynolds numbers in test cases such as a backward‐facing step, a square cavity and a channel with wavy boundaries.
A variable boundary model of storm surge flooding in generalized curvilinear grids
Authors: Shi Fengyan , Sun Wenxin 
Published: August 2005

AbstractIn this paper, generalized 2D shallow sea dynamic equations in movable curvilinear co‐ordinates are derived. Through a differential co‐ordinate transformation a self‐adaptive grid is proposed to treat a continuously deforming lateral boundary and a kinematical boundary condition is adopted. The self‐adaptive grid method (SAM) is used to simulate numerically the storm surge flooding in the Bohai Sea on 23 April 1969, which was one of the largest storm surge inundations in China.
A numerical study of flow over a confined backward‐facing step
Authors: Barton I. E. 
Published: August 2005

AbstractNumerical solutions using the SIMPLE algorithms for laminar flow over a backward‐facing step are presented. Five differencing schemes were used: hybrid; quadratic upwind (QUICK); second‐order upwind (SOUD); central‐differencing and a novel scheme named second‐order upwind biased (SOUBD). The SOUBD scheme is shown to be part of a family of schemes which include the central‐differencing, SOUD and QUICK schemes for uniform grids. The results of the backward‐facing step problem are presented and are compared with other numerical solutions and experimental data to evaluate the accuracy of the differencing schemes. The accuracy of the differencing schemes was ascertained by using uniform grids of various grid densities. The QUICK, SOUBD and SOUD schemes gave very similar accurate results. The hybrid scheme suffered from excessive diffusion except for the finest grids and the central‐differencing scheme only converged for the finest grids.
A comparison study on multivariant and univariant finite elements for three‐dimensional incompressible viscous flows
Authors: Sheu Tony W. H. , Wang Morten M. T. 
Published: August 2005

AbstractIn this paper, four quadratic hexahedron elements are considered and assessed for analysis of an incompressible viscous flow underlying the mixed finite element method. We classify the investigated elements as multivariant and univariant finite elements. With the same number of pressure unknowns, multivariant elements are more constrained when the number of elements per side is larger than 10, as compared with that of continuous pressure elements. In multivariant eléments, the coding is complicated by the appearance of restricted degrees of freedom at mid‐face and mid‐edge nodes. The comparison consequently should be made via numerical example against the analytical problem.
Generalized differential and integral quadrature and their application to solve boundary layer equations
Authors: Shu C. , Chew Y. T. , Richards B. E. 
Published: August 2005

AbstractBased on the work of generalized differential quadrature (GDQ), a global method of generalized integral quadrature (GIQ) is developed in this paper for approximating an integral of a function over a part of the closed domain. GIQ approximates the integral of a function over the part of the whole closed domain by a linear combination of all the functional values in the whole domain with higher order of accuracy. The weighting coefficients of GIQ can be easily determined from those of GDQ. Applications of GDQ and GIQ to solve boundary layer equations demonstrated that accurate numerical results can be obtained using just a few grid points.
Methylation of the O6‐methylguanine‐DNA methyltransferase promoter suppresses expression in mouse skin tumors and varies with the tumor induction protocol
Authors: Abdel‐Fattah Rana , Glick Adam , Rehman Ishtiaq , Maiberger Patrick , Hennings Henry 
Published: August 2005

AbstractHypermethylation of CpG sites within the promoter region of the O6‐methylguanine‐DNA methyltransferase (MGMT) gene occurs frequently in human cancer, preventing both MGMT expression and repair of alkylation damage. To assess the role of MGMT in the development of mouse skin tumors induced by initiation‐promotion protocols, methylation of the MGMT promoter was examined in tumor DNA using methylation‐specific PCR. To determine whether MGMT promoter methylation was affected by the tumor induction protocol, tumors were initiated by N‐methyl‐N′‐nitro‐N‐nitrosoguanidine (MNNG) or 7,12‐dimethylbenz[a]anthracene (DMBA) and promoted by 12‐O‐tetradecanoylphorbol‐13‐acetate (TPA) or mezerein. Although the MGMT promoter was not methylated in normal skin, promoter methylation was found in 56 of 136 papillomas (41.2%) and in 19 of 37 squamous cell carcinomas (51.4%). When methylation of the MGMT promoter was compared in the 4 treatment groups, hypermethylation was found more frequently in tumors initiated by DMBA and promoted by mezerein, a protocol associated with a high frequency of malignant conversion. Methylation was found in some tumors as early as 5 weeks after initiation, but the methylation frequency increased with time. MGMT promoter methylation reduced MGMT expression as determined by immunohistochemistry. Although MGMT promoter methylation was not generally correlated with ras mutations, the frequency of MGMT methylation was higher in MNNG‐initiated, mezerein‐promoted papillomas with mutations in Ha‐ras compared to papillomas with Ki‐ras. Methylation of the MGMT promoter, associated with reduced MGMT expression, is found in nearly half of mouse skin tumors, but varies with both the tumor initiator and tumor promoter, and may be a key step in the progression from papillomas to carcinomas. © 2005 Wiley‐Liss, Inc.
Prospective study on the expression of cancer testis genes and antibody responses in 100 consecutive patients with primary breast cancer
Authors: Mischo Axel , Kubuschok Boris , Ertan Kubilay , Preuss Klaus‐Dieter , Romeike Bernd , Regitz Evi , Schormann Claudia , de Bruijn Diederik , Wadle Andreas , Neumann Frank , Schmidt Werner , Renner Christoph , Pfreundschuh Michael 
Published: August 2005

AbstractTo determine the expression of cancer testis (CT) genes and antibody responses in a nonselected population of patients with primary breast cancer, we investigated the composite expression of 11 CT genes by RT‐PCR in fresh biopsies of 100 consecutive cases of primary breast carcinoma and by immunohistology in selected RT‐PCR‐positive cases. Antibody responses against 7 CT antigens were analyzed using recombinant antigen expression on yeast surface. In 98 evaluable cases, SCP‐1 and SSX‐4 were expressed most frequently (both 65%), followed by HOM‐TES‐85/CT‐8 (47%), GAGE (26%), SSX‐1 (20%), NY‐ESO‐1 (13%), MAGE‐3 (11%), SSX‐2 (8%), CT‐10 (7%), MAGE‐4 (4%) and CT‐7 (1%). One CT gene was expressed by 90% of the cases; 79% expressed ≥2, 48% ≥3, 29% ≥4, 12% ≥5, 6% ≥6, 3% ≥7, 2% ≥8 and one case coexpressed 9 antigens. Of 100 serum samples screened for CT antigen‐specific antibodies, antibodies against NY‐ESO‐1 were detected in 4 patients, against SCP‐1 in 6 patients and against SSX‐2 in 1 patient, while no antibodies were detected against MAGE‐3, CT‐7 and CT‐10. Expression of CT genes or antibody responses was not correlated with clinical parameters (menopausal status, tumor size, nodal involvement, grading, histology and estrogen receptor status) or the demonstration of CT gene expression at the protein level, by immunohistology. Our results show that breast carcinomas are among the tumors with the most frequent expression of CT antigens, rendering many patients potential candidates for vaccine trials. © 2005 Wiley‐Liss, Inc.
Src family kinase members have a common response to histone deacetylase inhibitors in human colon cancer cells
Authors: Hirsch Calley L. , Smith‐Windsor Erin L. , Bonham Keith 
Published: August 2005

AbstractHistone deacetylase inhibitors (HDIs) induce cell cycle arrest, differentiation and/or apoptosis in numerous cancer cell types and have shown promise in clinical trials. These agents are particularly novel, given their ability to selectively influence gene expression. Previously, we demonstrated that the HDIs butyrate and trichostatin A (TSA) directly repress c‐Src proto‐oncogene expression in many cancer cell lines. Activation and/or overexpression of c‐Src have been frequently observed in numerous malignancies, especially of the colon. Therefore, our observation was particularly interesting since butyrate is a naturally abundant component of the large intestine and has been suggested to be a cancer‐preventive agent. However, c‐Src is not the only Src family kinase (SFK) member to be implicated in the development of human cancers, including those of the colon. Therefore, the relative expression levels of known SFKs were examined in a panel of human colon cancer cell lines. We found a surprisingly diverse expression pattern but noted that most cell lines expressed relatively high levels of at least 2 SFKs. When the effects of butyrate and TSA were examined in representative cell lines, the expression of all SFKs was repressed in a dose‐ and time‐dependent manner. Further, detailed examination of Lck, Yes and Lyn demonstrated that this repression had a direct effect on transcription and was independent of new protein synthesis. These results mirror our earlier data obtained with c‐Src and suggest that SFKs are a major target of HDIs and likely account in part for the anticancer effects of these promising new drugs. © 2005 Wiley‐Liss, Inc.
Parental lung cancer as predictor of cancer risks in offspring: Clues about multiple routes of harmful influence?
Authors: Hemminki Kari , Chen Bowang 
Published: August 2005

AbstractThe carcinogenic effects of active smoking have been demonstrated for many sites, but the effects of passive smoking and exposures during pregnancy and breastfeeding are less well documented. We examined whether 0–70‐year‐old offspring of parents with lung cancer are at a risk of cancer that cannot be explained by their smoking or familial risk. It was assumed that known target sites for tobacco carcinogenesis would be affected, if any. The nationwide Swedish Family‐Cancer Database with cancers recorded from 1958 to 2002 was used to calculate age‐specific standardized incidence ratios (SIRs). Among offspring of affected mothers, increased risks were observed for upper aerodigestive (SIR 1.45), nasal (2.93), lung (1.71) and bladder (1.52) cancers and for kidney cancer (6.41) in one age group. The risk of bladder cancer was found in younger age groups than that of lung cancer. Cancers at many of these sites, but not the kidney or the bladder, were in excess in offspring of affected fathers. Nasal cancer was even increased when either parent was diagnosed with lung cancer; the highest risk was for nasal adenoid cystic carcinoma (7.73). The data suggest that passive smoking during childhood is associated with an increase risk of nasal cancer. For bladder and kidney cancers, a contribution by tobacco carcinogens is implicated through breastfeeding and in utero exposure. © 2005 Wiley‐Liss, Inc.
Inhibitory effect of linoleic acid on transformation of IEC6 intestinal cells by in vitro azoxymethane treatment
Authors: Sasaki Takamitsu , Yoshida Kazuhiro , Shimura Hideo , Ichiba Masayosi , Sasahira Tomonori , Shimomoto Takasumi , Denda Ayumi , Kuniyasu Hiroki 
Published: August 2005

AbstractThe effect of linoleic acid (LA) on growth and transformation of IEC6 intestinal cells was examined. IEC6 cells expressed mRNAs of 15‐lipooxygenase (LOX15) and peroxisome proliferator–activated receptor (PPAR)γ but not COX‐2. Cell growth was suppressed by LA in a dose‐dependent manner in IEC6 cells. Three‐week treatment with LA provided IEC6 cells a quiescent state. LA‐induced growth inhibition was abrogated by exposure to antisense S‐oligodeoxynucleotides (S‐ODNs) for LOX15 and/or PPARγ. In an in vitro carcinogenesis model, IEC6 cells, which had confirmed CYP2E1 expression and activity, were continuously treated with AOM and/or LA for 40 weeks. DNA injury in AOM‐treated cells was suppressed to the control level by concurrent LA treatment. Colony formation of AOM‐treated cells in soft agar was suppressed by treatment with LA, which was reversed by exposure to antisense S‐ODNs for LOX15 and/or PPARγ. AOM‐treated IEC6 cells formed s.c. tumors in 9 of 12 mice, whereas AOM+LA‐treated cells formed no tumor. IEC6 cells showed no remarkable alteration of protein production by AOM treatment, whereas cells treated with AOM+LA showed decreased epidermal growth factor receptor (EGFR) and phospho‐EGFR and increased BAX. These findings suggest that LA inhibited AOM‐induced transformation of COX‐2‐negative IEC6 cells, which was possibly mediated with PPARγ ligands generated by LOX15 from LA. © 2005 Wiley‐Liss, Inc.
Comparison of implantation and cytotoxicity testing for initially toxic biomaterials
Authors: Rosengren Agneta , Faxius Linda , Tanaka Noriho , Watanabe Mika , Bjursten Lars M. 
Published: August 2005

AbstractTo evaluate the predictive value of cytotoxicity testing, the present study compares the in vivo tissue responses to in vitro cytotoxicity before and after implantation. Material toxicity was caused by addition of the toxic substance Zincdiethyldithiocarbamate (ZDEC) that is used as a standard for in vitro cytotoxicity testing. Polyurethane discs with the addition of 0.5% or 1% ZDEC as well as nontoxic discs were inserted in the abdominal wall of rats for 1 day up to 6 weeks. After explantation the foreign body response was analyzed immunohistochemically. An in vitro reanalysis of the explanted reference materials (RMs) revealed remaining high concentrations of toxic compounds after 1‐week implantation, whereas no toxicity was seen after 6 weeks implantation. This was reflected in the foreign body response where a significantly thicker capsule and more inflammatory cells were seen at 1 week for the toxic implants. Over time, with decreasing toxicity, these differences disappeared. Test samples that only were subjected to in vitro extraction with water did not elute toxic compounds to the same extent as the in vivo conditions. It is concluded that many clinically useful implant materials may be unnecessarily rejected due to the results of in vitro tests. © 2005 Wiley Periodicals, Inc. J Biomed Mater Res, 2005
Permeable guidance channels containing microfilament scaffolds enhance axon growth and maturation
Authors: Cai Jie , Peng Xuejun , Nelson Kevin D. , Eberhart Robert , Smith George M. 
Published: August 2005

AbstractSuccessful peripheral nerve regeneration is still limited in artificial conduits, especially for long lesion gaps. In this study, porous poly(L‐lactide‐co‐DL‐lactide, 75:25) (PLA) conduits were manufactured with 16 poly(L‐lactide) (PLLA) microfilaments aligned inside the lumen. Fourteen and 18 mm lesion gaps were created in a rat sciatic nerve lesion model. To evaluate the combined effect of permeable PLA conduits and microfilament bundles on axon growth, four types of implants were tested for each lesion gap: PLA conduits with 16 filaments; PLA conduits without filaments; silicone conduits with 16 filaments; and silicone conduits without filaments. Ten weeks following implantation, regeneration within the distal nerve was compared between corresponding groups. Antibodies against the markers S100, calcitonin gene related peptide (CGRP), RMDO95, and P0 were used to identify Schwann cells, unmyelinated axons, myelinated axons, and myelin, respectively. Results demonstrated that the filament scaffold enhanced tissue cable formation and Schwann cell migration in all groups. The filament scaffold enhanced axonal regeneration toward the distal stump, especially across long lesion gaps, but significance was only achieved with PLA conduits. When compared to corresponding silicone conduits, permeable PLA conduits enhanced myelinated axon regeneration across both lesion gaps and achieved significance only in combination with filament scaffolds. Myelin staining indicated PLA conduits supported axon myelination with better myelin quantity and quality when compared to silicone conduits. © 2005 Wiley Periodicals, Inc. J Biomed Mater Res, 2005