bluuebunny/crossref_metadata_2025_split huggingface dataset:
Computational issues in large strain elasto‐plasticity: an algorithm for mixed hardening and plastic spin
Authors: Montáns Francisco Javier , Bathe Klaus‐Jürgen 
Published: February 2005

AbstractIn this paper an algorithm for large strain elasto‐plasticity with isotropic hyperelasticity based on the multiplicative decomposition is formulated. The algorithm includes a (possible) constitutive equation for the plastic spin and mixed hardening in which the principal stress and principal backstress directions are not necessarily preserved. It is shown that if the principal trial stress directions are preserved during the plastic flow (as assumed in some algorithms) a plastic spin is inadvertently introduced for the kinematic/mixed hardening case. If the formulation is performed in the principal stress space, a rotation of the backstress is inadvertently introduced as well. The consistent linearization of the algorithm is also addressed in detail. Copyright © 2005 John Wiley & Sons, Ltd.
Explicit Newmark/Verlet algorithm for time integration of the rotational dynamics of rigid bodies
Authors: Krysl P. , Endres L. 
Published: February 2005

AbstractWe reformulate the traditional velocity based vector‐space Newmark algorithm for the rotational dynamics of rigid bodies, that is for the setting of the SO(3) Lie group. We show that the most naive re‐write of the vector space algorithm possesses the properties of symplecticity and (almost) momentum conservation. Thus, we obtain an explicit algorithm for rigid body dynamics that matches or exceeds performance of existing algorithms, but which curiously does not seem to have been considered in the open literature so far. Copyright © 2005 John Wiley & Sons, Ltd.
Optimum design of structures against earthquake by discrete wavelet transform
Authors: Salajegheh Eysa , Heidari Ali , Saryazdi Saeid 
Published: February 2005

AbstractOptimum design of structures is achieved by a modified genetic algorithm. Some features of the simulated annealing are used to control various parameters of the genetic algorithm. The loads are considered as earthquake loads. A time history analysis is carried out for the dynamic analysis. To decrease the computational work of analysis, a discrete wavelet transform is used by which the number of points in the earthquake record is reduced. Then in the optimization process, the structures are analysed with these points. To reconstruct the actual responses of structures from the responses of these points, a reverse wavelet transform is employed. A number of structures are designed for minimum weight and the results are compared with optimal solution using exact dynamic analysis. Copyright © 2005 John Wiley & Sons, Ltd.
Proteome analysis of sugar beet leaves under drought stress
Authors: Hajheidari Mohsen , Abdollahian‐Noghabi Mohammad , Askari Hossein , Heidari Manzar , Sadeghian Seyed Y. , Ober Eric S. , Hosseini Salekdeh Ghasem 
Published: February 2005

AbstractDrought is one of the major factors limiting the yield of sugar beet (Beta vulgarisL.). The identification of candidate genes for marker‐assisted selection (MAS) could greatly improve the efficiency of breeding for increased drought tolerance. Drought‐induced changes in the proteome could highlight important genes. Two genotypes of sugar beet (7112 and 7219‐P.69) differing in genetic background were cultivated in the field. A line‐source sprinkler irrigation system was used to apply irrigated and water deficit treatments beginning at the four‐leaf stage. At 157 days after sowing, leaf samples were collected from well‐watered and drought‐stressed plants for protein extraction and to measure shoot biomass and leaf relative water content. Changes induced in leaf proteins were studied by two‐dimensional gel electrophoresis and quantitatively analyzed using image analysis software. Out of more than 500 protein spots reproducibly detected and analyzed, 79 spots showed significant changes under drought. Some proteins showed genotype‐specific patterns of up‐ or downregulation in response to drought. Twenty protein spots were analyzed by liquid chromatography‐tandem mass spectrometry (LC‐MS/MS), leading to identification of Rubisco and 11 other proteins involved in redox regulation, oxidative stress, signal transduction, and chaperone activities. Some of these proteins could contribute a physiological advantage under drought, making them potential targets for MAS.
High molecular mass proteome of androgen‐independent prostate cancer
Authors: Kuruma Hidetoshi , Egawa Shin , Oh‐Ishi Masamichi , Kodera Yoshio , Satoh Mamoru , Chen Weigiang , Okusa Hiroshi , Matsumoto Kazumasa , Maeda Tadakazu , Baba Shiro 
Published: February 2005

AbstractWe made a comprehensive study of protein expression of androgen‐independent (AI) prostate cancer by means of agarose two‐dimensional gel electrophoresis (agarose 2‐DE) followed by liquid chromatography‐tandem mass spectrometric analysis. The agarose 2‐DE method being good at separating high molecular mass (HMM) proteins and alkaline ones, so we were able to successfully reveal differences between the proteomes of androgen‐dependent (AD) tumors and those of AI tumors. During the creation of agarose 2‐DE protein maps, we successfully identified 295 proteins (91.0%) out of 324 spots excised in total. Excluding redundant and mouse serum proteins, we considered the remaining 225 proteins to be related to the cancer. We divided the 225 cancer‐related proteins into HMM and low molecular mass (LMM) groups by their molecular mass being above or below 80 kDa. Functional classification of the proteins in these two groups showed clear differences between the two: more than half (54.8%) of the HMM proteins, but less than one‐third (29.1%) of the LMM ones were classified among transcription‐ or translation‐related proteins. Eighteen proteins were regulated when the tumor progressed from an AD to an AI state. Five of these proteins, including antioxidant protein 2, superoxide dismutase 1, thioredoxin peroxidase, GTP‐binding protein beta chain homolog, and the ha1225 gene product, had a function to protect cells against oxidant stress‐induced apoptosis. We suggest that prevention against oxidative stress is one of the key points for prostate cancer to obtain androgen independency. We also found proteins that had not been previously reported in prostate cancer by use of genomic or conventional 2‐DE based proteomic approaches. The proteomic approach, using agarose 2‐DE focused on HMM proteins, has the capability to find novel biomarkers of prostate cancer.
Proteins of calcified endoskeleton: II Partial amino acid sequences of endoskeletal proteins and the characterization of proteinaceous organic matrix of spicules from the alcyonarian, Synularia polydactyla
Authors: Rahman M. Azizur , Isa Yeishin , Uehara Tsuyoshi 
Published: February 2005

AbstractCalcified organic substances in the skeleton contain a protein‐polysaccharide complex taking a key role in the regulation of bio‐calcification. However, information concerning the matrix proteins in alcyonarian and their effect on calcification process is still unknown. For this reason, we have studied the organic matrix of endoskeletal spicules from the alcyonarian coral, Synularia polydactyla, to analyze the proteins with their sequences and investigate the functional properties by a molecular approach. The separated spicules from the colony were identified by scanning electron microscope (SEM). The soluble organic matrix comprised 0.04% of spicule weight. By recording decline of pH in the experimental design, the inhibitory effect of the matrix on CaCO3 precipitation was revealed. Prior to electrophoresis, our analysis of proteins extracted from the soluble organic matrix of the spicules revealed an abundance of proteins in molecular weight. The sodium dodecyl sulfate‐polyacrylamide gel electrophoresis (SDS‐PAGE) analysis of the preparations showed seven bands of proteins with an apparent molecular mass of 109, 83, 70, 63, 41, 30 and 22 kDa. The proteins were electrophoresed on Tricine‐SDS‐PAGE after electro‐elution treatment, and then transferred to polyvinylidene difluoride (PVDF) membranes and their N‐termini were sequenced. Two bands of proteins of about 70 and 63 kDa successfully underwent N‐terminal amino acid sequencing. For the detection of calcium binding proteins, a Ca2+ overlay analysis was conducted on the extract by 45Ca autoradiography. The 109 and 63 kDa calcium binding proteins were found to be radioactive. Periodic acid schiff staining indicated that 83 and 63 kDa proteins were glycosylated. An assay for carbonic anhydrase, which is thought to play an important role in the process of calcification revealed low level of the activity. These findings suggest that the endoskeletal spicules of alcyonarian corals have protein‐rich organic matrices, which might be related to the calcification process.
Proteomic changes in rice leaves during development of field‐grown rice plants
Authors: Zhao Caifeng , Wang Jingqiang , Cao Mengliang , Zhao Kang , Shao Jianmin , Lei Tingting , Yin Jianning , Hill Gradford G , Xu Ningzhi , Liu Siqi 
Published: February 2005

AbstractOf the numerous factors affecting rice yield, how solar radiation is transformed into biomass through rice leaves is the most important. We have analyzed proteomic changes in rice leaves collected from six different developing stages (vegetative to ripening). We studied protein expression profiles of rice leaves by running two‐dimensional gel electrophoresis. Differential protein expression among the six phases were analyzed by image analysis, which allowed the identification of 49 significantly different gel spots. The spots were further verified by matrix‐assisted laser desorption/ionization‐time of flight mass spectrometry, in which 89.8% of them were confirmed to be rice proteins. Finally, we confirmed some of the interesting rice proteins by immunoblotting. Three major conclusions can be drawn from these experimental results. (i) Protein expression in rice leaves, at least for high or middle abundance proteins, is attenuated during growth (especially some chloroplast proteins). However, the change is slow and the expression profiles are relatively stable during rice development. (ii) Ribulose‐1,5‐bisphosphate carboxylase/oxygenase (RuBisCO), a major protein in rice leaves, is expressed at constant levels at different growth stages. Interestingly, a high ratio of degradation of the RuBisCO large subunit was found in all samples. This was confirmed by two approaches, mass spectrometry and immunoblotting. The degraded fragments are similar to other digested products of RuBisCO mediated by free radials. (iii) The expression of antioxidant proteins such as superoxide dismutase and peroxidase decline at the early ripening stage.
Proteomic profiling for cancer progression: Differential display analysis for the expression of intracellular proteins between regressive and progressive cancer cell lines
Authors: Hayashi Eiko , Kuramitsu Yasuhiro , Okada Futoshi , Fujimoto Masanori , Zhang Xiulian , Kobayashi Masanobu , Iizuka Norio , Ueyama Yoshiya , Nakamura Kazuyuki 
Published: February 2005

AbstractTumor development and progression consist of a series of complex processes involving multiple changes in gene expression (Paolo et al. Physiol. Rev., 1993, 73, 161–195; Lance et al. Cell., 1991, 64, 327–336). Tumor cells acquire an invasive and metastatic phenotype that is the main cause of death for cancer patients. Therefore, for early diagnosis and effective therapeutic intervention, we need to detect the alterations associated with transition from benign to malignant tumor cells on a molecular basis. To unravel alterations concerned with tumor progression, the proteomic approach has attracted great attention because it can identify qualitative and quantitative changes in protein composition, including post‐translational modifications. In this study, we performed proteomic differential display analysis for the expression of intracellular proteins in the regressive cancer cell line QR‐32 and the inflammatory cell‐promoting progressive cancer cell line QRsP‐11 of murine fibrosarcoma by two‐dimensional gel electrophoresis and mass spectrometry using an Agilent 1100 LC/MSD Trap XCT. We found 11 protein spots whose expression was different between QR‐32 and QRsP‐11 cells and identified nine proteins, seven of which, calreticulin precursor, tropomyosin 1 α chain, annexin A5, heat shock protein (HSP)90‐α, HSP90‐β, PEBP, and Prx II, were over‐expressed, and two, Anp32e and HDGF, which were down‐regulated. The results suggest an important complementary role for proteomics in identification of molecular abnormalities in tumor progression.
Clinical‐scale high‐throughput human plasma proteome analysis: Lung adenocarcinoma
Authors: Fujii Kiyonaga , Nakano Tomoyo , Kanazawa Mitsuhiro , Akimoto Shingo , Hirano Takashi , Kato Harubumi , Nishimura Toshihide 
Published: February 2005

AbstractClinical proteomics requires the stable and reproducible analysis of a large number of human samples. We report a high‐throughput comprehensive protein profiling system comprising a fully automated, on‐line, two‐dimensional microflow liquid chromatography/tandem mass spectrometry (2‐D µLC‐MS/MS) system for use in clinical proteomics. A linear ion‐trap mass spectrometer (ITMS) also known as a 2‐D ITMS instrument, which is characterized by high scan speed, was incorporated into the µLC‐MS/MS system in order to obtain highly improved sensitivity and resolution in MS/MS acquisition. This system was used to evaluate bovine serum albumin and human 26S proteasome. Application of these high‐throughput µLC conditions and the 2‐D ITMS resulted in a 10‐fold increase in sensitivity in protein identification. Additionally, peptide fragments from the 26S proteasome were identified three‐fold more efficiently than by the conventional 3‐D ITMS instrument. In this study, the 2‐D µLC‐MS/MS system that uses linear 2‐D ITMS has been applied for the plasma proteome analysis of a few samples from healthy individuals and lung adenocarcinoma patients. Using the 2‐D and 1‐D µLC‐MS/MS analyses, approximately 250 and 100 different proteins were detected, respectively, in each HSA‐ and IgG‐depleted sample, which corresponds to only 0.4 µL of blood plasma. Automatic operation enabled the completion of a single run of the entire 1‐D and 2‐D µLC‐MS/MS analyses within 11 h. Investigation of the data extracted from the protein identification datasets of both healthy and adenocarcinoma groups revealed that several of the group‐specific proteins could be candidate protein disease markers expressed in the human blood plasma. Consequently, it was demonstrated that this high‐throughput µLC‐MS/MS protein profiling system would be practically applicable to the discovery of protein disease markers, which is the primary objective in clinical plasma proteome projects.
α‐Cyanobenzyl dithioester reversible addition–fragmentation chain‐transfer agents for controlled radical polymerizations
Authors: Li Chunzhao , Benicewicz Brian C. 
Published: February 2005

AbstractA series of new reversible addition–fragmentation chain transfer (RAFT) agents with cyanobenzyl R groups were synthesized. In comparison with other dithioester RAFT agents, these new RAFT agents were odorless or low‐odor, and this made them much easier to handle. The kinetics of methyl methacrylate radical polymerizations mediated by these RAFT agents were investigated. The polymerizations proceeded in a controlled way, the first‐order kinetics evolved in a linear fashion with time, the molecular weights increased linearly with the conversions, and the polydispersities were very narrow (∼1.1). A poly[(methyl methacrylate)‐block‐polystyrene] block copolymer was prepared (number‐average molecular weight = 42,600, polydispersity index = 1.21) from a poly(methyl methacrylate) macro‐RAFT agent. These new RAFT agents also showed excellent control over the radical polymerization of styrenics and acrylates. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 1535–1543, 2005
Fluoropolymer Coating of Medical Grade Poly(vinyl chloride) by Plasma‐Enhanced Chemical Vapor Deposition Techniques
Authors: Balazs Dawn J. , Hollenstein Christophe , Mathieu Hans Jörg 
Published: February 2005

AbstractSummary: Medical grade poly(vinyl chloride) was modified by RF plasma‐deposition of teflon‐like coatings to create a platform for the physisorption of PEO‐containing copolymers, Pluronics®. Thin teflon‐like coatings were deposited in an RF‐plasma reactor by plasma‐enhanced chemical vapor deposition (PE‐CVD) methods, using hexafluoroethane (C2F6) as a precursor and H2 as a carrier gas. A systematic study of the deposition parameters, C2F6 percentage in the C2F6‐H2 gas feed, power input and pressure was completed using X‐ray Photoelectron Spectroscopy and water contact angle measurements to characterize the various coatings. The surface analysis results were further correlated to the existing ion‐activated growth model. XPS results indicated that the coatings which had the maximum fluorine incorporation, as determined by the F/C ratio, or CFx functional groups, had the highest surface hydrophobicity. The parameters that were determined to yield the maximum contact angle (104°) in the continuous power, RF regime were a high C2F6 percentage (80%) in the C2F6‐H2 gas feed and the mid‐range power input and pressure values tested (30 W and 0.4 mbar).Change in C 1s high resolution scans and contact angle achieved following teflon‐like deposition on native PVC.imageChange in C 1s high resolution scans and contact angle achieved following teflon‐like deposition on native PVC.
Cover Picture: Plasma Process. Polym. 2/2005
Authors: Besch Wilfried , Schröder Karsten , Ohl Andreas 
Published: February 2005

Cover: The photograph shows a micro‐moulded test specimen which facilitates surface analysis in high aspect ratio gap structures in polymeric microdevices after surface modification. After dismantling the specimen, side effect‐free access to internal surfaces is provided.Further details can be found in the Full Paper by W. Besch,* K. Schröder, and Andreas Ohl on page 97.
Efficient focusing with a concave lens based on a photonic crystal with an unusual effective index of refraction
Authors: Foca E. , Föll H. , Daschner F. , Sergentu V. V. , Carstensen J. , Frey S. , Knöchel R. , Tiginyanu I. M. 
Published: February 2005

AbstractThis work reports measurements with a concave lens based on a photonic crystal (PC) structure, which was designed to have an effective index of refraction neff < 1 or even < 0, and which is intended as a model system for future down‐scaled optical elements based on PCs with an unusual effective index. The dimensions of the model PC were optimized for experiments in the microwave regime around 10 GHz. Calculations for a material with no losses allowed to select the wavelengths for which the lens could be expected to behave as a homogeneous meta‐material with an unusual effective refractive index. The field distribution behind the lens was measured, and good focusing efficiencies for neff < 1 were found for perfect and strongly disturbed PC's in reasonable accordance with the predictions. The (down‐scaled) model system investigated thus can serve as a reference for testing PC‐based optical elements made from materials which so far elude reliable predictions, e.g. doped semiconductors, nanorod assemblies, or meta‐materials with anisotropic behavior. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Chemical sensitivity in positron annihilation with just one single Ge detector
Authors: Haaks Matz , Staab Torsten E. M. , Saarinen Kimmo , Maier Karl 
Published: February 2005

AbstractWe present a novel method for analyzing the data from momentum distribution measurements employing positron annihilation, using just one single Ge‐detector, but employing a mathematically sufficiently well suited model for background subtraction. For a variety of high purity metals the resulting momentum distributions have exactly the same shapes up to 35 × 10–3 m0c as those obtained with coincidence Doppler broadening of the annihilation radiation using a two‐detector system. This data analysis applies to any positron source without high energy gammas or a slow positron beam system with just a single Ge‐detector and enables the possibility of analysing the chemical surrounding at the positron trapping site without any additional hardware. In particular, in combination with a slow positron microbeam, it allows a spatially resolved measurement of the electron's momentum distribution. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Gallium nitride nanowires with a metal initiated metal‐organic chemical vapor deposition (MOCVD) approach [phys. stat. sol. (b) 241, 2775 (2004)]
Authors: Lee Sang‐Kwon , Choi Heon‐Jin , Pauzauskie Peter , Yang Peidong , Cho Nam‐Kyu , Park Hyo‐Derk , Suh Eun‐Kyung , Lim Kee‐Young , Lee Hyung‐Jae 
Published: February 2005

AbstractThe authors add a missing reference to the article published in phys. stat. sol. (b) 241, 2775 (2004), referring to one of their own earlier papers in Nano Lett. 3, 1063 (2003). (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Searching for auxetics with DYNA3D and ParaDyn
Authors: Hoover Wm. G. , Hoover C. G. 
Published: February 2005

AbstractThe present special issue of physica status solidi (b), guest‐edited by Krzysztof W. Wojciechowski, Andrew Alderson, Arkadiusz Brańka, and Kim L. Alderson, is dedicated to Auxetics and Related Systems – materials which exhibit negative Poisson's ratio behaviour. Most papers were presented at a workshop which was held in Poznań–Będlewo, 27–30 June 2004.In our Editor's Choice [1] novel simulations with a parallel finite element program, ParaDyn, have been conducted to study the formation of auxetic materials. Structures composed of either brick elements (hexahedra) or shell elements are constructed in a regular array of panels. These structures are compressed and relaxed to form an initial state for an auxetic (foam‐like) material. The foam structure shown is composed of 208896 shell elements arranged in four by four panels. Applying a uniaxial compression to this structure characterizes the material behaviour of the lateral surfaces as normal (expanding) or auxetic (compressing).The first author, William G. Hoover, has been working in areas such as statistical and applied mechanics, nonlinear and molecular dynamics and is now pursuing, as he states on his own webpage, an “active retired research career” as Professor Emeritus of UC Davis.
Electronic and structural properties of C59Si on the monohydride Si(100) surface
Authors: Zanella Ivana , Fazzio A. , Da Silva Antônio J. R. 
Published: February 2005

AbstractWe propose the use of the Si atom in the C59Si molecule as a possible way to controllably anchor fullerene molecules on an Si surface, due to the formation of a strong bond to one of the Si surface atoms. We considered a monohydride Si(100) surface with the H removed from one of the Si surface atoms, and the C59Si was adsorbed at this site. Through ab initio calculations based on Density Functional Theory, we obtained a final Sisurface–SiC59Si bond distance of 2.37 Å, and a binding energy of –3.0 eV. Considering the reaction Hsurface + C59SiH → (C59Si)adsorbed + (H2)gas, we find this process to be exothermic by 0.41 eV. Upon adsorption of an isolated molecule, we find four levels in the gap, three empty and one singly occupied, all of them being basically localized at the C59Si molecule. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005