bluuebunny/crossref_metadata_2025_split huggingface dataset:
Binary spatial partitioning of the central‐difference time integration scheme for explicit fast transient dynamics
Authors: Casadei Folco , Halleux Jean‐Pierre 
Published: December 2008

AbstractThis paper proposes a generalization of the explicit central‐difference time integration scheme, using a time step variable not only in time but also in space. The solution at each element/node is advanced in time following local rather than global stability limitations. This allows substantial saving of computer time in realistic applications with non‐uniform meshes, especially in multi‐field problems like fluid–structure interactions. A binary scheme in space is used: time steps are not completely arbitrary, but stay in a constant ratio of two when passing from one partition level to the next one. This choice greatly facilitates implementation (via an integer‐based logic), ensures inherent synchronization and avoids any interpolations, necessary in other partitioning schemes in the literature, but which may reduce numerical stability. The mesh partition is automatically built up and continuously updated by simple spatial adjacency considerations. The resulting algorithm deals automatically with large variations in time of stability limits. The paper introduces the core spatial partitioning technique in the Lagrangian formulation. Some academic numerical examples allow a detailed comparison with the standard, spatially uniform algorithm. A final more realistic example shows the application of partitioning in simulations with arbitrary Lagrangian Eulerian formulation and fully‐coupled boundary conditions (fluid–structure interaction). Copyright © 2008 John Wiley & Sons, Ltd.
Frameshift mutations of autophagy‐related genes ATG2B, ATG5, ATG9B and ATG12 in gastric and colorectal cancers with microsatellite instability
Authors: Kang Mi Ran , Kim Min Sung , Oh Ji Eun , Kim Yoo Ri , Song Sang Yong , Kim Sung Soo , Ahn Chang Hyeok , Yoo Nam Jin , Lee Sug Hyung 
Published: December 2008

AbstractMounting evidence indicates that alterations of autophagy processes are directly involved in the development of many human diseases, including cancers. Autophagy‐related gene (ATG) products are main players in the autophagy process. In humans there are 16 known ATG genes, of which four (ATG2B, ATG5, ATG9B and ATG12) have mononucleotide repeats with seven or more nucleotides. Frameshift mutations of genes with mononucleotide repeats are features of cancers with microsatellite instability (MSI). It is not known whether ATG genes with mononucleotide repeats are altered by frameshift mutations in gastric and colorectal carcinomas with MSI. For this, we analysed the mononecleotide repeats in ATG2B, ATG5, ATG9B and ATG12 in 32 gastric carcinomas with high MSI (MSI‐H), 13 gastric carcinomas with low MSI (MSI‐L), 43 colorectal carcinomas with MSI‐H and 15 colorectal carcinomas with MSI‐L by a single‐strand conformation polymorphism (SSCP) analysis. We found ATG2B, ATG5, ATG9B and ATG12 mutations in 10, 2, 13 and 0 cancers, respectively. The mutations were detected in MSI‐H cancers but not in MSI‐L cancers. Gastric and colorectal cancers with MSI‐H harboured one or more ATG mutations in 28.1% and 27.9%, respectively. Our data indicate that frameshift mutations in ATG genes with mononucleotide repeats are common in gastric and colorectal carcinomas with MSI‐H, and suggest that these mutations may contribute to cancer development by deregulating the autophagy process. Copyright © 2008 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
A combined experimental and theoretical investigation on the oxygenation of organic sulfides by oxo(salen)chromium(V) ion
Authors: Venkataramanan Natarajan Sathiyamoothy , Rajagopal Seenivasan , Suvitha Ambigapathy , Kawazoe Yoshiyuki 
Published: December 2008

AbstractThe mechanism of oxygenation of organic sulfide by oxo(salen)chromium(V) complexes has been studied experimentally and by the density functional theory (DFT) method. Spectral studies show DMSO ligands bind with the Cr center of oxidant and the adduct formed was responsible for the oxygenation reaction. The reaction was first order with respect to oxidant and substrate. Hammett plot shows the formation of positive charge over sulfur atom and the development of negative charge over the oxidant in the transition state (TS). For the substrate ρ values are in the range from −1.5 to −1.8. The geometry has been correctly predicted by the B3LYP function, and it gives better results for spin states, harmonic frequencies, and thermodynamic energies for the system. DFT results indicate the existence of oxo(salen)chromium(V) and Cr(III)–salen at doublet and quartet as ground state, respectively. Binding of donor ligand weakens the CrO bond. TS structures show an increase in the negative charge and spin density over Cr atom indicating the involvement of spin inversion and radical character. The low activation energy and high free energy change are responsible for the enhancement of the reaction rate and product yield in the presence of DMSO donor ligand, while the rebound mechanism and the direction of substrate approach perpendicular to the salen plane are responsible for their higher selectivity. From this combined study, a mechanism involving consecutive two‐electron transfer from the oxo(salen)chromium(V) ion to the electron‐rich sulfur atom is proposed. Copyright © 2008 John Wiley & Sons, Ltd.
Copolymerization of tetradecene‐1 and octene‐1 with silyl‐protected 10‐undecen‐1‐ol using a Cs‐symmetry hafnium metallocene catalyst. A route to functionalized poly(α‐olefins)
Authors: Kotzabasakis Vasilios , Petzetakis Nikolaos , Pitsikalis Marinos , Hadjichristidis Nikos , Lohse David J. 
Published: December 2008

AbstractStatistical copolymers of tetradecene‐1 and octene‐1 with 1‐tert‐butyldimethylsilyloxy‐10‐undecene were synthesized by metallocene catalyzed copolymerization. The Cs‐symmetry hafnium metallocene [(p‐Et3Si)Ph]2C(2,7‐di‐tert‐BuFlu)(Cp)Hf(CH3)2 and tetrakis(pentafluorophenyl) borate dimethylanilinium salt ([B(C6F5)4]−[Me2NHPh]+) were employed as the catalytic system, in the presence of trioctylaluminum (TOA) as a scavenger. The monomer reactivity ratios were calculated using the Finemann‐Ross, inverted Finemann‐Ross, and Kelen‐Tüdos graphical methods. The structural parameters of the different copolymers were obtained from the calculation of the dyad monomer sequence fractions and the mean sequence lengths derived via the reactivity ratios. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 876–886, 2009
Kinetic pathway investigations of three‐component photoinitiator systems for visible‐light activated free radical polymerizations
Authors: Kim Dongkwan , Stansbury Jeffrey W. 
Published: December 2008

AbstractThree‐component photoinitiator systems generally include a light‐absorbing photosensitizer (PS), an electron donor, and an electron acceptor. To investigate the key factors involved with visible‐light activated free radical polymerizations involving three‐component photoinitiators and 2‐hydroxyethyl methacrylate, we used thermodynamic feasibility and kinetic considerations to study photopolymerizations initiated with either rose bengal or fluorescein as the PS. The Rehm–Weller equation was used to verify the thermodynamic feasibility for the photo‐induced electron transfer reaction. It was concluded that key kinetic factors for efficient visible‐light activated initiation process are summarized in two ways: (1) to retard back electron transfer and recombination reaction steps and (2) to use a secondary reaction step for consuming dye‐based radical and regenerating the original PS (dye). Using the thermodynamic feasibility and kinetic data, we suggest three different kinetic mechanisms, which are (i) photo‐reducible series mechanism, (ii) photo‐oxidizable series mechanism, and (iii) parallel‐series mechanism. Because the photo‐oxidizable series mechanisms most efficiently allow the key kinetic factors, this kinetic pathway showed the highest conversion and rate of polymerization. The kinetic data measured by near‐IR and photo‐differential scanning calorimeter verified that the photo‐oxidizable series mechanism provides the most efficient kinetic pathway in the visible‐light activated free radical polymerizations. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 887–898, 2009
Ring‐opening polymerization of benzylated 1,6‐anhydro‐β‐D‐lactose and specific biological activities of sulfated (1→6)‐α‐D‐lactopyranans
Authors: Han Shuqin , Kanematsu Yuji , Hattori Kazuyuki , Nakashima Hideki , Yoshida Takashi 
Published: December 2008

AbstractA new anhydro disaccharide monomer, 1,6‐anhydro‐2,3‐di‐o‐benzyl‐4‐o‐(2′,3′,4′,6′‐tetra‐o‐benzyl‐β‐D‐galactopyranosyl)‐β‐D‐glucopyranose (benzylated 1,6‐anhydro lactose (LSHBE)), was synthesized from D‐lactose to investigate the polymerizability and biological activities of the resulting branched polysaccharides. The ring‐opening polymerization of LSHBE was carried out with phosphorus pentafluoride as a catalyst under high vacuum to give a stereoregular benzylated (1 → 6)‐α‐D‐lactopyranan. The molecular weights of poly(LSHBE)s increased with an increase in the amount of CH2Cl2 solvent, and polymerization temperatures were affected in both molecular weights and yields of the polymers. The copolymerization of LSHBE with benzylated 1,6‐anhydro‐β‐D‐glucopyranose (LGTBE) gave the corresponding copolysacchrides having different proportions of lactose and glucose units in good yields. After debenzylation to recover hydroxyl groups and then sulfation, sulfated homopoly(lactose)s and copoly(lactose and glucose)s were obtained. Sulfated homopoly(lactose)s had moderate anti‐HIV (EC50 = 5.9 and 1.3 μg/mL) and blood anticoagulant activities (AA = 18 and 13 unit/mg), respectively. Sulfated copoly(lactose and glucose) having 15 mol % lactose units gave high anti‐HIV and blood anticoagulant activities of 0.3 μg/mL and 54 unit/mg, respectively. These biological results suggest that the distance between branched units on the main chain plays an important role in the anti‐HIV and blood anticoagulant activities. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 913–924, 2009
Equations of state for polyamide‐6 and its nanocomposites. 1. Fundamentals and the matrix
Authors: Utracki L. A. 
Published: December 2008

AbstractThe pressure‐volume‐temperature (PVT) surface of polyamide‐6 (PA‐6) was determined in the range of temperature T = 300–600 K and pressure P = 0.1–190 MPa. The data were analyzed separately for the molten and the noncrystalline phase using the Simha‐Somcynsky (S‐S) equation of state (eos) based on the cell‐hole theory. At Tg(P) ≤ T ≤ Tm(P), the “solid” state comprises liquid phase with crystals dispersed in it. The PVT behavior of the latter phase was described using Midha‐Nanda‐Simha‐Jain (MNSJ) eos based on the cell theory. The data fitting to these two theories yielded two sets of the Lennard‐Jones interaction parameters: ε*(S‐S) = 34.0 ± 0.3 and ε*(MNSJ) = 22.8 ± 0.3 kJ/mol, whereas v*(S‐S) = 32.00 ± 0.1 and v*(MNSJ) = 27.9 ± 0.2 mL/mol. The raw PVT data were numerically differentiated to obtain the thermal expansion and compressibility coefficients, α and κ, respectively. At constant P, κ followed the same dependence on both sides of the melting zone near Tm. By contrast, α = α(T) dependencies were dramatically different for the solid and molten phase; at T < Tm, α linearly increased with increasing T, then within the melting zone, its value step‐wise decreased, to slowly increase at higher temperatures. © 2008 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 47: 299–313, 2009
Beyond the psychotherapy and survival debate: the challenge of social disparity, depression and treatment adherence in psychosocial cancer care
Authors: Kissane David 
Published: December 2008

AbstractThe psychotherapy and cancer survival debate generated great interest in the psychoneuroimmunological and bio‐behavioral mechanisms that might mediate any gain in survival. Recent methodologically‐improved cognitive‐existential, supportive‐expressive and psycho‐educational group interventions for patients with breast cancer and melanoma have not extended survival times. Shorter survival has been associated with social disparity and untreated clinical depression, potentially mediated by poorer adherence to anti‐cancer treatments. Group therapy both prevents and treats depression. Future research could address these bio‐behavioral mechanisms. Copyright © 2008 John Wiley & Sons, Ltd.
Nanocomposites of Electrospun Poly[(D,L‐lactic)‐co‐(glycolic acid)] and Plasma‐Functionalized Single‐Walled Carbon Nanotubes for Biomedical Applications
Authors: Yoon Ok J. , Kim Hyun W. , Kim Duck J. , Lee Hyun J. , Yun Ji Y. , Noh Yoo H. , Lee Do Y. , Kim Do H. , Kim Sung S. , Lee Nae‐Eung 
Published: December 2008

AbstractThe conductance of amine‐functionalized SWCNTs (a‐SWCNTs), obtained by inductively coupled N2/H2 plasma treatment of commercially available carboxyl‐functionalized SWCNTs (c‐SWCNTs), was decreased compared to that of the c‐SWCNTs. As a result, the diameter and surface energy of electrospun PLGA/a‐SWCNT nanocomposites decreased and increased, respectively, compared to those of electrospun PLGA/c‐SWCNT nanocomposites. The results also showed that the a‐SWCNTs were well dispersed in the nanocomposites, improved adhesion of SWCNTs to the surrounding polymer matrix and thereby enhanced the tensile modulus of electrospun PLGA/c‐SWCNT and PLGA/a‐SWCNT nanocomposites by 127 and 226%, respectively, compared to that of electrospun PLGA membranes.magnified image
The vitamin D receptor agonist elocalcitol inhibits IL‐8‐dependent benign prostatic hyperplasia stromal cell proliferation and inflammatory response by targeting the RhoA/Rho kinase and NF‐kB pathways
Authors: Penna Giuseppe , Fibbi Benedetta , Amuchastegui Susana , Corsiero Elisa , Laverny Gilles , Silvestrini Enrico , Chavalmane Aravinda , Morelli Annamaria , Sarchielli Erica , Vannelli Gabriella Barbara , Gacci Mauro , Colli Enrico , Maggi Mario , Adorini Luciano 
Published: December 2008

AbstractBACKGROUNDBenign prostatic hyperplasia (BPH) is characterized by an important inflammatory component. Stimulation of human prostate stromal cells from BPH tissues with proinflammatory cytokines leads to secretion of IL‐8, a chemokine involved in BPH pathogenesis. The vitamin D receptor (VDR) agonist elocalcitol can arrest prostate growth in BPH patients, but its mechanism of action in this pathology is still incompletely understood.METHODSIL‐8 levels were measured by real‐time RT‐PCR and ELISA. NF‐κB translocation and COX‐2 expression were evaluated by confocal microscopy. RhoA and Rho‐kinase (ROCK) gene expression and functional activity were studied by real‐time RT‐PCR, immuno‐kinase assays, Western blot analysis, confocal microscopy, and cell invasion.RESULTSStimulation of BPH cells with IL‐8 activates the calcium‐sensitizing RhoA/ROCK pathway, as demonstrated by the increased membrane translocation of RhoA and by phosphorylation of the ROCK substrate myosin phosphatase target subunit 1 (MYPT‐1). In agreement with these data, C3 exoenzyme, a selective RhoA inhibitor, inhibits IL‐8‐induced invasion of BPH cells. The VDR agonist elocalcitol significantly inhibits IL‐8 production by BPH cells stimulated with inflammatory cytokines, and IL‐8‐induced proliferation of BPH cells. In addition, elocalcitol inhibits IL‐8‐induced membrane translocation of RhoA and MYPT‐1 phosphorylation in BPH cells, and inhibits dose‐dependently their IL‐8‐dependent invasion. The inhibition induced by elocalcitol of IL‐8 production by BPH cells is accompanied by decreased COX‐2 expression and PGE2 production and by arrest of NF‐κB p65 nuclear translocation, associated with inhibition of the RhoA/ROCK pathway.CONCLUSIONSThese data provide a mechanistic explanation for the anti‐proliferative and anti‐inflammatory properties of elocalcitol in BPH cells. Prostate 69:480–493, 2009. © 2008 Wiley‐Liss, Inc.
Butanol fraction containing berberine or related compound from nexrutine® inhibits NFκB signaling and induces apoptosis in prostate cancer cells
Authors: Muralimanoharan Sri Balasubashini , Kunnumakkara A.B. , Shylesh Bhaskaran , Kulkarni Kaustubh H. , Haiyan Xu , Ming Hu , Aggarwal Bharat B. , Rita Ghosh , Kumar Addanki P. 
Published: December 2008

AbstractBACKGROUNDEpidemiological and laboratory studies support the hypothesis that several plant components influence prostate carcinogenesis and holds promise for disease prevention. Previously we reported that Nexrutine® (bark extract from Phellodendron amurense) inhibits proliferation of prostate cancer cells and prostate tumor development in the transgenic adenocarcinoma of mouse prostate (TRAMP) model through modulation of Akt signaling pathway. In the present investigation we conducted studies to further define the mechanism of action of Nexrutine® and to identify the active component associated with its biological activity.METHODSAndrogen‐responsive, androgen‐independent human prostate cancer cell lines and tissues from TRAMP mice fed Nexrutine® were used in these studies. Activity guided fractionation identified butanol fraction recapitulating the activities of Nexrutine® assessed by proliferation assays, apoptotic assays (DAPI and TUNEL staining), transient transfections, gel shift assays and Western blotting. In addition ultra‐performance liquid chromatography (UPLC) of butanol fraction was used to identify active component of Nexrutine®.RESULTSButanol fraction recapitulated the activities of Nexrutine® in (i) inhibiting proliferation; (ii) inducing apoptosis; and (iii) modulating transcriptional activity of NFκB in prostate cancer cells. Our data also indicates that both Nexrutine® and butanol fraction modulates NFκB transcriptional activity by inhibiting IκBα phosphorylation. Expression of p65 and phosphorylated IκBα are high in tumors from TRAMP mice. In contrast dietary administration of Nexrutine® reduced expression of p65 and phosphorylated IκBα in prostate from TRAMP mice. In addition using UPLC, we have identified berberine or closely related compound in the butanol fraction.CONCLUSIONThe results suggest that berberine or closely related component of butanol fraction may be responsible for the observed biological activities and induce apoptosis in prostate cancer cells by targeting critical cell survival signaling pathways both in vitro and in vivo. Prostate 69:494–504, 2009. © 2008 Wiley‐Liss, Inc.
Conserved structural and dynamics features in the denatured states of drosophila SUMO, human SUMO and ubiquitin proteins: Implications to sequence‐folding paradigm
Authors: Kumar Dinesh , Chugh Jeetender , Sharma Shilpy , Hosur Ramakrishna V. 
Published: December 2008

AbstractWe have characterized here the structural and dynamics properties of urea‐denatured state of dSmt3 by multidimensional NMR at 27°C and pH 5.6. The various results suggest that hydrophobic clusters as well as different native and non‐native secondary structural elements are transiently formed. The backbone in the regions Gln26‐Lys31 and Gly47‐Gln60 shows conformationally restricted motions. The AABUF profile of the sequence reflected that this region has the highest tendency to undergo hydrophobic clustering and may thus assist the formation of transient structures. The secondary chemical shifts and coupling constants indicated that this region has strong tendency to occupy the broad β‐domain of (ϕ,ψ) space. A number of NMR parameters indicated that the region Asp58‐Gln60 (corresponding to β3‐β4 turn in the folded state) has residual turn‐like structure. The present structural and dynamics results on urea‐denatured dSmt3 have been compared with the previously published results on denatured states of similar fold proteinse.g. human SUMO‐1 (55% homologous), ubiquitin (13.8% homologous) and GB1. Although the sequence homology is rather poor between them, the residual structure in all cases seems to be largely native type. The implications of these to sequence‐folding paradigm and initial folding processes have been discussed. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Characterization of a diagnostic Fab fragment binding trimeric Lewis X
Authors: de Geus Daniël C. , van Roon Anne‐Marie M. , Thomassen Ellen A. J. , Hokke Cornelis H. , Deelder André M. , Abrahams Jan Pieter 
Published: December 2008

AbstractLewis X trisaccharides normally function as essential cell–cell interaction mediators. However, oligomers of Lewis X trisaccharides expressed by the parasite Schistosoma mansoni seem to be related to its evasion of the immune response of its human host. Here we show that monoclonal antibody 54‐5C10‐A, which is used to diagnose schistosomiasis in humans, interacts with oligomers of at least three Lewis X trisaccharides, but not with monomeric Lewis X. We describe the sequence and the 2.5 Å crystal structure of its Fab fragment and infer a possible mode of binding of the polymeric Lewis X from docking studies. Our studies indicate a radically different mode of binding compared to Fab 291‐2G3‐A, which is specific for monomeric Lewis X, thus providing a structural explanation of the diagnostic success of 54‐5C10‐A. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Description and recognition of regular and distorted secondary structures in proteins using the automated protein structure analysis method
Authors: Ranganathan Sushilee , Izotov Dmitry , Kraka Elfi , Cremer Dieter 
Published: December 2008

AbstractThe Automated Protein Structure Analysis (APSA) method, which describes the protein backbone as a smooth line in three‐dimensional space and characterizes it by curvature κ and torsion τ as a function of arc length s, was applied on 77 proteins to determine all secondary structural units via specific κ(s) and τ(s) patterns. A total of 533 α‐helices and 644 β‐strands were recognized by APSA, whereas DSSP gives 536 and 651 units, respectively. Kinks and distortions were quantified and the boundaries (entry and exit) of secondary structures were classified. Similarity between proteins can be easily quantified using APSA, as was demonstrated for the roll architecture of proteins ubiquitin and spinach ferridoxin. A twenty‐by‐twenty comparison of all α domains showed that the curvature‐torsion patterns generated by APSA provide an accurate and meaningful similarity measurement for secondary, super secondary, and tertiary protein structure. APSA is shown to accurately reflect the conformation of the backbone effectively reducing three‐dimensional structure information to two‐dimensional representations that are easy to interpret and understand. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Estimating flame speeds for use with the BST blast curves
Authors: Melton Timothy A. , Marx Jeffrey D. 
Published: December 2008

AbstractThe Baker‐Strehlow‐Tang (BST) vapor cloud explosion model is one of the most common methods used to estimate overpressures for the purpose of locating buildings in relation to process units. This model suffers from a problem common to all simplified explosion models: the user is required to pick the “strength” of the explosion using one or more simple parameters. In the BST model, the fuel reactivity, flame expansion, and obstacle density parameters are used to select a flame speed from a limited matrix of possible values. This article presents the Quest Model for estimation of flame speeds (QMEFS), a systematic approach to estimating flame speed that does not rely on the BST categories. It provides for a continuous range of flame speeds that can then be used with the existing BST blast curves to calculate the characteristics of the vapor cloud explosion. The QMEFS approach provides the user with a method for describing a vapor cloud explosion that is more detailed than the BST model, and establishes a more refined system for predicting the consequences of vapor cloud explosions. © 2008 American Institute of Chemical Engineers Process Saf Prog, 2009