bluuebunny/crossref_metadata_2025_split huggingface dataset:
Application of hierarchical matrices to the simulation of wave propagation in fluids
Authors: Lehmann L. , Rüberg T. 
Published: December 2005

AbstractThis paper deals with a coupled finite element/scaled boundary finite element method (FE/SBFEM) and its application to wave propagation problems in fluids in the time domain. This method is already well established and has proven to be an efficient technique for treating radiation problems. In its application to time domain problems, convolution integrals arise. For each time step ti, i matrix–vector multiplications have to be performed, where the involved influence matrix—due to the non‐locality in space—is fully populated. This numerical evaluation becomes a significant, time‐consuming task for long time calculations, thus decreasing the attractiveness of the method. In this paper, the application of hierarchical matrices (ℋ︁‐matrices) is to overcome this drawback. ℋ︁‐Matrices represent an octree‐based clustered low‐rank approximation of the original, fully populated matrix and allow a considerable increase in efficiency for matrix–vector products encountered, e.g. in convolution integrals. The application of ℋ︁‐matrices to this method results in an increase in efficiency without noticeable loss in accuracy. Since convolution integrals arise in various large‐scale engineering computations the application of ℋ︁‐matrix techniques might turn out to be a highly promising way to pursue. Copyright © 2005 John Wiley & Sons, Ltd.
An effective spectral collocation method for the direct solution of high‐order ODEs
Authors: Mai‐Duy N. 
Published: December 2005

AbstractThis paper reports a new Chebyshev spectral collocation method for directly solving high‐order ordinary differential equations (ODEs). The construction of the Chebyshev approximations is based on integration rather than conventional differentiation. This use of integration allows the multiple boundary conditions to be incorporated more efficiently. Numerical results show that the proposed formulation significantly improves the conditioning of the system and yields more accurate results and faster convergence rates than conventional formulations. Copyright © 2005 John Wiley & Sons, Ltd.
User tools and languages for graph‐based Grid workflows
Authors: Hoheisel Andreas 
Published: December 2005

AbstractThis article presents a graph‐based Grid workflow language that is based on the formalism of Petri nets and the corresponding workflow enactment machine, developed by the author within the Fraunhofer Resource Grid in Germany. The workflow enactment machine supports dynamic refinement of workflows during runtime and automatic mapping of abstract jobs onto concrete Grid resources, which are accessed by means of the Globus Toolkit. Copyright © 2005 John Wiley & Sons, Ltd.
Grid‐Flow: a Grid‐enabled scientific workflow system with a Petri‐net‐based interface
Authors: Guan Zhijie , Hernandez Francisco , Bangalore Purushotham , Gray Jeff , Skjellum Anthony , Velusamy Vijay , Liu Yin 
Published: December 2005

AbstractAdvances in computer technologies have enabled scientists to explore research issues in their respective domains at scales greater and finer than ever before. The availability of efficient data collection and analysis tools presents researchers with vast opportunities to process heterogeneous data within a distributed environment. To support the opportunities enabled by massive computation, a suitable scientific workflow system is needed to help the users to manage data and programs, and to design reusable procedures of scientific experimental tasks. In this paper, the design and prototype implementation of a scientific workflow infrastructure, called Grid‐Flow, is presented. Grid‐Flow assists researchers in specifying scientific experiments using a Petri‐net‐based interface. The Grid‐Flow infrastructure is designed as a Service Oriented Architecture with multi‐layer component models. The contributions of Grid‐Flow are as follows: (1) a new, lightweight, programmable Grid workflow language, Grid‐Flow Description Language, is provided to describe the workflow process in a Grid environment; (2) a Petri‐net‐based user interface, based on the Generic Modeling Environment, is demonstrated to help the user design the workflow process with a Petri‐net model; and (3) a program integration component of the Grid‐Flow system is presented to integrate all possible programs into the system. Copyright © 2005 John Wiley & Sons, Ltd.
GAUGE: Grid Automation and Generative Environment
Authors: Hernández Francisco , Bangalore Purushotham , Gray Jeff , Guan Zhijie , Reilly Kevin 
Published: December 2005

AbstractThe Grid has proven to be a successful paradigm for distributed computing. However, constructing applications that exploit all the benefits that the Grid offers is still not optimal for both inexperienced and experienced users. Recent approaches to solving this problem employ a high‐level abstract layer to ease the construction of applications for different Grid environments. These approaches help facilitate construction of Grid applications, but they are still tied to specific programming languages or platforms. A new approach is presented in this paper that uses concepts of domain‐specific modeling (DSM) to build a high‐level abstract layer. With this DSM‐based abstract layer, the users are able to create Grid applications without knowledge of specific programming languages or being bound to specific Grid platforms. An additional benefit of DSM provides the capability to generate software artifacts for various Grid environments. This paper presents the Grid Automation and Generative Environment (GAUGE). The goal of GAUGE is to automate the generation of Grid applications to allow inexperienced users to exploit the Grid fully. At the same time, GAUGE provides an open framework in which experienced users can build upon and extend to tailor their applications to particular Grid environments or specific platforms. GAUGE employs domain‐specific modeling techniques to accomplish this challenging task. Copyright © 2005 John Wiley & Sons, Ltd.
A Grid workflow infrastructure
Authors: Cybok Dieter 
Published: December 2005

AbstractIn this paper we propose a Grid workflow infrastructure, which serves as the base for specifying and executing collaborative interactive workflows within computational Grids. The infrastructure is based on the Open Grid Services Architecture (OGSA) and leverages the concepts of the Business Process Execution Language for Web Services (BPEL4WS). Using OGSA enables the exploitation of advanced Grid features such as factories, lifecycle management and notifications. Leveraging BPEL4WS to a Grid enabled workflow language has the advantage that basic workflow functionalities, which are similar for Grid and Web services, do not have to be developed again. The result is a state‐of‐the‐art Grid workflow infrastructure that was developed within a relatively short period. The main building blocks of the infrastructure are the specification of the Grid Workflow Execution Language (GWEL) notation and the implementation of a Grid workflow execution engine, using Globus Toolkit 3 (GT3) technology, for processing e‐Science specific workflows specified in GWEL documents. The workflow engine itself is a high‐level Grid service, hence automatically Grid aware, which can be used within any GT3 environment. Copyright © 2005 John Wiley & Sons, Ltd.
Workflow applications in GridLab and PROGRESS projects
Authors: Kosiedowski Michal , Kurowski Krzysztof , Mazurek Cezary , Nabrzyski Jarek , Pukacki Juliusz 
Published: December 2005

AbstractIn this paper we present our motivations and ideas for workflow management based on our experiences gained in two projects: GridLab and PROGRESS. In these projects we have been dealing with real use cases and end users' requirements for workflow management. Therefore, we were able to define and implement functional workflow extensions to the Grid(Lab) Resource Management System (GRMS). GRMS is a resource management system with a workflow engine that executes and manages jobs on remote Grid resources. One can submit to GRMS workflow experiments based on an XML workflow schema, defining flexible mechanisms for dynamic workflow control, including various types of precedence constraints, different locations of the final data products and executables, etc. All of these features allow end users to speed up remote workflow calculations and improve data management mechanisms. Copyright © 2005 John Wiley & Sons, Ltd.
Concave 1,10‐Phenanthrolines as Tailored Ligands for Copper(I)‐Catalyzed Diastereoselective Cyclopropanations
Authors: Lüning Ulrich , Fahrenkrug Frank 
Published: December 2005

AbstractAlkenyloxy‐substituted aryl bridgeheads have been connected to 2,9‐dichloro‐1,10‐phenanthroline (11) either by Suzuki coupling or by nucleophilic aromatic substitution. The resulting di‐ or tetraalkenes 12 or 17 have been cyclized by ring‐closing metathesis to give concave 1,10‐phenanthrolines 14 and 19, differing from other concave 1,10‐phenanthrolines 1 in their geometries. The influence of the shapes of these ligands and those of the related concave 1,10‐phenanthrolines 1a–f and 2 on the stereochemistry of the copper(I)‐catalyzed cyclopropanation of indene (3) and styrene (4) has been investigated, identifying factors that favour the formation of thermodynamically less stable syn‐cyclopropanes 6 and 7. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006)
A functional polymorphism in the matrix metalloproteinase‐1 gene promoter is associated with susceptibility and aggressiveness of head and neck cancer
Authors: O‐charoenrat Pornchai , Leksrisakul Piyavadee , Sangruchi Supatra 
Published: December 2005

AbstractMatrix metalloproteinases (MMPs) play an important role in several steps of cancer development. A single guanine insertion polymorphism (2G) in the MMP1 promoter sequence at −1,607 creates an Ets binding site and thus results in enhancing transcriptional activity. This study aimed to evaluate the contribution of this 2G polymorphism on susceptibility and aggressiveness of HNSCC. A panel of HNSCC cell lines and peritumoral fibroblasts were examined for the MMP1 genotypes and expression levels. Genomic DNA was extracted from peripheral blood of 300 patients with newly diagnosed HNSCC and from 300 age‐ and gender‐matched cancer‐free controls. Genotyping was carried out using a PCR‐RFLP assay. The levels of MMP1 mRNA expression were evaluated by the quantitative RT‐PCR and a correlation with different genotype was determined. Odds ratio (OR) for cancer risk were calculated using multivariate logistic regression. In addition, a correlation between the 2G/2G genotype and clinicopathological parameters was examined. Eleven out of 18 HNSCC cell lines showed the 2G/2G genotype (61%) and only 1 cell line had the 1G/1G genotype (5.6%). Cell lines with the 2G/2G genotype expressed significantly higher mean MMP1 mRNA level than those with other genotypes. In clinical model, subjects carrying the homozygous 2G/2G genotype had a higher risk of head and neck cancer compared with subjects with other genotypes (adjusted OR: 2.28; 95% CI: 1.58–3.27), controlling for major confounders. A correlation between promoter polymorphisms and the levels of MMP1 expression in cancer tissues was found, and this 2G/2G genotype was correlated with the adverse clinicopathological parameters. Finally, the highest level of MMP1 enhancement was demonstrated in the coculture of tumor cells and peritumoral fibroblasts of 2G homozygotes. These findings suggest that the presence of 2G polymorphism at the MMP1 promoter is associated with the development and progression of HNSCC. © 2005 Wiley‐Liss, Inc.
Enhancing effects of simultaneous treatment with sodium nitrite on 2‐amino‐3‐methylimidazo[4,5‐f]quinoline‐induced rat liver, colon and Zymbal's gland carcinogenesis after initiation with diethylnitrosamine and 1,2‐dimethylhydrazine
Authors: Kitamura Yasuki , Umemura Takashi , Okazaki Kazushi , Kanki Keita , Imazawa Takayoshi , Masegi Toshiaki , Nishikawa Akiyoshi , Hirose Masao 
Published: December 2005

AbstractCombined effects of sodium nitrite (NaNO2) and 2‐amino‐3‐methylimidazo[4,5‐f]quinoline (IQ) on liver, colon and Zymbal's gland carcinogenesis were assessed using a rat two‐stage carcinogenesis model, with a focus on involvement of oxidative stress. Male 6‐week‐old F344 rats were given a single intraperitoneal injection of 200 mg/kg of diethylnitrosamine and 4 subcutaneous injections of 40 mg/kg of 1,2‐dimethylhydrazine for initiation. Then, they were administered 0 or 300 ppm IQ in the diet or 0, 0.1 or 0.2% NaNO2 in their drinking water for 27 weeks. The treatment with NaNO2 + IQ significantly enhanced colon and Zymbal's gland carcinogenesis and tended to enhance hepatocarcinogenesis. The incidence of lung tumors in the IQ‐treated groups was significantly increased as compared with the initiation alone group. In a second experiment, male rats were given IQ or NaNO2 under the same conditions as before for 1 week, and at sacrifice, their liver and colon tissue or mucosa were collected for analysis of 8‐hydroxydeoxyguanosine (8‐OHdG), thiobarbituric acid reactive substances (TBARS), acrolein‐modified protein and the bromodeoxyuridine‐labeling index (BrdU‐LI) (in the colon). In the colon, 8‐OHdG, acrolein‐modified protein levels and BrdU‐LI were significantly increased by the combined treatment. These results indicate that the treatment with NaNO2 enhances IQ‐induced colon and Zymbal's gland carcinogenesis in rats and that oxidative DNA damage and lipid peroxidation may partly be involved, especially in the colon. In addition, this experiment showed that IQ can act as a potent lung carcinogen in rats. © 2005 Wiley‐Liss, Inc.
Celecoxib induces anoikis in human colon carcinoma cells associated with the deregulation of focal adhesions and nuclear translocation of p130Cas
Authors: Casanova Isolda , Parreño Matilde , Farré Lourdes , Guerrero Sílvia , Céspedes M. Virtudes , Pavon Miguel Angel , Sancho Francesc J. , Marcuello Eugenio , Trias Manuel , Mangues Ramon 
Published: December 2005

AbstractCelecoxib, a selective cyclooxygenase‐2 (COX‐2) inhibitor, is effective as chemopreventive against colon cancer and it is the only nonsteoroidal antiinflammatory drug approved by the FDA for adjuvant therapy in patients with familial adenomatous polyposis. It is also being evaluated, within Phase II and III clinical trials, in combination with standard chemotherapy to treat sporadic colorectal cancer. Nevertheless, its antitumor mechanism of action is still not fully understood. In this study, we have evaluated thein vitrogrowth inhibitory effect of celecoxib in colon carcinoma cells and analyzed its mechanism of action. We report that the deregulation of the focal adhesion assembly protein Crk‐associated substrate 130 kDa (p130Cas) by celecoxib plays a relevant role in the cytotoxic effect of this drug. Thus, celecoxib induces the proteolysis of p130Cas and the nuclear translocation of the 31 kDa generated fragment leading to apoptosis. Furthermore, overexpression of wild‐type p130Cas reverts, in part, the growth inhibitory effect of celecoxib. In contrast, FAK and AKT do not appear to be involved in this activity. Our data suggest, for the first time, that the antitumor mechanism of action of celecoxib includes the induction of anoikis, an effect that is not related to COX‐2 inhibition. Besides providing new insights into the antitumor effect of celecoxib, this novel mechanism of action holds potential relevance in drug development. Indeed, our results open the possibility to develop new celecoxib derivatives that induce anoikis without COX‐2 inhibition so as to avoid the cardiovascular toxicity recently described for the COX‐2 inhibitors. © 2005 Wiley‐Liss, Inc.
Enhancement of human papilloma virus type 16 E7 specific T cell responses by local invasive procedures in patients with (pre)malignant cervical neoplasia
Authors: Visser Jeroen , van Baarle Debbie , Hoogeboom Baukje Nynke , Reesink Nathalie , Klip Harry , Schuuring Ed , Nijhuis Esther , Pawlita Michael , Bungener Laura , de Vries‐Idema Jacqueline , Nijman Hans , Miedema Frank , Daemen Toos , van der Zee Ate 
Published: December 2005

AbstractIt has been suggested that local invasive procedures may alter the natural course of (pre)malignant cervical disease. This could be due to partial excision of the lesions, or via induction of cellular immunity against human papillomavirus (HPV) by the local invasive procedures. We studied the influence of local invasive procedures on HPV‐16 E7 specific immune responses in patients with different grades of cervical intra‐epithelial neoplasia (CIN) and different stages of cervical cancer. Blood was obtained at intake and after invasive procedures from patients with CIN or cervical cancer. Antigen specific T‐cell responses were measured by IFN‐γ ELISPOT analysis, after stimulation with recombinant HPV‐16 E7 protein. As expected, HPV‐16 E7 specific IFN‐γ T cell responses were more frequent in HPV‐16 DNA positive patients compared with that in HPV‐16 DNA negative patients (39/50 vs. 16/36, (p = 0.006, χ2 test). After invasive procedures, a small number of HPV‐16 DNA positive CIN patients, but a considerable proportion of HPV‐16 DNA positive cervical cancer patients, showed an enhancement of T cell responses against HPV‐16 E7. Induction of T cell reactivity was most pronounced in cervical cancer patients who had undergone previous invasive procedures. Both CD4+ and CD8+ T cells showed E7 specific IFN‐γ production upon in‐vitro stimulation. Our study shows that invasive procedures may enhance HPV‐specific cell‐mediated immunity in a considerable number of patients with cervical cancer, but in only a minority of CIN patients. Our data indicate that invasive procedures should be considered as possible confounding factors when analyzing the effectiveness of therapeutic immunization studies, especially, when induction of HPV‐specific immune responses is used as intermediate end‐point. © 2005 Wiley‐Liss, Inc.
Combination of a monoclonal anti‐phosphatidylserine antibody with gemcitabine strongly inhibits the growth and metastasis of orthotopic pancreatic tumors in mice
Authors: Beck Adam W. , Luster Troy A. , Miller Andrew F. , Holloway Shane E. , Conner Chris R. , Barnett Carlton C. , Thorpe Philip E. , Fleming Jason B. , Brekken Rolf A. 
Published: December 2005

AbstractPancreatic cancer continues to have a dismal prognosis and novel therapy is needed. In this study, we evaluate a promising new target for therapy, phosphatidylserine (PS). PS is an anionic phospholipid located normally on the inner leaflet of the plasma membrane in mammalian cells. In the tumor microenvironment, PS becomes externalized on vascular endothelium. The monoclonal antibody 3G4 binds PS and promotes an inflammatory response against tumor blood vessels, resulting in reduction of tumor growth. Mice with orthotopic pancreatic tumors were treated with 3G4, gemcitabine or a combination of both drugs. Tumor burden including pancreas weight and metastatic lesions (liver, lymph node and peritoneal) were reduced 3‐ to 5‐fold by the combination therapy as compared with 1.5‐ to 2‐fold with 3G4 and gemcitabine alone, respectively. Treatment of tumor‐bearing animals with the combination therapy increased macrophage infiltration into the tumor mass 10‐fold and reduced microvessel density in the tumor by 2.5‐fold compared with tumors from untreated animals. Gemcitabine alone and 3G4 alone were less effective than the combination of the 2 agents together. The additive therapeutic effect of both agents appears to be because chemotherapy increases PS exposure on tumor vascular endothelium and amplifies the target for attack by 3G4. In conclusion, 3G4 enhanced the anti‐tumor and anti‐metastatic activity of gemcitabine without contributing to toxicity. © 2005 Wiley‐Liss, Inc.
Sonography of the first dorsal metatarsal artery of the foot
Authors: Zhu Jiaan , Hu Bing 
Published: December 2005

AbstractPurposeTo describe the gray‐scale and Doppler sonographic examination technique and appearances of the first dorsal metatarsal artery (FDMA) of the foot and discuss its clinical significance.MethodsThe dorsal arteries of foot—including the FDMA and the first plantar metatarsal artery—of 374 feet were studied using gray‐scale and color Doppler sonography. Due to the difficulty of detecting the FDMA, a majority of them were identified by studying the web area just distal to the intermetatarsal space. The interosseous muscle was identified to determine the classification of the anatomic type of the FDMA. The sonographic results of 152 feet were compared with surgical findings.ResultsThe average caliber of the FDMA was 1.0 ± 0.5 mm. The FDMA was classified into 3 groups of variants based on its relationship with the first dorsal interosseous muscle. The groups were identified as the superficial artery (54.5%), intramuscular artery (39.6%), and submuscular artery (9%) variants. The rates of visualization of the distal and proximal portions of the FDMA were 86.6% and 47%, respectively. In the first intermetatarsal space, there were anastomoses between the FDMA and the first plantar metatarsal arteries in 87.6% of the feet.ConclusionsThe FDMA varies greatly; however, sonography can clearly show its morphologic characteristics, such as caliber and location. Sonography also provides valuable preoperative information in microsurgery of the foot. © 2006 Wiley Periodicals, Inc. J Clin Ultrasound 34:1–4, 2006
Unusually asymmetric venous engorgement of the breast after long‐term hemodialysis
Authors: Kim Min Jung , Kim Eun‐Kyung , Oh Ki Keun 
Published: December 2005

AbstractVenous engorgement of the breast demonstrated on mammography is usually considered a minor sign of malignancy. We report the sonographic and mammographic findings in an unusual case of asymmetric enlargement of the mammary veins in a middle‐aged patient as a complication of long‐term hemodialysis. © 2006 Wiley Periodicals, Inc. J Clin Ultrasound 34:27–29, 2006
Differentiation of diiodothyronines using electrospray ionization tandem mass spectrometry
Authors: Zhang Yuntao , Conrad Abigail H. , Thoma Rudy , Conrad Gary W. 
Published: December 2005

AbstractDiiodothyronines 3,5‐diiodothyronine (3,5‐T2), 3′,5′‐diiodothyronine (3′,5′‐T2), and 3,3′‐diiodothyronine (3,3′‐T2) are important metabolites of 3,5,3′‐triiodothyronine (T3) and 3,3′,5′‐triiodothyronine (rT3; reverse T3). In this paper, a novel and rapid method for identifying and quantifying 3,5‐T2, 3′,5′‐T2 and 3,3′‐T2 has been introduced using electrospray ionization tandem mass spectrometry (ESI‐MS/MS). Fragmentation patterns were proposed on the basis of our data obtained by ESI‐MS/MS. MS2 spectra in either negative ionization mode or positive ionization mode can be used to differentiate 3,5‐T2, 3′,5′‐T2 and 3,3′‐T2. On the basis of the relative abundance of fragment ions in MS2 spectra under the positive ionization mode, quantification of the 3,5‐T2, 3′,5′‐T2 and 3,3′‐T2 isomers in mixtures is also achieved without prior separation. Copyright © 2005 John Wiley & Sons, Ltd.