bluuebunny/crossref_metadata_2025_split huggingface dataset:
Numerical investigation of flow in a channel obstructed by an array of square rods (2nd report, Investigation of a criterion for judging the uniqueness and validity of numerical results)
Authors: Murata Hiroyuki , Sawada Ken‐Ichi , Suzuki Kenjiro 
Published: April 2007

AbstractTwo‐dimensional numerical computation is performed for unsteady laminar flow. Spatially periodic boundary conditions are adopted in the streamwise direction, and in particular, a criterion for judging the uniqueness of the numerical solution is studied. The following results were obtained. When the numerical result fluctuates with the computational domain size, various low‐frequency components are markedly observed in the streamwise velocity of the calculated result. Compared with the channel flow obstructed by a single rod of the same size, the intensities of velocity fluctuation in this study are relatively high, and their distribution throughout the flow field is rather uniform. The spatially averaged kinematic energy of the velocity fluctuation is adopted as a key parameter, and a discrimination map of the uniqueness of the numerical solution is presented using a timescale ratio between mean flow and velocity fluctuation, the rod pitch, and the blockage ratio. The timescale ratio is well correlated with a geometric parameter obtained from the flow configuration, and the discrimination map can be converted such that the geometric parameter and the channel Reynolds number describe it. © 2007 Wiley Periodicals, Inc. Heat Trans Asian Res, 36(3): 113–126, 2007; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/htj.20152
Family history of gallstones and the risk of biliary tract cancer and gallstones: A population‐based study in Shanghai, China
Authors: Hsing Ann W. , Bai Yan , Andreotti Gabriella , Rashid Asif , Deng Jie , Chen Jinbo , Goldstein Alisa M. , Han Tian‐Quan , Shen Ming‐Chang , Fraumeni Joseph F. , Gao Yu‐Tang 
Published: April 2007

AbstractCancers of the biliary tract arise from the gallbladder, extrahepatic bile ducts and ampulla of Vater. Although relatively uncommon, the incidence of biliary tract cancer rose more than 100% in Shanghai, China between 1972 and 1994. Gallstones are the predominant risk factor for biliary tract cancers, with over 60% of the cancer cases having gallstones. A familial tendency to gallstones has been reported and may elevate the risk of gallbladder cancer further. As part of a large population‐based case–control study of biliary tract cancers in Shanghai, China, we examined the association between a family history of gallstones and biliary tract cancers as well as biliary stones. A total of 627 biliary tract cancers (368 gallbladder, 191 bile duct, 68 ampulla of Vater), 1,037 biliary stone cases (774 gallbladder, 263 bile duct) and 959 healthy subjects randomly selected from the population were included in this study. Information on family history of gallstones among first‐degree relatives (i.e., parents, siblings, offspring) was obtained through a self‐reported history during in‐person interviews. A family history of gallstones was associated with increased risks of biliary stones [odds ratio (OR) = 2.8, 95% confidence interval (CI) = 2.1–3.8], gallbladder cancer (OR = 2.1, 95% CI = 1.4–3.3) and bile duct cancer (OR = 1.5, 95% CI = 0.9–2.5), after adjustment for age, gender, marital status, education, smoking, alcohol drinking and body mass index. For gallbladder cancer, subjects with gallstones but without a family history of gallstones had a 21‐fold risk (95% CI 14.8–30.1), while those with both gallstones and a positive family history had a 57‐fold risk (95% CI 32.0–110.5). Significant risks for gallbladder cancer persisted after additional adjustment for gallstones, and when the analysis was restricted to subjects with first‐degree relatives whose gallstones were treated with cholecystectomy. The significant associations with a family history of gallstones were seen for all first‐degree relatives, including parents, siblings and offspring, but not spouses. This large population‐based study not only supports the role of gallstones in biliary carcinogenesis but also suggests that the underlying genetic or lifestyle determinants of stones within families contribute to the risk of biliary tract cancer. © 2007 Wiley‐Liss, Inc.
Protein C inhibitor inhibits breast cancer cell growth, metastasis and angiogenesis independently of its protease inhibitory activity
Authors: Asanuma Kunihiro , Yoshikawa Tomoaki , Hayashi Tatsuya , Akita Nobuyuki , Nakagawa Norimi , Hamada Yasuhiko , Nishioka Junji , Kamada Haruhiko , Gabazza Esteban C. , Ido Masaru , Uchida Atsumasa , Suzuki Koji 
Published: April 2007

AbstractProtein C inhibitor (PCI) regulates the anticoagulant protein C pathway and also inhibits urinary plasminogen activator (uPA), a mediator of tumor cell invasion. In the present study, we evaluated the effect of human PCI and its inactive derivatives on tumor growth and metastasis of human breast cancer (MDA‐231) cells, and on angiogenesis in vivo. The invasiveness of MDA‐231 cells was inhibited by recombinant intact PCI, but not by reactive site‐modified PCI (R354APCI) or by the N‐terminal fragment of protease‐cleaved PCI (NTPCI). The in vitro invasiveness of MDA‐231 cells expressing intact PCI (MDA‐PCI) was significantly decreased as compared to MDA‐231 cells expressing R354APCI (MDA‐R354APCI) or NTPCI (MDA‐NTPCI). Further, in vivo growth and metastatic potential of MDA‐PCI, MDA‐R354APCI and MDA‐NTPCI cells in severe combined immunodeficient (SCID) mice were significantly decreased as compared to MDA‐Mock cells. Angiogenesis was also significantly decreased in Matrigel implant containing MDA‐PCI, MDA‐R354APCI or MDA‐NTPCI cells as compared to that containing MDA‐Mock cells. In vivo angiogenesis in rat cornea and in vitro tube formation were also inhibited by recombinant intact PCI, R354APCI and NTPCI. Furthermore, the anti‐angiogenic activity of PCI was strong as cleaved antithrombin (AT), and slightly stronger than that of plasminogen activator inhibitor (PAI)‐1 and pigment epithelium‐derived factor (PEDF). Overall, this study showed that, in addition to a reactive site‐dependent mechanism, PCI may also regulate tumor growth and metastasis independently of its protease inhibitory activity by inhibiting angiogenesis. © 2007 Wiley‐Liss, Inc.
A gene expression signature associated with metastatic cells in effusions of breast carcinoma patients
Authors: Dupont Virginie N. , Gentien David , Oberkampf Marine , De Rycke Yann , Blin Nathalie 
Published: April 2007

AbstractMalignant effusion in invasive breast carcinoma is associated with poor prognosis. To decipher molecular events leading to metastasis and to identify reliable markers for targeted therapies are of crucial need. Therefore, we have used cDNA microarrays to delineate molecular signatures associated with metastasis and relapse in breast carcinoma effusions. Taking advantage of an immunomagnetic method, we have purified to homogeneity EpCAM‐positive cells from 34 malignant effusions. Immunopurified cells represented as much as 10% of the whole cell fraction and their epithelial and carcinoma features were confirmed by immunofluorescence labeling. Gene expression profiles of 19 immunopurified effusion samples, were analyzed using human pan‐genomic microarrays, and compared with those of 4 corresponding primary tumors, 8 breast carcinoma effusion‐derived cell lines, and 4 healthy mammary tissues. Principal component and multiple clustering analyses of microarray data, clearly identified distinctive molecular portraits corresponding to the 4 categories of specimens. Of uppermost interest, effusion samples were arranged in 2 subsets on the basis of their gene expression patterns. The first subset partly shares a gene expression signature with the different cell lines, and overexpresses CD24, CD44 and epithelial cytokeratins 8,18,19. The second subset overexpresses markers related to aggressive invasive carcinoma (uPA receptor, S100A4, vimentin, CXCR4). These findings demonstrate the importance of using pure cell fractions to accurately decipher in silico gene expression of clinical specimens. Further studies will lead to the identification of genes of oustanding importance to diagnose malignant effusion, predict survival and tailor appropriate therapies to the metastatic effusion disease in breast carcinoma patients. © 2007 Wiley‐Liss, Inc.
Coffee consumption and risk of colorectal cancer in a population‐based prospective cohort of Japanese men and women
Authors: Lee Kyung‐Jae , Inoue Manami , Otani Tetsuya , Iwasaki Motoki , Sasazuki Shizuka , Tsugane Shoichiro ,   for the JPHC Study Group
Published: April 2007

AbstractWe prospectively examined the association between coffee consumption and the risk of developing colorectal cancer in a large population‐based cohort study (the JPHC Study) of Japanese men and women. Data were analyzed from a population‐based cohort of 96,162 subjects (46,023 men and 50,139 women). A total of 1,163 incident colorectal cancers were identified during the follow‐up period, including 763 cases of colon cancer and 400 of rectal cancer. We observed a significant inverse association between coffee consumption and the risk of developing invasive colon cancer among women. Compared with those who almost never consumed coffee, women who regularly consumed 3 or more cups of coffee per day had a RR of 0.44 (95% CI = 0.19–1.04; p for trend = 0.04) after adjustment for potential confounding factors. However, no significant association was found for rectal cancer in women. In men, no significant decrease was observed in any colorectal cancer site. Further, additional analyses on the association of green tea consumption with colorectal cancer risk found no significant association in men or women. These findings suggest that coffee consumption may lower the risk of colon cancer among Japanese women. © 2007 Wiley‐Liss, Inc.
Chondrocyte‐alginate bioconstructs: An nuclear magnetic resonance relaxation study
Authors: Fantazzini Paola , Garavaglia Carla , Gomez Santiago , Toffanin Renato , Vittur Franco 
Published: April 2007

AbstractProton nuclear magnetic resonance (NMR) relaxometry can give informations about hydrogel scaffold properties. As these properties can be modified with culture time and conditions according to scaffold biodegradability and new tissue biosynthesis, the aim of this research was to test the efficiency of this noninvasive NMR technique in the follow‐up of 3D cultures for tissue engineering. The distributions of proton relaxation times T1 and T2 have been measured on cylindrical gel samples of different types of alginate, in the presence or absence of hyaluronate, in gels or bioconstructs with encapsulated chondrocytes cultured for 30 days in normal or reduced weight conditions. It was found that T2 increases with the mannuronate/guluronate ratio in alginate samples and with the presence of hyaluronate. The distributions of both T1 and T2 result wider for bioconstructs cultured in normal gravity than for those cultured in reduced weight conditions. Neither cell growing nor collagen production but only GAG neosynthesis have been demonstrated in our experimental conditions. In conclusion, T2 is sensitive to the gel properties (possibly to the rigidity of macromolecular components). The homogeneity of bioconstructs can be monitored by the distribution of T1 and T2. We propose that nonspatially resolved NMR relaxometry can efficiently be used in monitoring tissue development in a biodegradable scaffold for tissue engineering. © 2007 Wiley Periodicals, Inc. J Biomed Mater Res 2007
Phenotype and gene expression pattern of osteoblast‐like cells cultured on polystyrene and hydroxyapatite with pre‐adsorbed type‐I collagen
Authors: Hanagata Nobutaka , Takemura Taro , Monkawa Akira , Ikoma Toshiyuki , Tanaka Junzo 
Published: April 2007

AbstractHydroxyapatite and type‐I collagen are major components of bone matrix. We compared phenotype and gene expression pattern of osteoblast‐like cells cultured on HAp and HAp with pre‐adsorbed type‐I collagen from neutral solutions (HAp/NCs) with those of tissue culture grade polystyrene (TCPS) and TCPS with the collagen (TCPS/NCs). In initial cell attachment, the cells tensely spread on TCPS, while loosely spread on TCPS/NCs, HAp, and HAp/NCs. The levels of expressed integrin α2 and α5 subunits were not significantly different among any surfaces. Although the cells on HAp/NCs directly attached with the same collagen molecules as TCPS/NCs, mineralization was observed in only TCPS/NCs. The basal substrates (TCPS and HAp) greatly influenced osteoblast maturation even in the surfaces with pre‐adsorbed collagen, since mineralization was induced by TCPS, but not by HAp. Gene expression pattern analyzed with DNA microarray also supported greater influence of basal substrates than pre‐adsorbed collagen. In addition, comprehensive gene expression analyses revealed that HAp and HAp/NCs specifically up‐regulated Ly6a and Tmem37 genes, while down‐regulated Ifitm5 gene. © 2007 Wiley Periodicals, Inc. J Biomed Mater Res 2007
Impedimetric sensing of cells on polypyrrole‐based conducting polymers
Authors: Ateh D.D. , Waterworth A. , Walker D. , Brown B.H. , Navsaria H. , Vadgama P. 
Published: April 2007

AbstractPolypyrrole (PPy) is a conducting polymer that may be electrochemically generated with the incorporation of any anionic species, including net‐negatively charged biological molecules such as proteins and polysaccharides. In this article, dermatan and chloride‐loaded PPy films were prepared on gold sputter‐coated coverslips and various skin derived cells were studied on them by electrochemical impedance spectroscopy. Impedance spectra in the frequency range 1–100 kHz were either determined at specific times or impedance was monitored continuously at specific frequencies. An equivalent impedance circuit was fitted to the recorded impedance spectra to obtain parameters whose contributions could be mapped to intracellular and intercellular current pathways, and the membrane properties of cells. Results show cell‐induced impedance changes were detected over PPy modified electrodes and were dependent on cell density and type, monitoring frequency, material composition, and treatment. Lower cell densities were detected on PPy when compared with bare gold. Keratinocyte confluence, as determined by impedimetric analysis, was reached more rapidly on PPy than on gold. This was consistent with previous, more cumbersome, biochemical assays. Electrical equivalent circuit analysis provided evidence that the technique may be extended to discriminate cell type because of the intracellular and intercellular resistance, and cell membrane capacitance being related to cell morphology. © 2007 Wiley Periodicals, Inc. J Biomed Mater Res 2007
Quaternized chitosan/alginate nanoparticles for protein delivery
Authors: Li Tao , Shi Xiao‐Wen , Du Yu‐Min , Tang Yu‐Feng 
Published: April 2007

AbstractQuaternized chitosan (QCS)/alginate (AL) nanoparticles (QCS/AL) were successfully prepared in neutral condition for the oral delivery of protein. The physicochemical structure of the QCS/AL nanoparticles was characterized by IR spectroscopy and transmission electron microscopy. The diameter of the nanoparticles with a positive surface charge was about 200 nm. The load of bovine serum albumin (BSA) was affected by the concentration and the molecular parameters, i.e. degree of substitution (DS) and weight‐average molecular weight (Mw) of QCS, as well as the concentration of BSA. The release of BSA from nanoparticles was pH‐dependent. Quick release occurred in 0.1M phosphate buffer solution (PBS, pH = 7.4), while the release was slow in 0.1M HCl (pH = 1.2). The DS and Mw of QCS play important roles in the release of BSA in vitro. QCS with high Mw accelerated the release of BSA in acid, while high DS retarded the release of BSA in both 0.1M HCl and 0.1M PBS. © 2007 Wiley Periodicals, Inc. J Biomed Mater Res 2007
Structural, electronic, and optical properties of 9‐heterofluorenes: A quantum chemical study
Authors: Chen Run‐Feng , Zheng Chao , Fan Qu‐Li , Huang Wei 
Published: April 2007

AbstractDensity‐functional theory studies were applied to investigate the structural, electronic, and optical properties of 9‐heterofluorenes achieved by substituting the carbon at 9 position of fluorene with silicon, germanium, nitrogen, phosphor, oxygen, sulfur, selenium, or boron. These heterofluorenes and their oligomers up to pentamers are highly aromatic and electrooptically active. The alkyl and aryl substituents of the heteroatom have limited influence, but the oxidation of the atom has significant influence on their molecular structures and properties. The highest occupied molecular orbital (HOMO)‐lowest occupied molecular orbital (LUMO) interaction theory was successfully applied to analyze the energy levels and the frontier wave functions of these heterofluorenes. Most heterofluorenes belong to type B of interaction with low‐lying LUMO and have the second kind of wave function. Carbazole and selenafluorene have type C of interaction with high‐lying HOMO and the third kind of wave function. Types C and D of heterofluorenes, such as carbazole, oxygafluorene, sulfurafluorene, and selenafluorene also have high triplet state energies. The extrapolated HOMO and LUMO for polyheterofluorenes indicate that polyselenonafluorene has the lowest LUMO; polycarbazole has the highest HOMO; polyselenafluorene has the highest bandgap (Eg); and polyborafluorene has the lowest Eg. Heterofluorenes and their oligomers and polymers are of great experimental interests, especially those having extraordinary properties revealed in this study. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007
A combined electronegativity equalization and electrostatic potential fit method for the determination of atomic point charges
Authors: Berente Imre , Czinki Eszter , Náray‐szabó Gábor 
Published: April 2007

AbstractWe report an approach for the determination of atomic monopoles of macromolecular systems using connectivity and geometry parameters alone. The method is appropriate also for the calculation of charge distributions based on the quantum mechanically determined wave function and does not suffer from the mathematical instability of other electrostatic potential fit methods. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007
New six‐site acetonitrile model for simulations of liquid acetonitrile and its aqueous mixtures
Authors: Nikitin Alexei M. , Lyubartsev Alexander P. 
Published: April 2007

AbstractA new six site flexible acetonitrile molecular model is developed. The AMBER force field was used for description of intramolecular parameters, the atomic charges were calculated from a high level ab initio theory and finally the Lennard–Jones parameters were tuned to fit the experimental density and evaporation heat. The obtained in this way model reproduces correctly densities of water–acetonitrile mixtures as well as provides qualitative description of the dielectric permittivity and self‐diffusion coefficients. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007
Algorithm to evaluate rate constants for polyatomic chemical reactions. I. Theory and computational details
Authors: González Javier , Giménez Xavier , Bofill Josep Maria 
Published: April 2007

AbstractA classical reaction path, Liouville algorithm, as previously developed by the authors, has been reformulated in a more efficient form, based on the time‐dependent first integral method from the theory of partial differential equations. Both the theory and computational details are presented. The formulation is based on solving the complete rate constant problem, concerning both the density distribution as well as the reactive flux, by means of solving the classical Liouville equation. The numerical implementation is discussed in detail, including some specifics concerning the reaction path calculation. The formulation is tested with the well‐known Müller–Brown bidimensional potential energy surface. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007
Complete maps of molecular‐loop conformational spaces
Authors: Porta Josep M. , Ros Lluís , Thomas Federico , Corcho Francesc , Cantó Josep , Pérez Juan Jesús 
Published: April 2007

AbstractThis paper presents a numerical method to compute all possible conformations of distance‐constrained molecular loops, i.e., loops where some interatomic distances are held fixed, while others can vary. The method is general (it can be applied to single or multiple intermingled loops of arbitrary topology) and complete (it isolates all solutions, even if they form positive‐dimensional sets). Generality is achieved by reducing the problem to finding all embeddings of a set of points constrained by pairwise distances, which can be formulated as computing the roots of a system of Cayley–Menger determinants. Completeness is achieved by expressing these determinants in Bernstein form and using a numerical algorithm that exploits such form to bound all root locations at any desired precision. The method is readily parallelizable, and the current implementation can be run on single‐ or multiprocessor machines. Experiments are included that show the method's performance on rigid loops, mobile loops, and multiloop molecules. In all cases, complete maps including all possible conformations are obtained, thus allowing an exhaustive analysis and visualization of all pseudo‐rotation paths between different conformations satisfying loop closure. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007
Protein structure prediction aided by geometrical and probabilistic constraints
Authors: Porwal Gaurav , Jain Swapnil , Babu S. Dhilly , Singh Deepak , Nanavati Hemant , Noronha Santosh 
Published: April 2007

AbstractDatabase‐assistedab initioprotein structure prediction methods have exhibited considerable promise in the recent past, with several implementations being successful in community‐wide experiments (CASP). We have employed combinatorial optimization techniques toward solving the protein structure prediction problem. A Monte Carlo minimization algorithm has been employed on a constrained search space to identify minimum energy configurations. The search space is constrained by using radius of gyration cutoffs, the loop backbone dihedral probability distributions, and various secondary structure packing conformations. Simulations have been carried out on several sequences and 1000 conformations have been initially generated. Of these, 50 best candidates have then been selected as probable conformations. The search for the optimum has been simplified by incorporating various geometrical constraints on secondary structural elements using distance restraint potential functions. The advantages of the reported methodology are its simplicity, and modifiability to include other geometric and probabilistic restraints. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007