bluuebunny/crossref_metadata_2025 huggingface dataset:
Bayesian meta‐modelling of engineering design simulations: a sequential approach with adaptation to irregularities in the response behaviour
Authors: Farhang‐Mehr A. , Azarm S.
Published: February 2005

Among current meta‐modelling approaches, Bayesian‐based interpolative methods have received significant attention in the literature. These methods are particularly known for their capability to adapt to the response function behaviour in order to generate good meta‐models with fewer experiments. Current Bayesian adaptation techniques, however, are mainly based on the assumption that some variables are more important (or sensitive) than others. These less sensitive variables are weighted less or ignored to reduce the dimension of the design space. This assumption limits the scope and applicability of these models since in many practical cases none of the variables can be completely ignored or weighted less than others.

This paper proposes a pragmatic approach that identifies regions of the design space where more experiments are needed based on the response function behaviour. The proposed approach adaptively utilizes the information obtained from previous experiments, builds interim meta‐models, and identifies ‘irregular’ regions in which more experiments are needed. The behaviour of the interim meta‐model is then quantified as a spatial function and incorporated into the next stage of the design to sequentially improve the accuracy of the obtained meta‐model. The performance of the new approach is demonstrated using a numerical and an engineering example. Copyright © 2005 John Wiley & Sons, Ltd.
Simulation of light‐weight membrane structures by wrinkling model
Authors: Rossi Riccardo , Lazzari Massimiliano , Vitaliani Renato , Oñate Eugenio
Published: February 2005

The computational challenge in dealing with membrane systems is closely connected to the lack of bending stiffness that constitutes the main feature of this category of structures. This manifests numerically in badly conditioned or singular systems requiring the use of stabilized solution procedures, in our case of a ‘pseudo‐dynamic’ approach. The absence of the flexural stiffness makes the membrane very prone to local instabilities which manifest physically in the formation of little ‘waves’ in ‘compressed’ areas. Current work presents an efficient, sub‐iteration free ‘explicit’, penalty material based, wrinkling simulation procedure suitable for the solution of ‘static’ problems. The procedure is stabilized by taking full advantage of the pseudo‐dynamic solution strategy, which allows to retain the elemental quadratic convergence properties inside the single solution step. Results are validated by comparison with published results and by setting up ‘numerical experiments’ based on the solution of test cases using dense meshes. Copyright © 2005 John Wiley & Sons, Ltd.
Vibration analyses of a portal frame under the action of a moving distributed mass using moving mass element
Authors: Wu Jia‐Jang
Published: February 2005

Four kinds of moving mass elements, 1st‐node, 2nd‐node, full and short‐range mass elements, are presented, where the 1st‐node (or 2nd‐node) mass element refers to that with mass distributed from the first node (or second node) to the arbitrary position of a two‐node beam element, the full mass element is the special case of the 1st‐node (or 2nd‐node) mass element with mass distributed over the full length of the beam element, while the short‐range mass element is the case with its location arbitrary on a beam element. If the total range of a distributed mass is denoted by R and the length of each beam element is denoted by 𝓁, then, for the case of R⩾𝓁, one may model the distributed mass on the beam using the combination of the 1st‐node, 2nd‐node and full mass elements, while for the case of R<𝓁, one may model the distributed mass using the short‐range mass element. It has been found that the effects of the vertical (ȳ) and horizontal (x̄) inertia forces, Coriolis force and centrifugal force induced by the moving distributed mass can be easily taken into the formulations by means of the last concept. To illustrate the application of the presented theory, the dynamic analysis of a pinned–pinned beam and that of a portal frame under the action of a moving uniformly distributed mass are performed by means of the finite element method and the Newmark integration method. Numerical results show that some pertinent factors, such as Coriolis force, centrifugal force, acceleration, velocity and total range of the moving distributed mass, have significant influences on the vertical (ȳ) and horizontal (x̄) response of a structure. Copyright © 2005 John Wiley & Sons, Ltd.
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

In 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

We 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

Optimum 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

Drought 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

We 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

Calcified 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

Of 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

Tumor 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

Clinical 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

A 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

Summary: 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.

image

Change 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

This 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

We 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

The 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

The 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

We 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
Sequence similarity between part of human retinoblastoma susceptibility gene product and a neurofilament protein subunit
Authors: Hong Frank , Lee Wen-Hwa
Published: February 2005

Retinoblastoma, is a highly malignant but readily treatable cancer of the retina, which occurs at an incidence of 1 in 20,000 live births in young children. The retinoblastoma gene that determines susceptibility to this cancer encodes a nuclear phosphoprotein which has been extensively characterized. Yet, to this date, its function remains unknown. We report here that RB amino acids 307–435 shows similarity to the rod domain of the neurofilament L-type subunit (NF-L).
TGF‐β Signaling in Colon Cancer Cells
Authors: Li Fazhi , Cao Yanna , Townsend Courtney M. , Ko Tien C.
Published: February 2005

Transforming growth factor‐betas (TGF‐βs), cytokines expressed in the colon, play important roles as tumor suppressors and tumor promoters during colorectal carcinogenesis. TGF‐β signaling pathway involves activation of Smad2 and Smad3 by the type I receptor and formation of Smad2/3/4 heteromeric complexes that enter the nucleus to regulate transcription. Most human colorectal cancers are resistant to the tumor suppressor effects of TGF‐β, and a subset of human colorectal cancers have mutations in Smad2 and Smad4. The purpose of this study was to determine whether Smads are required for TGF‐β signaling in colon cancer cells. First, we selected a colon cancer cell line (MC‐26) that has a functional TGF‐β signaling pathway. We found that MC‐26 cells expressed Smad2, Smad3, and Smad4 mRNAs by reverse transeription‐polymerase chain reaction and confirmed that the TGF‐β signaling pathway is functional using a transient transfection assay with 3TP‐Lux reporter plasmid. TGF‐β also inhibited cell growth and induced apoptosis in MC‐26 cells. When MC‐26 cells were transiently transfected with dominant‐negative carboxyl‐terminal truncation mutants of Smad2, Smad3, and Smad4, TGF‐β‐induced 3TP‐Lux reporter activity was significantly reduced, suggesting that Smad2, Smad3, and Smad4 are attractive novel therapeutic targets for regulating TGF‐β signaling in colorectal cancers. Because MC‐26 cells express TGF‐β activated Smads, have a functional TGF‐β signaling pathway, and are sensitive to the growth inhibitory and apoptotic effects of TGF‐β, they can serve as an excellent model to examine TGF‐β signaling in colorectal cancers.
Production of the English past tense by children with language comprehension impairments
Authors: NATION KATE , SNOWLING MARGARET J. , CLARKE PAULA
Published: February 2005

Three experiments investigated the ability of eight-year old children with poor language comprehension to produce past tense forms of verbs. Twenty children selected as poor comprehenders were compared to 20 age-matched control children. Although the poor comprehenders performed less well than controls on a range of tasks considered to tap verbal-semantic abilities, the two groups showed equivalent phonological skills. Poor comprehenders performed as well as control children when asked to inflect novel verbs and regular verbs. In contrast, poor comprehenders were less skilled than controls at inflecting both high frequency and low frequency irregular verbs. Although the predominant error pattern for all children was to over-regularize, this was most marked in the poor comprehenders; control children were more likely to produce errors that contained knowledge of the irregular form than poor comprehenders. In addition, the ability to inflect irregular verbs was related to individual differences in verbal-semantic skills. These findings are discussed within a framework in which verb inflection is related to underlying language skills in both the phonological and semantic domains.
Phonological specificity in children at 1;2
Authors: BALLEM KATE D. , PLUNKETT KIM
Published: February 2005

The specificity of infants' phonological representations is examined by comparing their sensitivity to mispronunciations of novel and familiar words, using the preferential looking task. 29 children at 1;2 were trained and tested on familiar and novel word–object pairs. Children showed evidence of sensitivity to mispronunciations of novel and familiar words, indicating detailed phonological representations. Discrepancies between this study and earlier investigations are discussed with reference to differences between habituation and preferential looking tasks.
The relationship between prosodic and syntactic organization in early multiword speech
Authors: BEHRENS HEIKE , GUT ULRIKE
Published: February 2005

Several descriptions of the transition from single to multiword utterances use prosody as an important diagnostic criterion. For example, in contrast to successive single-word utterances, ‘real’ two-word utterances are supposed to be characterized by a unifying intonation contour and a lack of an intervening pause. Research on the acquisition of prosody, however, revealed that control of the phonetic parameters pitch, loudness, and duration is far from complete at such an early stage. In this study, we examine the interaction between the development of different types of syntactic structures and their prosodic organization. Data from a detailed production record of a monolingual German-learning boy is analysed both auditorily and acoustically with a focus on four different types of two-word utterances produced between 2;0 and 2;3. Two major findings are reported here. First, the different types of two-word utterances undergo individual trajectories of prosodic (re-)organization, in part depending on the time course in which they become productive. This suggests that different types of multiword utterances become prosodically fluent at different points in time. Second, the variability of prosodic features such as pauses and stress pattern is very high at the onset of combinatorial speech. Consequently, fluency or disfluency of individual examples should not be used as a reliable criterion for their syntactic status and we recommend caution when taking prosody as a cue for syntactic development.
Productivity and beyond: mastering the Polish genitive inflection
Authors: DĄBROWSKA EWA
Published: February 2005

This study charts the development of the genitive masculine inflection, one of the most irregular parts of the Polish case-marking system. 72 Polish children aged from 2;3 to 10;8 participated in a nonce word production experiment testing their ability to supply the genitive form and their sensitivity to the semantic factors determining the choice of ending. Results indicate that productivity, or the ability to supply the inflected form of some nonce words, emerges early: 78% of the two-year-olds were able to inflect at least one test item. However, mastery, or the ability to consistently supply the correct ending, takes considerably longer to develop, and adultlike levels of provision are not reached until about age 10;0.
‘Word-learning wizardry’ at 1;6
Authors: HOUSTON-PRICE CARMEL , PLUNKETT KIM , HARRIS PAUL
Published: February 2005

This article explores whether infants are able to learn words as rapidly as has been reported for preschoolers. Sixty-four infants aged 1;6 were taught labels for either two moving images or two still images. Each image–label pair was presented three times, after which comprehension was assessed using an adaptation of the intermodal preferential looking paradigm. Three repetitions of each label were found to be sufficient for learning to occur, fewer than has previously been reported for infants under two years. Moreover, contrary to a previous finding, learning was equally rapid for infants who were taught labels for moving versus still images. The findings indicate that infants in the early stages of acquiring a vocabulary learn new word-referent associations with ease, and that the learning conditions that allow such learning are less restricted that was previously believed.
Large constituent families help children parse compounds
Authors: KROTT ANDREA , NICOLADIS ELENA
Published: February 2005

The family size of the constituents of compound words, or the number of compounds sharing the constituents, has been shown to affect adults' access to compound words in the mental lexicon. The present study was designed to see if family size would affect children's segmentation of compounds. Twenty-five English-speaking children between 3;7 and 5;9 were asked to explain the meaning of existing compounds with constituents of varying family size to an alien puppet. The results showed that children were more likely to mention the modifier of compounds if they came from large constituent families than if they came from small constituent families. Other variables were also shown to have some, but smaller effects on children's parsing, including the frequency of the constituent words and the compounds, whether the compounds were already known, and age. These results suggest that children's segmentation of compounds might be facilitated by analogy with other compounds already in their vocabularies.
Maternal responsive and directive behaviours and utterances as predictors of children's lexical development
Authors: MASUR ELISE FRANK , FLYNN VALERIE , EICHORST DOREEN L.
Published: February 2005

Predictive relations were examined between measures of 20 mothers' behavioural and verbal general and specific responsiveness and intrusive and supportive directiveness and their children's subsequent expressive vocabularies during three developmental periods with endpoints at the beginning, middle, and end of the second year: 0;10 to 1;1, 1;1 to 1;5, and 1;5 to 1;9. Regression analyses, controlling for mothers' utterance frequencies and children's initial lexicons, revealed considerable consistency between reported and observed lexicons but changing patterns of predictive relations with development. During the first period, behavioural, but not verbal, measures of maternal responsiveness and supportive directiveness were positively predictive. In period two, verbal, but not behavioural, measures predicted children's vocabularies, with specific responsiveness and supportive directiveness as positive predictors and intrusive directiveness as a negative predictor. During the final period, mothers' behavioural and verbal responsiveness and behavioural supportive directiveness positively predicted and their verbal intrusive directiveness negatively predicted children's lexical growth.
Object name learning and object perception: a deficit in late talkers
Authors: JONES SUSAN S. , SMITH LINDA B.
Published: February 2005

Two experiments examined the relation between early object name learning and the ability to represent objects by their abstract shapes. In Experiment 1, two-year-old children with productive vocabularies in the bottom 20th percentile – ‘late talkers' – were compared with (1) same-age children with larger vocabularies, and (2) younger children matched for productive vocabulary, on their ability to recognize named common objects. Object categories were represented two ways: by lifelike, perceptually rich toys, and by grey caricatures of those objects' abstract shapes. All 3 groups recognized lifelike objects equally well. Both typically-developing control groups were better than late talkers at recognizing shape caricatures of objects whose names they knew. In Experiment 2, late talkers and age-matched controls identified named objects represented by lifelike toys and by duplicates of those toys covered in grey textured paint. Age-matched controls knew more of the object names overall, but both they and the late talkers performed equally well on both kinds of test objects. Thus, late talkers had some difficulty in Experiment 1 recognizing objects from abstract shape cues, but no difficulty in Experiment 2 when the shape cues were realistic. The findings imply a relation between the growth of productive vocabulary and the emergence of the ability to represent object categories by abstract shape.
When children reach beyond their grasp: why some children make pronoun case errors and others don't
Authors: RISPOLI MATTHEW
Published: February 2005

This research addresses the question of why some children are disposed to making a large number of pronoun case errors and others are not. The answer proposed is that when pronoun paradigm building outstrips the development of INFL, children become especially vulnerable to erring in the choice of pronominal word form, resulting in pronoun case error. On the other hand, when pronoun paradigm building proceeds more conservatively, the risk of error is reduced. The spontaneous sentence production of children observed in naturalistic caregiver – child interaction from a cross-section of 44 children (2;0–4;0) is used to support this proposal. The data show that pronoun case error was minimal among children who had strong INFL. However, among children with weak INFL there was a wide range of variation, some children making many errors and others making none. Analysis of variance confirmed that this variation was strongly related to the dispersion of production attempts across an extended pronoun paradigm, such that, the fewer cells attempted, the lower the error rate. These findings show that pronoun case errors are not an inevitable result of grammatical development, but may conceivably be avoided altogether if paradigm building proceeds at a rate commensurate with the child's development of INFL.
The influence of object pre-exposure on two-year-olds' disambiguation of novel labels
Authors: GRAHAM SUSAN A. , TURNER JUANITA N. , HENDERSON ANNETTE M. E.
Published: February 2005

We investigated whether manipulating the perceived novelty of nameless objects would influence two-year-olds' tendency to map novel words to these objects. In Experiment 1, children who had been pre-exposed to target nameless objects were more likely to map novel words onto those objects than children who were not pre-exposed to the objects or children who were pre-exposed to non-target members of the nameless object categories. In Experiment 2, children who were pre-exposed to a nameless object were more likely to assign the novel label to that object than to either a familiar object or an unfamiliar object that had not been pre-exposed. The results of these studies suggest that reducing the novelty of nameless objects increases two-year-olds' tendency to map a novel word to a nameless object.
Testing the role of semantic similarity in syntactic development
Authors: NINIO ANAT
Published: February 2005

The study explored early syntactic development, and tested the hypothesis that children use similarity of meaning in order to move beyond the learning of individual item-based multiword constructions. The first 6 types of verb–object (VO) constructions in Hebrew-speaking children were analysed for the occurrence of transfer of learning and facilitation, as well as for the semantic similarity of the direct objects (DO). Longitudinal naturalistic speech corpora of 20 children (1;06–2;06) were analysed. We found facilitation (increased rate of learning) among the first 6 types of VO constructions (each type built on a different verb) as evidenced by the accelerating growth curves. Next, we measured the semantic similarity of the DOs using an 8-category system including Patient, Theme and Object of Result. The first 6 DO types represented 3·95 different semantic roles. On the average, after the first VO construction was learned, 3 out of the following 5 constructions produced were not preceded by another VO construction where the DO was of the same semantic category. The results indicate that facilitation of learning of early syntax is most probably NOT mediated by semantic similarity.
Multiple sclerosis: MHC associations and therapeutic implications
Authors: Holmes Samantha , Friese Manuel A. , Siebold Christian , Jones E. Yvonne , Bell John , Fugger Lars
Published: February 2005

Multiple sclerosis (MS) is an autoimmune disease with an important genetic component. The strongest genetic association is with the major histocompatibility complex (MHC) region. Several MHC alleles predispose to the disease, the most prominent of which are certain alleles in the HLA-DR2 haplotype. Functional and structural studies have helped to explain the molecular basis of these associations. Although there is currently no curative treatment for MS, an increased understanding of the disease has aided the design of immunotherapies that act on the immune system more specifically than the longstanding drugs. Many of these therapies work at the antigen-specific level, disrupting the interaction between T-cell receptors and MHC molecules that leads to disease.
Chemical weathering in high‐sediment‐yielding watersheds, New Zealand
Authors: Lyons W. Berry , Carey Anne E. , Hicks D. Murray , Nezat Carmen A.
Published: February 2005

We have determined the chemical erosion yields for fifteen watersheds in New Zealand, ranging in size from 12.2 to 2928 km2. These rates, coupled with previously measured physical erosion yields, allow us to compare these two modes of landscape denudation. The physical erosion yields are some of the highest measured in the world. Although in most instances the chemical erosion yields are only a small fraction of the total erosion yields, the absolute values are very high. Our data strongly support the notion that chemical erosion rates are greatly influenced by the yield of physical erosion and that the rapid production of fresh surfaces as a result of high physical erosion rates and subsequent denudation is critical to the high chemical erosion yields observed.
Adiabat_1ph: A new public front‐end to the MELTS, pMELTS, and pHMELTS models
Authors: Smith Paula M. , Asimow Paul D.
Published: February 2005

The program adiabat_1ph is a simple text‐menu driver for subroutine versions of the algorithms MELTS, pMELTS, and pHMELTS [Asimow et al., 2004; Ghiorso et al., 2002; Ghiorso and Sack, 1995]. It may be used to calculate equilibrium assemblages along a thermodynamic path set by the user and can simultaneously calculate trace element distributions. The MELTS family of algorithms is suitable for multicomponent systems, which may be anhydrous, water‐undersaturated, or water‐saturated, with the options of buffering oxygen fugacity and/or water activity. A wide variety of calculations can be performed either subsolidus or with liquid(s) present; melting and crystallization may be batch, fractional, or continuous. The software is suitable for Linux, MacOS X, and Windows, and many aspects of program execution are controlled by environment variables. Perl scripts are also provided that may be used to invoke adiabat_1ph with some command line options and to produce output that may be easily imported into spreadsheet programs, such as Microsoft Excel. Benefits include a batch mode, which allows almost complete automation of the calculation process when suitable input files are written. This technical brief describes version 1.04, which is provided as ancillary material. Binaries, scripts, documentation, and example files for this and future releases may be downloaded at http://www.gps.caltech.edu/∼asimow/adiabat. On a networked computer, adiabat_1ph automatically checks whether a newer version is available.
Three‐dimensional finite difference time domain modeling of the Earth‐ionosphere cavity resonances
Authors: Yang Heng , Pasko Victor P.
Published: February 2005

Comparison of results from a three‐dimensional (3‐D) finite difference time domain (FDTD) model of Schumann resonances (SR) with a set of classical eigenfrequency and quality factor solutions for laterally uniform spherically symmetric Earth‐ionosphere cavity and recent SR observations during solar proton events (SPEs) and X‐ray bursts demonstrate the potential and applicability of the FDTD technique for studies of realistic SR problems.