bluuebunny/crossref_metadata_2025_split huggingface dataset:
A proteomic analysis during serial subculture and osteogenic differentiation of human mesenchymal stem cell
Authors: Sun Hyun Jin , Bahk Young Yil , Choi Yon Rak , Shim Jung Hye , Han Seung Hwan , Lee Jin Woo 
Published: August 2006

AbstractAlthough previous studies have reported the effects of extensive subculturing on proliferation rates and osteogenic potential of human mesenchymal stem cells (hMSCs), the results remain controversial. The aim of our study was to characterize the proliferation and osteogenic potential of hMSCs during serial subculture, and also to identify proteins that are differentially regulated in hMSCs during serial subculture and osteogenic differentiation using proteome analysis. Here we show that the proliferation and osteogenic capacity of hMSCs decrease during serial subculturing. Several proteins were shown to be differentially regulated during serial subculture; among these the expression of T‐complex protein 1 α subunit (TCP‐1α), a protein known to be associated with cell proliferation, cell cycle, morphological changes, and apoptosis, gradually decreased during serial subculture. Among proteins that were differentially regulated during osteogenic differentiation, chloride intracellular channel 1 (CLIC1) was downregulated only during the early passages eukaryotic translation elongation factor, and acidic ribosomal phosphoprotein P0 was downregulated during the middle passages, while annexin V, LIM, and SH3 domain protein 1 (LASP‐1), and 14‐3‐3 protein gamma (YWHAG) were upregulated during the later passage. These studies suggest that differentially regulated passage‐specific proteins may play a role in the decrease of osteogenic differentiation potential under serial subculturing. © 2006 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 24:2059–2071, 2006
Late Pleistocene and Holocene environmental changes in the coastal zone of northwestern Portugal
Authors: de Carvalho G. Soares , Granja H. M. , Loureiro E. , Henriques R. 
Published: August 2006

AbstractThis paper examines the Quaternary changes in the coastal zone of northwestern Portugal through the relationship between sediments and landforms. By interpolating the available data from geomorphology, lithostratigraphy, sedimentology and geochronology, it was possible to reconstruct existing palaeoenvironments, the oldest of which date back to the last interglacial. The main landforms are a high and a low platform bounded by scarps. River sands and silty sediments formed in a lacustrine environment (Antas Formation, MIS 5) are associated with the high platform. Two deposits are associated with the low platform: the Cepães Formation (MIS 3) consisting of a lower set of river sand beds and an upper gravel beach bed, and the Aguçadoura Formation (MIS 1) consisting of Holocene lagoonal beds. Copyright © 2006 John Wiley & Sons, Ltd.
Rheology Pathway to Macroscale Ordered Nanostructures of Polymeric Nanotemplates: Nanopores, Nanosheets and Nanofibers
Authors: Fahmi Amir W. , Gutmann Jochen S. , Vogel Roland , Gindy Nabil , Stamm Manfred 
Published: August 2006

AbstractSummary: The creation of nanotemplates under dynamic shear flow conditions is described. The structures used are based on the self‐organization of comb‐coil‐like diblock copolymer systems with two intrinsic length scales, resulting from combining diblock copolymers with hydrogen‐bonding amphiphiles. Rheological data of polymeric supramolecular order formation are studied under oscillating shear flow conditions and it was observed that the order of the polymeric nanodomains can be extended to macroscopic distances. It is proposed that the key success factor to obtain highly ordered samples is to perform the orientation process using appropriate rheological conditions (temperature, frequency and strain) selected such that the ratio of the elastic component G′ to the viscous component G″ is larger than 1. This observation was used to select the rheological parameters for the three different samples investigated, where three different types of nanotemplates are observed after extracting the hydrogen‐bonding amphiphile; nanosheets, hollow cylinders and nanofibres. SAXS is primarily used to inspect the resulting structures. Additionally, AFM and TEM were utilized to image the morphologies and to further act as visual proof for the efficiency of the rheological orientation process.AFM phase image of PS‐b‐P4VP nanosheets on Si wafer substrate after extracting the PDP.magnified imageAFM phase image of PS‐b‐P4VP nanosheets on Si wafer substrate after extracting the PDP.
Kinetics of Cationic Photopolymerizations of UV‐Curable Epoxy‐Based SU8‐Negative Photoresists With and Without Silica Nanoparticles
Authors: Cho Jung‐Dae , Ju Hyoung‐Tae , Park Young‐Sik , Hong Jin‐Who 
Published: August 2006

AbstractSummary: This paper reports on the photocuring kinetics of protonic‐acid‐initiated cationic polymerizations of UV‐curable epoxy‐based SU8‐negative photoresist systems with and without silica nanoparticles, as assessed using photo‐DSC, FTIR spectroscopy, UV‐vis spectroscopy, and SEM. Photo‐DSC analysis using an autocatalytic kinetic model demonstrated that the cross‐link density and cure rate increased as the concentration of silica nanoparticles with surface silanol groups increased to 2.5 wt.‐%. This result was confirmed by FTIR spectroscopy, and suggests that the presence of silica nanoparticles of up to 2.5 wt.‐% promoted the cure conversion and cure rate of the UV‐curable hybrid organic/inorganic negative photoresists due to the synergistic effect of silica nanoparticles acting both as an effective flow or diffusion‐aid agent and as a proton‐donor cocatalyst during the cationic photopolymerization process. The decrease in the cross‐link density that occurred when the silica content was higher than 2.5 wt.‐% was attributed to aggregation between silica nanoparticles due to their high surface energy.SEM photograph at the film‐air interface of the UV‐cured hybrid organic/inorganic photoresist containing 10 wt.‐% silica nanoparticles.magnified imageSEM photograph at the film‐air interface of the UV‐cured hybrid organic/inorganic photoresist containing 10 wt.‐% silica nanoparticles.
Effect of diffusion in inhomogeneous magnetic fields on balanced steady‐state free precession
Authors: Bieri O. , Scheffler K. 
Published: August 2006

AbstractIn this work, the effects of susceptibility variation from dilute, micron‐sized spherical field perturbers and diffusion on balanced steady‐state free precession (bSSFP) are analyzed. Predictions from Monte Carlo simulations are in good agreement with experiments and reveal that, for diffusing protons, susceptibility variation becomes apparent as a reduction in the overall bSSFP signal intensity. This reduction depends on microsphere parameters (radius and susceptibility difference), as well as on sequence‐related parameters (repetition time and flip angle) and on relaxation times. Specific Monte Carlo results from one set of parameter values can be extrapolated to another set of values by means of a scaling law and a substitution model. The scaling law, derived from the Bloch–Torrey equation, captures the dependencies of bSSFP signal reduction on susceptibility and diffusion‐related changes and on repetition time, whereas the substitution model describes those on flip angle and relaxation times. Copyright © 2006 John Wiley & Sons, Ltd.
Clustered generalized finite element methods for mesh unrefinement, non‐matching and invalid meshes
Authors: Duarte C. A. , Liszka T. J. , Tworzydlo W. W. 
Published: August 2006

AbstractIn spite of significant advancements in automatic mesh generation during the past decade, the construction of quality finite element discretizations on complex three‐dimensional domains is still a difficult and time demanding task.In this paper, the partition of unity framework used in the generalized finite element method (GFEM) is exploited to create a very robust and flexible method capable of using meshes that are unacceptable for the finite element method, while retaining its accuracy and computational efficiency. This is accomplished not by changing the mesh but instead by clustering groups of nodes and elements. The clusters define a modified finite element partition of unity that is constant over part of the clusters. This so‐called clustered partition of unity is then enriched to the desired order using the framework of the GFEM.The proposed generalized finite element method can correctly and efficiently deal with: (i) elements with negative Jacobian; (ii) excessively fine meshes created by automatic mesh generators; (iii) meshes consisting of several sub‐domains with non‐matching interfaces. Under such relaxed requirements for an acceptable mesh, and for correctly defined geometries, today's automated tetrahedral mesh generators can practically guarantee successful volume meshing that can be entirely hidden from the user. A detailed technical discussion of the proposed generalized finite element method with clustering along with numerical experiments and some implementation details are presented. Copyright © 2006 John Wiley & Sons, Ltd.
Exact dynamic stiffness matrix for a thin‐walled beam of doubly asymmetric cross‐section filled with shear sensitive material
Authors: Rafezy B. , Howson W. P. 
Published: August 2006

AbstractAn exact dynamic stiffness matrix is developed for the flexural motion of a three‐dimensional, bi‐material beam of doubly asymmetric cross‐section. The beam comprises a thin walled outer layer that encloses and works compositely with its shear sensitive core material. The outer layer may have the form of an open or closed section and provides flexural, warping and Saint‐Venant rigidity, while the core material provides Saint‐Venant and shear rigidity. The uniform distribution of mass in the member is accounted for exactly and thus necessitates the solution of a transcendental eigenvalue problem. This is accomplished using the Wittrick–Williams algorithm, which enables the required natural frequencies to be converged upon to any required accuracy with the certain knowledge that none have been missed. Such a formulation enables the powerful modelling features associated with the finite element technique to be utilized when establishing structural models. Three examples are included to validate and illustrate the method. The work also holds considerable potential in its application to the approximate analysis of asymmetric, multi‐storey, three‐dimensional wall‐frame structures. Copyright © 2006 John Wiley & Sons, Ltd.
Comparative proteomic studies on the pathogenesis of human ulcerative colitis
Authors: Hsieh Sen‐Yung , Shih Tsung‐Chieh , Yeh Chien‐Yuh , Lin Chun‐Jung , Chou Yun‐Ying , Lee Ying‐Shiung 
Published: August 2006

AbstractUlcerative colitis (UC) is a chronic inflammatory disorder primarily affecting the colon mucosa. Its etiology and pathogenesis remain unclear. We used 2‐DE and MS to identify differentially expressed proteins among the UC active, UC inactive, nonspecific colitis, and normal colon mucosa. Thirteen down‐regulated and six up‐regulated proteins were identified. Of the down‐expressed proteins, eight (heat‐shock protein 90 (HSPA9B), heat‐shock protein 60 (HSPD1), H+‐transporting two‐sector ATPase (ATP5B), prohibitin (PHB), mitochondrial malate dehydrogenase (MDH2), voltage‐dependent anion‐selective channel protein 1 (VDAC1), thioredoxin peroxidase (PRDX1), and thiol‐specific antioxidant (PRDX2)) were mitochondrial proteins, three (ATP5B, MDH2, triosephosphate isomerase) were involved in energy generation, three (PRDX1, PRDX2, SELENBP1) were cellular antioxidants, and six (HSPD1, HSPA9B, PRDX1, PRDX2, PHB, VDAC1) were stress‐response proteins. Transmission electron microscopy revealed pathological alterations of mitochondrial ultrastructures even before the global colonocyte changes in the UC colon mucosa. PHB, an essential mitochondrial component protein, was down‐expressed in the disease active as well as inactive colon mucosa from the patients of UC, indicative of an early event of mitochondrial changes during UC development. In contrast, aberrant activation of NFAT and ectopic expression of potential immunogenic proteins (tumor rejection antigen 1 and poliovirus receptor related protein 1) were found in the UC‐diseased colon mucosa. Our findings suggest the implications of colonocyte mitochondrial dysfunction and perturbed mucosa immune regulation in the pathogenesis of UC and provide potential targets for the development of a new therapy.
Effect of fungal polysaccharides on the modulation of plasma proteins in streptozotocin‐induced diabetic rats
Authors: Kim Sang Woo , Hwang Hye Jin , Kim Hyun Mi , Lee Myung Chul , Shik Lee Myung , Choi Jang Won , Yun Jong Won 
Published: August 2006

AbstractTo search out novel biomarkers for monitoring diabetes prognosis, we examined the effect of hypoglycemic fungal exopolysaccharides (EPS) on the differential levels of plasma proteins in streptozotocin‐induced diabetic rats. The orally administrated EPS exhibited an excellent hypoglycemic effect, lowering the average plasma glucose level, and increasing insulin secretion in diabetic rats. The 2‐DE analysis of rat plasma demonstrated that about 500 visualized spots were differentially regulated, of which 20 spots were identified as principal diabetes‐associated proteins. The distinct effect of diabetes induction on the pattern of rat plasma proteins includes the down‐regulation of albumin, apolipoprotein E (Apo E), α1‐inhibitor‐3, fetuin β, Gc‐globulin, hemopexin, vitronectin, and transthyretin (TTR) monomer, and the up‐regulation of Apo A‐I, Apo A‐IV, ceruloplasmin, α1‐antitrypsin, serine protease inhibitor III, and transferrin. Those protein levels were interestingly restored to those of healthy rats by EPS treatment, although the order of magnitude of the changes differed widely. Two proteins of interest showed distinct differential expression with opposite trends: TTR tetramer was significantly down‐regulated and immunoglobulin (Ig) kappa light chain was significantly up‐regulated upon diabetes induction, both of which were also normalized to those of healthy groups after EPS treatment.
Proteomic analysis of individual variation in normal livers of human beings using difference gel electrophoresis
Authors: Zhang Xuequn , Guo Yuanbiao , Song Yanping , Sun Wei , Yu Chaohui , Zhao Xiaohang , Wang Hongyang , Jiang Hongchi , Li Youming , Qian Xiaohong , Jiang Ying , He Fuchu 
Published: August 2006

AbstractNormal Chinese Liver Proteome Expression Profile is one of the major parts of Human Liver Proteome Project. Before starting the studies, it is necessary to examine the interindividual variation of normal liver proteome and evaluate the minimal size of samples for proteomic analysis. In this study, normal liver samples from ten individual volunteers were collected and the proteome profiles of these samples were analyzed using 2‐D difference gel electrophoresis (DIGE) combined with MALDI‐TOF/TOF MS. The individual liver tissue lysates were labeled with Cy3 and Cy5 while the pooled sample was labeled with Cy2 as an internal standard, which minimized gel‐to‐gel variation. After analysis by the DeCyder software, up to 2056 protein spots were detected on the master gel. The CV of standardized abundance was calculated for the protein spots that were matched across all ten gels. The CV values of these protein spots ranged from 6.4 to 108.5% and the median CV was ∼19%, which demonstrated that the protein expression of normal liver among different individuals was relatively stable. The eight proteins with CV values over 50% were identified which would be a caveat when considering these proteins as potential disease‐related markers. Moreover, the one‐way ANOVA feature showed a correlation between sample size and individual variations. The results showed that when the sample size exceeded 7, the individual variations were not significant to the whole pool. Our results are an important basis for liver protein expression profiles and comparative proteomics of liver disease.
Mechanism and kinetics of dithiobenzoate‐mediated RAFT polymerization. I. The current situation
Authors: Barner‐Kowollik Christopher , Buback Michael , Charleux Bernadette , Coote Michelle L. , Drache Marco , Fukuda Takeshi , Goto Atsushi , Klumperman Bert , Lowe Andrew B. , Mcleary James B. , Moad Graeme , Monteiro Michael J. , Sanderson Ronald D. , Tonge Matthew P. , Vana Philipp 
Published: August 2006

AbstractInvestigations into the kinetics and mechanism of dithiobenzoate‐mediated Reversible Addition–Fragmentation Chain Transfer (RAFT) polymerizations, which exhibit nonideal kinetic behavior, such as induction periods and rate retardation, are comprehensively reviewed. The appreciable uncertainty in the rate coefficients associated with the RAFT equilibrium is discussed and methods for obtaining RAFT‐specific rate coefficients are detailed. In addition, mechanistic studies are presented, which target the elucidation of the fundamental cause of rate retarding effects. The experimental and theoretical data existing in the literature are critically evaluated and apparent discrepancies between the results of different studies into the kinetics of RAFT polymerizations are discussed. Finally, recommendations for further work are given. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 5809–5831, 2006
Molecular dynamics study of the stabilities of consensus designed ankyrin repeat proteins
Authors: Yu Haibo , Kohl Andreas , Binz H. Kaspar , Plückthun Andreas , Grütter Markus G. , van Gunsteren Wilfred F. 
Published: August 2006

AbstractTwo designed ankyrin repeat (AR) proteins (E3_5 and E3_19) are high homologous (with about 87% sequence identity) and their crystal structures have a Cα atom‐positional root‐mean‐square difference of about 0.14 nm. However, it was found that E3_5 is considerably more stable than E3_19 in guanidinium hydrochloride and thermal denaturation experiments. With the goal of providing insights into the various factors contributing to the stabilities of the designed AR proteins and suggesting possible mutations to enhance their stabilities, homology modeling and molecular dynamics (MD) simulations with explicit solvent have been performed. Because the crystal structure of E3_19 was solved later than that of E3_5, a homology model of E3_19 based on the crystal structure of E3_5 was also used in the simulations. E3_5 shows a very stable trajectory in both crystal and solution simulations. In contrast, the C‐terminal repeat of E3_19 unfolds in the simulations starting from either the modeled structure or the crystal structure, although it has a sequence identical to that of E3_5. A continuum electrostatic model was used to estimate the effect of single mutations on protein stability and to study the interaction between the internal ARs and the C‐terminal capping AR. Mutations involving charged residues were found to have large effects on stability. Due to the difference in charge distribution in the internal ARs of E3_19 and E3_5, their interaction with the C‐terminal capping AR is less favorable in E3_19. The simulation trajectories suggest that the stability of the designed AR proteins can be increased by optimizing the electrostatic interactions within and between the different repeats. Proteins 2006. © 2006 Wiley‐Liss, Inc.
Specificity of molecular interactions in transient protein–protein interaction interfaces
Authors: Cho Kyu‐il , Lee KiYoung , Lee Kwang H. , Kim Dongsup , Lee Doheon 
Published: August 2006

AbstractIn this study, we investigate what types of interactions are specific to their biological function, and what types of interactions are persistent regardless of their functional category in transient protein–protein heterocomplexes. This is the first approach to analyze protein–protein interfaces systematically at the molecular interaction level in the context of protein functions. We perform systematic analysis at the molecular interaction level using classification and feature subset selection technique prevalent in the field of pattern recognition. To represent the physicochemical properties of protein–protein interfaces, we design 18 molecular interaction types using canonical and noncanonical interactions. Then, we construct input vector using the frequency of each interaction type in protein–protein interface. We analyze the 131 interfaces of transient protein–protein heterocomplexes in PDB: 33 protease‐inhibitors, 52 antibody‐antigens, 46 signaling proteins including 4 cyclin dependent kinase and 26 G‐protein. Using kNN classification and feature subset selection technique, we show that there are specific interaction types based on their functional category, and such interaction types are conserved through the common binding mechanism, rather than through the sequence or structure conservation. The extracted interaction types are Cα H···OC interaction, cation···anion interaction, amine···amine interaction, and amine···cation interaction. With these four interaction types, we achieve the classification success rate up to 83.2% with leave‐one‐out cross‐validation at k = 15. Of these four interaction types, CαH···OC shows binding specificity for protease‐inhibitor complexes, while cation–anion interaction is predominant in signaling complexes. The amine ··· amine and amine···cation interaction give a minor contribution to the classification accuracy. When combined with these two interactions, they increase the accuracy by 3.8%. In the case of antibody–antigen complexes, the sign is somewhat ambiguous. From the evolutionary perspective, while protease‐inhibitors and sig‐naling proteins have optimized their interfaces to suit their biological functions, antibody–antigen interactions are the happenstance, implying that antibody–antigen complexes do not show distinctive interaction types. Persistent interaction types such as π···π, amide‐carbonyl, and hydroxyl‐carbonyl interaction, are also investigated. Analyzing the structural orientations of the π···π stacking interactions, we find that herringbone shape is a major configuration in transient protein–protein interfaces. This result is different from that of protein core, where parallel‐displaced configurations are the major configuration. We also analyze overall trend of amide‐carbonyl and hydroxyl‐carbonyl interactions. It is noticeable that nearly 82% of the interfaces have at least one hydroxyl‐carbonyl interactions. Proteins 2006. © 2006 Wiley‐Liss, Inc.
Spectroscopic ellipsometry study of FePt nanoparticle films
Authors: Lee S. J. , Lo C. C. H. , Yu A. C. C. , Fan M. 
Published: August 2006

AbstractThe optical properties of a FePt nanoparticle film were investigated using spectroscopic ellipsometry. The FePt nanoparticle film of thickness about 15 nm was prepared by deposition of FePt nanoparticles directly on a Si substrate. The nanoparticle film was annealed at 600 °C in vacuum for two hours before the measurements. The optical properties of the FePt nanoparticle film showed distinctively different spectra from those obtained from the bulk and thin film FePt samples, in particular in the low photon energy range (below 3.5 eV) where the nanoparticle film exhibited a relatively flat refractive index and a substantially lower extinction coefficient than the bulk and epitaxial thin film samples. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)