bluuebunny/crossref_metadata_2025_split huggingface dataset:
A time‐accurate pseudo‐compressibility approach based on an unstructured hybrid finite volume technique applied to unsteady turbulent premixed flame propagation
Authors: Dourado Wladimyr M. C. , Bruel Pascal , Azevedo João L. F. 
Published: March 2004

AbstractA preconditioning approach based on the artificial compressibility formulation is extended to solve the governing equations for unsteady turbulent reactive flows with heat release, at low Mach numbers, on an unstructured hybrid grid context. Premixed reactants are considered and a flamelet approach for combustion modelling is adopted using a continuous quenched mean reaction rate. An overlapped cell‐vertex finite volume method is adopted as a discretisation scheme. Artificial dissipation terms for hybrid grids are explicitly added to ensure a stable, discretised set of equations. A second‐order, explicit, hybrid Runge–Kutta scheme is applied for the time marching in pseudo‐time. A time derivative of the dependent variable is added to recover the time accuracy of the preconditioned set of equations. This derivative is discretised by an implicit, second‐order scheme. The resulting scheme is applied to the calculation of an infinite planar (one‐dimensional) turbulent premixed flame propagating freely in reactants whose turbulence is supposed to be frozen, homogeneous and isotropic. The accuracy of the results obtained with the proposed method proves to be excellent when compared to the data available in the literature. Copyright © 2004 John Wiley & Sons, Ltd.
Three‐dimensional incompressible flow calculations using the characteristic based split (CBS) scheme
Authors: Nithiarasu P. , Mathur J. S. , Weatherill N. P. , Morgan K. 
Published: March 2004

AbstractIn this paper, the characteristic based split scheme is employed for the solution of three‐dimensional incompressible viscous flow problems on unstructured meshes. Many algorithm related issues are discussed. Fully explicit and semiimplicit forms of the scheme are explained and employed in the calculation of both isothermal and nonisothermal incompressible flows simulation. The extension of the scheme to porous medium flows is also demonstrated with relevant examples. Copyright © 2004 John Wiley & Sons, Ltd.
Simulation of interface and free surface flows in a viscous fluid using adapting quadtree grids
Authors: Greaves Deborah 
Published: March 2004

AbstractA new adaptive quadtree method for simulating laminar viscous fluid problems with free surfaces and interfaces is presented in this paper. The Navier–Stokes equations are solved with a SIMPLE‐type scheme coupled with the Compressive Interface Capturing Scheme for Arbitrary Meshes (CICSAM) (Numerical prediction of two fluid systems with sharp interfaces, Ph.D. Thesis, Imperial College of Science, Technology and Medicine, London, 1997) volume of fluid (VoF) method and PLIC reconstruction of the volume fraction field during refinement and derefinement processes. The method is demonstrated for interface advection cases in translating and shearing flow fields and found to provide high interface resolution at low computational cost. The new method is also applied to simulation of the collapse of a water column and the results are in excellent agreement with other published data. The quadtree grids adapt to follow the movement of the free surface, whilst maintaining a band of the smallest cells surrounding the surface. The calculation is made on uniform and adapting quadtree grids and the accuracy of the quadtree calculation is shown to be the same as that made on the equivalent uniform grid. Copyright © 2004 John Wiley & Sons, Ltd.
High resolution Godunov‐type schemes with small stencils
Authors: Guinot Vincent 
Published: March 2004

AbstractHigher‐order Godunov‐type schemes have to cope with the following two problems: (i) the increase in the size of the stencil that make the scheme computationally expensive, and (ii) the monotony‐preserving treatments (limiters) that must be implemented to avoid oscillations, leading to strong damping of the solution, in particular linear waves (e.g. acoustic waves). When too compressive, limiting procedures may also trigger the instability of oscillatory numerical solutions (e.g. in advection–dispersion phenomena) via the artificial amplification of the shorter modes. The present paper proposes a new approach to carry out the reconstruction. In this approach, the values of the flow variable at the edges of the computational cells are obtained directly from the reconstruction within these cells. This method is applied to the MUSCL and DPM schemes for the solution of the linear advection equation. The modified DPM scheme can capture contact discontinuities within one computational cell, even after millions of time steps at Courant numbers ranging from 1 to values as low as 10‐4. Linear waves are subject to negligible damping. Application of the method to the DPM for one‐dimensional advection–dispersion problems shows that the numerical instability of oscillatory solutions caused by the over compressive, original DPM limiter is eliminated. One‐ and two‐dimensional shallow water simulations show an improvement over classical methods, in particular for two‐dimensional problems with strongly distorted meshes. The quality of the computational solution in the two‐dimensional case remains acceptable even for mesh aspect ratios Δx/Δy as large as 10. The method can be extend to the discretization of higher‐order PDEs, allowing third‐order space derivatives to be discretized using only two cells in space. Copyright © 2004 John Wiley & Sons, Ltd.
Adaptive strategy of the supersonic turbulent flow over a backward‐facing step
Authors: Yang Shih‐Ying 
Published: March 2004

AbstractAn adaptive strategy incorporating mesh remeshing and refining is developed to study the supersonic turbulent flow over a backward‐facing step on a mixed quadrilateral–triangular mesh. In the Cartesian co‐ordinate system, the unsteady Favre‐averaged Navier–Stokes equations with a low‐Reynolds‐number k–εturbulence model are solved using a locally implicit scheme with an anisotropic dissipation model. In the present adaptive strategy, two error indicators for both mesh remeshing and refining, respectively, are presented. The remeshing error indicator incorporates unified magnitude of substantial derivative of pressure and that of vorticity magnitude, whereas the refining error indicator incorporates unified magnitude of substantial derivative of pressure and that of weighted vorticity magnitude. To assess the present approach, the transonic turbulent flow around an NACA 0012 airfoil is performed. Based on the comparison with the experimental data, the accuracy of the present approach is confirmed. According to the high‐resolutional result on the adaptive mesh, the structure of backstep corner vortex, expansion wave and oblique shock wave is distinctly captured. Copyright © 2004 John Wiley & Sons, Ltd.
Molecular pathogenesis of uterine smooth muscle tumors from transcriptional profiling
Authors: Quade Bradley J. , Wang Tao‐Yeuan , Sornberger Kris , Cin Paola Dal , Mutter George L. , Morton Cynthia C. 
Published: March 2004

AbstractUterine smooth muscle tumors range from the very common benign leiomyoma to the uncommon, but frequently lethal, leiomyosarcoma. Morphological and clinical differences between these tumors are presumed to result from differences in gene expression. To test this hypothesis, RNAs from four normal uterine myometria, seven uterine leiomyomas, and nine uterine leiomyosarcomas were profiled using microarrays of oligonucleotides representing about 7,000 unique probe sets. RNAs whose levels distinguished any of the three sample types were selected by analysis of variance (ANOVA). The 153 (2.2% of the total) probe sets representing 146 unique genes with the highest test statistic selected for further analysis met minimum ratio and range thresholds between groups. Cluster analysis distinguished benign and malignant samples at the first node, and myometrium and leiomyoma were resolved in a secondary node. Downregulation of specific genes in uterine leiomyosarcoma was the most common pattern of differential gene expression selected by the three‐way ANOVA. Four extrauterine leiomyosarcomas had profiles most similar to that of the uterine leiomyosarcomas. Functional analysis of the 146 genes did not reveal any strong biological theme. These genes were distributed throughout the genome, but there was slight overrepresentation of genes on 1p and 2q. These genes define a tumor signature for uterine smooth muscle neoplasia, and they suggest that the molecular pathways in leiomyoma and leiomyosarcoma are distinct. © 2004 Wiley‐Liss, Inc.
Gene expression profiling and identification of novel prognostic marker genes in neuroblastoma
Authors: Takita Junko , Ishii Masami , Tsutsumi Shuichi , Tanaka Yukichi , Kato Keisuke , Toyoda Yasunori , Hanada Ryoji , Yamamoto Keiko , Hayashi Yasuhide , Aburatani Hiroyuki 
Published: March 2004

AbstractTo investigate the various genetic characteristics of and differences between early‐ and advanced‐stage neuroblastoma (NB) and to identify candidate genes involved in NB progression, we performed DNA microarray analysis on 20 primary tumors. Two‐way clustering analysis based on the expression pattern of approximately 500 of 1,700 genes revealed genetic subgroups in these NB tumors. Although 9 of the 13 early‐stage tumors (69%) and 4 of the 6 advanced‐stage tumors (67%) were classified as being in the same cluster, the remaining tumors showed different expression profiles. This indicates that both the early‐ and advanced‐stage tumors were heterogeneous. Based on the microarray data, we identified the BIRC, CDKN2D, and SMARCD3 genes as those that are predominantly expressed in either the early or the advanced stage of NB. These genes have been reported to be associated with apoptosis, cell cycles, and the transcriptional activator, respectively. To better assess the prognostic value of the expression of these genes in NB, real‐time polymerase chain reaction was carried out on 50 primary tumors. The expression of both the BIRC3 and CDKN2D genes was significantly higher in the early‐stage group than in the advanced‐stage group (P = 0.002 and 0.003, respectively), whereas the expression of the SMARCD3 gene was significantly reduced in the early‐stage group (P = 0.02). Therefore, the BIRC, CDKN2D, and SMARCD3 genes are possible candidates for being novel prognostic markers for NB. © 2004 Wiley‐Liss, Inc.
Type I MOZ/CBP (MYST3/CREBBP) is the most common chimeric transcript in acute myeloid leukemia with t(8;16)(p11;p13) translocation
Authors: Rozman María , Camós Mireia , Colomer Dolors , Villamor Neus , Esteve Jordi , Costa Dolors , Carrió Ana , Aymerich Marta , Aguilar Josep Lluis , Domingo Alícia , Solé Francesc , Gomis Federico , Florensa Lourdes , Montserrat Emili , Campo Elias 
Published: March 2004

AbstractThe t(8;16)(p11;p13) fuses the MOZ (MYST3) gene at 8p11 with CBP (CREBBP) at 16p13 and is associated with an infrequent but well‐defined type of acute myeloid leukemia (AML) that has unique morphocytochemical findings (monocytoid blast morphology with erythrophagocytosis and simultaneously positive for myeloperoxidase and nonspecific esterases). RT‐PCR amplification of MOZ/CBP (MYST3/CREBBP) chimera has proved difficult, with four different transcripts found in four reported cases. We studied 7 AML‐t(8;16) patients, 5 with cytogenetically demonstrated t(8;16) and 2 with similar morphocytochemical and immunophenotypical characteristics. Clinically, 3 cases presented as therapy‐related leukemia. Extramedullar involvement was observed at presentation in 2 patients and coagulopathy in 4. The clinicobiological findings confirmed the distinctiveness of this entity. Of note is the erythrophagocytosis in 5 of 7 cases and the immunological negativity for CD34 and CD117 and positivity for CD56. Using a new RT‐PCR strategy, we were able to amplify a specific band of 212 bp in six cases in which sequence analysis confirmed the presence of the previously described MOZ/CBP fusion transcript type I. This is the largest molecularly studied AML‐t(8;16) series, which demonstrates that MOZ/CBP breakpoints are usually clustered in intron 16 of MOZ and intron 2 of CBP. The newly designed single‐round PCR provides a simple tool for the molecular confirmation of MOZ/CBP rearrangement. © 2004 Wiley‐Liss, Inc.
Novel germ‐line deletion of SNF5/INI1/SMARCB1 gene in neonate presenting with congenital malignant rhabdoid tumor of kidney and brain primitive neuroectodermal tumor
Authors: Kusafuka Takeshi , Miao Jiangyong , Yoneda Akihiro , Kuroda Seika , Fukuzawa Masahiro 
Published: March 2004

AbstractWe describe a neonate who had a rare tumor combination of a malignant rhabdoid tumor of the kidney (MRTK) and a brain primitive neuroectodermal tumor (PNET). Genetic alterations of the SNF5/INI1/SMARCB1 gene were investigated by PCR–single‐strand conformation polymorphism (SSCP), loss of heterozygosity (LOH), sequence, and karyotyping analyses, and the gene expression level was determined by real‐time quantitative RT‐PCR analysis. PCR band signals of each exon of the hSNF5/INI1 were weak or nearly undetectable in both MRTK and PNET, whereas those of the corresponding normal kidney were clearly detected. Aberrantly migrating SSCP bands led to identification of a nucleotide change in intron 8. Although this was regarded as a polymorphism, only the changed nucleotide was observed in the normal kidney of the patient. Allelic states in the parents were heterozygous for the polymorphism in the father and homozygous for the normal sequence in the mother. Thus, it was evident that a substantial genetic part of the maternal normal allele including SNF5/INI1 was deleted as a de novo germ‐line mutation. In both tumors, LOH at microsatellite loci on the long arm of chromosome 22 was evident, and expression of SNF5/INI1 mRNA was drastically decreased compared to that in control tissues (0.7–3.9 vs. 123.6–153.5). Deletion of a substantial genetic part demonstrated in our patient is the novel appearance of a germ‐line deletion of the SNF5/INI1 gene. Additional large somatic deletions resulted in total inactivation of the gene in both tumors. Our patient provides evidence for an important role of SNF5/INI1germ‐line mutation in predisposing patients to multiple rhabdoid tumors. © 2004 Wiley‐Liss, Inc.
Correlation between histone acetylation and expression of the MYO18B gene in human lung cancer cells
Authors: Tani Masachika , Ito Jun , Nishioka Michiho , Kohno Takashi , Tachibana Ken , Shiraishi Masahiko , Takenoshita Seiichi , Yokota Jun 
Published: March 2004

AbstractRecently, we isolated a candidate tumor‐suppressor gene, MYO18B, which was inactivated in approximately 50% of human lung cancers by deletion, mutation, and promoter methylation. However, more frequent reduction or loss of MYO18B expression and restoration of MYO18B expression by trichostatin A (TSA) treatment suggested the contribution of other mechanisms, especially histone deacetylation, for epigenetic inactivation of the MYO18B gene. In this study, we examined histone modification of the promoter region of the MYO18B gene in 8 human lung cancer cell lines by a chromatin immunoprecipitation assay. In 6 of 7 cell lines with reduced or silenced MYO18B expression, the levels of histones H3 and H4 acetylation surrounding the MYO18B promoter region were lower than those in a cell line with MYO18B expression. By treatment with TSA, the levels of histone H3 and H4 acetylation were increased in all 6 cell lines whose MYO18B expression was restored by TSA, whereas neither H3 nor H4 acetylation was increased in cells whose MYO18B expression was not restored by TSA. Significant correlations were observed between the levels of histone H3/H4 acetylation and MYO18B expression. These results suggest that acetylation of both histones H3 and H4 contributes to regulation of MYO18B expression in lung cancer cells and that histone deacetylation surrounding the promoter region plays an important role in MYO18B silencing and is involved in lung carcinogenesis. © 2004 Wiley‐Liss, Inc.
Oligodendrocytes are susceptible to apoptotic cell death induced by prion protein‐derived peptides
Authors: Sponne Isabelle , Fifre Alexandre , Koziel Violette , Kriem Badreddine , Oster Thierry , Olivier Jean‐Luc , Pillot Thierry 
Published: March 2004

AbstractNeurodegenerative prion diseases, characterized by a progressive dementia, are associated with the accumulation of abnormal forms of the prion (PrPc) protein, potentially due to an aberrant regulation of PrPc biogenesis and/or topology. One of these forms, termed ctmPrP, displays a transmembrane conformation and might trigger neuronal cell death in Gerstmann‐Straüssler‐Scheinker (GSS) syndrome and other prion‐associated diseases in humans. Although the primary target cells involved in the progression of prion diseases remain unidentified, it was recently suggested that modifications of the oligodendroglial cells occur early in prion diseases. In the present study, we demonstrate that a putative transmembrane domain of the human PrPc, i.e., amino acids 118–135, induces oligodendrocyte (OLG) death in vitro in a time‐ and dose‐dependent manner. The process leading to OLG death and induced by the PrP[118–135] peptide was characterized by DNA fragmentation, cytoskeletal disruption, and caspase activation. Protection against the PrP[118–135] peptide‐induced OLG apoptosis by several antioxidant molecules, such as probucol, propylgallate, and promethazine, suggests that oxidative injuries contribute to the PrP[118–135] cytotoxicity to OLGs. These results suggest a potential pathophysiological role of the ctmPrP‐ and/or PrP fragment‐mediated OLG cytotoxicity in spongiform encephalopathies. © 2004 Wiley‐Liss, Inc.
Odontogenic ghost cell carcinoma
Authors: Goldenberg David , Sciubba James , Tufano Ralph P. 
Published: March 2004

AbstractBackground.Odontogenic ghost cell carcinoma (OGCC), a malignant counterpart of the calcifying odontogenic cyst (COC), is exceedingly rare. Previous descriptions of this tumor were based on identification of malignant histologic characteristics such as infiltration, cellular pleomorphism, numerous mitoses, and necrosis concurrent with classical benign COC or its solid benign variant, the odontogenic ghost cell tumor.Methods.We present a case of a young Asian man who underwent multiple local excisions of a recurring maxillary COC. After one such excision, a rapid onset of painful swelling ensued, and the patient was referred to our institution for definitive surgery.Results.The patient underwent a right subtotal maxillectomy. Intraoperatively, a 5‐cm tumor was found to be extending into the right maxillary sinus and nasal cavity. The excised tumor was diagnosed as an OGCC. The tumor was excised with clear margins, and no adjunctive radiotherapy was given. The patient was free of residual or recurrent disease 18 months after surgery.Conclusions.On the basis of this case and prior cases found in the literature, OGCCs show a spectrum of growth from slow growing locally invasive tumors to highly aggressive, rapidly growing, infiltrative tumors. Wide local excision with histologically clean margins is the recommended mode of treatment. We recommend close long‐term surveillance of recurrent or long‐standing benign COCs and OGCC. © 2003 Wiley Periodicals, Inc. Head Neck 26: 378–381, 2004
MUC4 and ERBB2 expression in major and minor salivary gland mucoepidermoid carcinoma
Authors: Weed Donald T. , Gomez‐Fernandez Carmen , Pacheco Jeffrey , Ruiz Jose , Hamilton‐Nelson Kara , Arnold David J. , Civantos Francisco J. , Zhang Jin , Yasin Mohammed , Goodwin W. Jarrard , Carraway Kermit L. 
Published: March 2004

AbstractBackground.Peptide sequence homology between the gene product of human MUC4 and rat sialomucin complex (SMC) has recently been reported. Each contains a mucin subunit with antiadhesive activity linked to the plasma membrane by means of a transmembrane subunit with two epidermal growth factor (EGF)–like domains that act as ligand for ErbB2. This study investigates MUC4 and ErbB2 receptor expression in major and minor salivary gland mucoepidermoid carcinoma and correlates patterns of expression with clinical outcomes.Methods.MUC4 antigens and ErbB2 receptor expression are localized by immunohistochemical studies that use archival formalin‐fixed and paraffin‐embedded tissue. Clinical outcomes are determined by retrospective chart review of all patients (n = 28) with available archived pathologic specimens at the University of Miami–affiliated hospitals treated between 1994 and 2000.Results.Median survival time was 24 months (range, 2–60 months) among the nine patients who died, whereas median follow‐up time in the remaining 19 patients is 33.4 months (range, 4.7–73 months). A trend toward a reduction in MUC4 antigen expression in high‐grade tumors (55% expression) compared with low‐grade (91% expression) and intermediate‐grade (100% expression) tumors is identified (chi square, p = .0975). Patients with tumors expressing MUC4 antigens are at reduced risk of death (hazard ratio [HR], 0.20; p = .0531). Adjustment for pathologic grade, T stage, and age results in a much higher risk of death for patients whose tumors do not express MUC4 antigens, although this does not meet statistical significance (HR, 26.6; p = .1). Analysis of recurrence adjusting for T stage reveals that patients whose tumors do not express MUC4 antigens are at increased risk of recurrence compared with patients whose tumor expresses MUC4 antigens (HR, 6.37; p = .03). ErbB2 receptor staining is noted in seven of 28 patients, with five of these seven showing 2+ and 3+ membrane‐staining patterns. Adjustment for pathologic grade and age suggests that patients whose tumors express high levels of ErbB2 (2+, 3+) are at increased risk of death compared with patients with low or no expression of ErbB2 (HR, 2.29; p = .32). MUC4 antigen positivity is seen in two of the five cases with 2+ and 3+ staining for ErbB2.Conclusions. These findings suggest MUC4 antigen positivity is associated with reduced risk of death and reduced risk of recurrence and may identify a subset of patients with more favorable prognosis. Although limited by small sample size, analysis reveals ErbB2 overexpression is not consistently associated with MUC4 antigen positivity and might be associated with increased risk of death © 2004 Wiley Periodicals, Inc. Head Neck 26: 353–364, 2004