bluuebunny/crossref_metadata_2025_split huggingface dataset:
Oscillatory crack tip triangular elements for finite element analysis of interface cracks
Authors: Liu C. H. , Huang Chunta 
Published: October 2003

AbstractIn this paper a special crack tip element has been developed in which displacements and stresses have the same behaviour as those of bi‐material interface cracks with open tips. The element degenerates into a traditional triangular quarter point element in cases of homogeneous cracks. An isoparametric co‐ordinate system (ρ, t) is defined in this study, and numerical techniques using these co‐ordinates to evaluate Jacobian matrices, shape function derivatives, and element stiffness matrices are developed. Also, equations calculating the complex stress intensity factor using displacements are obtained in this study. Numerical results are in good agreement with known analytical solutions in two examples. Copyright © 2003 John Wiley & Sons, Ltd.
A new rigid‐viscoplastic model for simulating thermal strain effects in metal‐forming processes
Authors: Dvorkin Eduardo N. , Toscano Rita G. 
Published: October 2003

AbstractA new rigid‐viscoplastic model that includes the effect of thermal strains when modelling steady‐state metal‐forming processes was developed. A symmetric approximation to the resulting non‐symmetric stiffness matrix was derived. The thermo‐mechanical flow formulation was implemented using the pseudo‐concentrations technique. The new formulation was numerically tested showing that it provides reliable results. Copyright © 2003 John Wiley & Sons, Ltd.
Studies in elastic fracture mechanics based on the material force method
Authors: Denzer Ralf , Barth Franz Josef , Steinmann Paul 
Published: October 2003

AbstractThe object of this work is to discuss a further improvement of the material force method for non‐linear hyperelastostatic fracture mechanics. We investigate the accuracy of the material force method within a ‘modified boundary layer’‐formulation using a Ramberg–Osgood material type for the sake of comparison. The proposed improvement leads to a reliable and very accurate method to compute the vectorial J‐integral in fracture mechanics. Copyright © 2003 John Wiley & Sons, Ltd.
Earthquake response analysis in the time domain for 2D soil–structure systems using analytical frequency‐dependent infinite elements
Authors: Kim Doo Kie , Yun Chung‐Bang 
Published: October 2003

AbstractThis paper presents a time domain method for soil–structure interaction analysis under seismic excitations. It is based on the finite element formulation incorporating analytical frequency‐dependent infinite elements for the far‐field soil region. Equivalent earthquake input forces are calculated based on the free‐field responses along the interface between the near‐ and far‐field soil regions using the fixed exterior boundary method in the frequency domain. Then, the input forces are transformed into the time domain by using inverse Fourier transform. The dynamic stiffness matrices of the far‐field soil region formulated using the analytical frequency‐dependent infinite elements in the frequency domain can be easily transformed into the corresponding matrices in the time domain. Hence, the response can be analytically computed in the time domain. A recursive procedure is proposed to compute the interaction forces along the interface and the responses of the soil–structure system in the time domain. Earthquake response analyses have been carried out on a multi‐layered half‐space and a tunnel embedded in a layered half‐space, and results are compared with those obtained by the conventional method in the frequency domain. Copyright © 2003 John Wiley & Sons, Ltd.
Tetrahedral mesh generation based on advancing front technique and optimization scheme
Authors: Choi Woo‐Young , Kwak Dae‐Young , Son Il‐Heon , Im Yong‐Taek 
Published: October 2003

AbstractIn recent years, demand for three‐dimensional simulations has continued to grow in the field of computer‐aided engineering. Especially, in the analysis of forming processes a fully automatic and robust mesh generator is necessary for handling complex geometries used in industry. For three‐dimensional analyses, tetrahedral elements are commonly used due to the advantage in dealing with such geometries. In this study, the advancing front technique has been implemented and modified using an optimization scheme. In this optimization scheme, the distortion metric determines ‘when and where’ to smooth, and serves as an objective function. As a result, the performance of the advancing front technique is improved in terms of mesh quality generated. Copyright © 2003 John Wiley & Sons, Ltd.
Work narratives: Gender and race in professional personhood
Authors: Dombeck Mary‐Therese 
Published: October 2003

AbstractAn ethnographic study was conducted to explore how nurses construe and understand their professional culture and their professional personhood. The sample was 36 nurses ranging in age from 26 to 63 (12 African American women, 11 White women, 13 men 12 White and 1 Caribbean Islander). Data were gathered through participant observation, audiotaped individual conversations, a process of seven consecutive group sessions, and short narratives written by the nurses in group sessions. The data were analyzed: (a) by a coding system that focused on the formal and informal roles, rules, and relationships in work and school settings; and (b) by examining the changes in participants' narratives about their professional identity during the process of the group meetings. All the nurses in the sample had been profoundly affected by the socially accepted “feminine” images of nursing. The findings also revealed racial issues in the nursing profession. The implications of this study point to the need for new models of nursing education and nursing leadership to overcome old images and to make nursing attractive to those from diverse backgrounds. © 2003 Wiley Periodicals, Inc. Res Nurs Health 26:351–365, 2003
Validation of measures of middle schoolers' self‐efficacy for physical and emotional health, and academic tasks
Authors: Bray Christell O. , Nash Kathleen , Froman Robin D. 
Published: October 2003

AbstractThe development and psychometric study of a measure of middle schoolers' perceptions of self‐efficacy for physical, emotional, and academic behaviors appropriate to their age and developmental tasks are described. The validation of the Middle School Self‐Efficacy Questionnaire (MISSE) included the adaptation of existing items and the generation of new ones. Items were subjected to judges' review by two expert panels and were tested with a large, geographically diverse sample of youngsters aged 11–14. Statistical analyses included factor analysis, internal consistency estimations,ttests, and analyses of variance for hypothesis testing related to construct validity. Results showed support for the expected factors and provided evidence of the validity of the MISSE. © 2003 Wiley Periodicals, Inc. Res Nurs Health 26:376–386, 2003
A new methodological approach in nursing research: An actor, partner, and interaction effect model for family outcomes
Authors: Rayens Mary Kay , Svavarsdottir Erla Kolbrun 
Published: October 2003

AbstractMethodological and statistical challenges have been identified in family research when the parental dyad is under study. The purposes of this article are to review the literature on methodological and statistical procedures in research on families, and to introduce an analysis technique that is new to the nursing literature, the actor–partner interdependence model (APIM). The use and interpretation of the APIM method is illustrated through an example of families of young children with asthma. In the APIM an actor effect is the impact a person has on his or her own outcome, whereas a partner effect is the impact a member of a dyad has on his or her partner's outcome. The main findings from the data example indicate that family adaptation is influenced by the actor effect of resiliency factors (sense of coherence and family hardiness), the partner effect of caregiving demands, as well as by both the actor and partner effects of family demands. The APIM method gives new insight into how parental data can be analyzed by taking both the individual and the partner contribution into account when studying family phenomena. Knowing how outcomes may be influenced not only by individuals (via an actor effect) but also by their partners (through a partner effect) enriches our understanding of how families function. © 2003 Wiley Perioicals, Inc. Res Nurs Health 26:409–419, 2003
Alzheimer's disease caregiving information and skills. Part I: Care recipient issues and concerns
Authors: Farran Carol J. , Loukissa Dimitra , Perraud Suzanne , Paun Olimpia 
Published: October 2003

AbstractIncreasing attention has been given to testing clinical trials with family caregivers of the elderly. More recent intervention studies indicated that caregiver skill‐building interventions may be more effective than information/support interventions. Researchers have given considerable attention to the content and support needed by family caregivers, but we know less about how this content and support translates into caregiver skills. This is the first in a series of three articles on a study in which qualitative methods were used to analyze summaries from the group component of a larger caregiver clinical trial. In this article we identify content and skills that dementia family caregivers need in addressing three major care recipient issues and concerns: (a) difficult behaviors and emotional responses, (b) personal and instrumental activities of daily living, and (c) cognitive decline. © 2003 Wiley Periodicals, Inc. Res Nurs Health 26:366–375, 2003
Smoking and adolescence: Narratives of identity
Authors: Johnson Joy L. , Lovato Chris Y. , Maggi Stefania , Ratner Pamela A. , Shoveller Jean , Baillie Lynne , Kalaw Cecilia 
Published: October 2003

AbstractThe purpose of this study was to understand the identities that youth hold in relation to smoking, as revealed in narrative accounts of their smoking experiences. The analysis was a narrative inquiry, a qualitative approach based on the propensity of people to narrate or tell stories about the experiences in their daily lives. A purposeful sample of 35 youths ages 14–18 years with a variety of smoking histories (all had tried smoking) participated in in‐depth interviews. A detailed analysis of the transcripts revealed the key identities communicated by the youths including theconfident nonsmoker, thevulnerable nonsmoker, theardent nonsmoker, theaccepting nonsmoker, thein‐control smoker, theconfirmed smoker, and thecontrite smoker. Tobacco control interventions for youth must be designed to respond to and incorporate multiple smoking identities. © 2003 Wiley Periodicals, Inc. Res Nurs Health 26:387–397, 2003
Adverse events in acute care: An integrative literature review
Authors: Kellogg Victoria A. , Havens Donna Sullivan 
Published: October 2003

AbstractAn integrative literature review was conducted to investigate studies on adverse events reported in medical, health services, and nursing literature. The review was guided by the method proposed by Jackson (1980) and Ganong (1987). Three questions shaped the review: (a) What terms are used to denote adverse events? (b) What purposes drive adverse events research? and (c) What data sources are used to study adverse events? Adverse events was the dominant term, the study of adverse events as an outcome variable was the prevailing research purpose, and monitoring or screening the patient clinical record and self‐reported incidents by health care professionals were the main data sources. Future research is recommended to conceptualize and study adverse events. © 2003 Wiley Periodicals, Inc. Res Nurs Health 26:398–408, 2003
Unfolding of the cold shock protein studied with biased molecular dynamics
Authors: Morra Giulia , Hodoscek Milan , Knapp Ernst‐Walter 
Published: October 2003

AbstractThe cold shock protein from Bacillus caldolyticus is a small β‐barrel protein that folds in a two‐state mechanism. For the native protein and for several mutants, a wealth of experimental data are available on stability and folding, so that it is an optimal system to study this process. We compare data from unfolding simulations (trajectories of 5 and up to 12 ns) obtained with a bias potential at room temperature and from unbiased thermal unfolding simulations with experimental data. The unfolding patterns derived from the trajectories starting from different native‐like conformations and subject to different unfolding conditions agree. The transition state found in the simulations of unfolding is close to the native structure in agreement with experiment. Moreover, a lower value of the free energy barrier of unfolding was found for the mutant R3E than for the mutant E46A and the native protein, as indicated by experimental data. The first unfolding event involves the three‐stranded β‐sheet whose decomposition corresponds to the transition state. In contrast to conclusions drawn from experiments, we found that the two‐stranded β‐strand forms the most stable substructure, which decomposes very late in the unfolding process. However, assuming that this structure forms very early in the folding process, our findings would not contradict the experiments but require a different interpretation of them. Proteins 2003;53:000–000. © 2003 Wiley‐Liss, Inc.
Importance of sequence specificity for predicting protein folding pathways: Perturbed Gaussian chain model
Authors: Kameda Tomoshi 
Published: October 2003

AbstractRecent experimental and theoretical studies suggest that rates and pathways of protein folding are largely decided by topology of the native structures, at least for small proteins. However, some exceptions are known; for example, protein L and protein G have the same topology, but exhibit different characteristics of the TSE. Thus, folding pathways of some proteins are critically affected by detailed information on amino acid sequences. To investigate the sequence specificity, we calculate folding pathways of 20 small proteins using the perturbed Gaussian chain model developed by Portman et al. (Phys Rev Lett 1998;81:5237–5240; J Chem Phys 2001;114:5069–5081). Characteristics of the TSE predicted by the model are in good agreement with experimental ϕ‐value data for many proteins at coarse‐grained level. Especially, estimation of folding TSE for protein G and protein L based on both topology and additional sequence information are consistent with experimental ϕ‐value data. With only topology information, however, the model predicts the TSE of protein G incorrectly. Moreover, the model that uses topology and sequence information describes free energy profiles of two‐state and three‐state folders consistently with experiment, whereas the topology only model predicts free energy profiles of some proteins incorrectly. This indicates that sequence specificity also has critical roles in determining the folding pathways for some proteins. Proteins 2003. © 2003 Wiley‐Liss, Inc.
Atomic contact vectors in protein‐protein recognition
Authors: Mintseris Julian , Weng Zhiping 
Published: October 2003

AbstractThe ability to analyze and compare protein‐protein interactions on the structural level is critical to our understanding of various aspects of molecular recognition and the functional interplay of components of biochemical networks. In this study, we introduce atomic contact vectors (ACVs) as an intuitive way to represent the physico‐chemical characteristics of a protein‐protein interface as well as a way to compare interfaces to each other. We test the utility of ACVs in classification by using them to distinguish between homodimers and crystal contacts. Our results compare favorably with those reported by other authors. We then apply ACVs to mine the PDB for all known protein‐protein complexes and separate transient recognition complexes from permanent oligomeric ones. Getting at the basis of this difference is important for our understanding of recognition and we achieved a success rate of 91% for distinguishing these two classes of complexes. Although accessible surface area of the interface is a major discriminating feature, we also show that there are distinct differences in the contact preferences between the two kinds of complexes. Illustrating the superiority of ACVs as a basic comparison measure over a sequence‐based approach, we derive a general rule of thumb to determine whether two protein‐protein interfaces are redundant. With this method, we arrive at a nonredundant set of 209 recognition complexes—the largest set reported so far. Proteins 2003. © 2003 Wiley‐Liss, Inc.
The tissue factor/factor VIIa/factor Xa complex: A model built by docking and site‐directed mutagenesis
Authors: Norledge Brian V. , Petrovan Ramona J. , Ruf Wolfram , Olson Arthur J. 
Published: October 2003

AbstractFactor X is activated to factor Xa (fXa) in the extrinsic coagulation pathway by the tissue factor (TF)/factor VIIa (fVIIa) complex. Upon activation, the fXa molecule remains associated with the TF/fVIIa complex, and this ternary complex is known to activate protease‐activated receptors (PARs) 1 and 2. Activation of fVII in the TF complex by fXa is also seen at physiologic concentrations. The ternary complexes TF/fVII/fXa, TF/fVIIa/fX, and TF/fVIIa/fXa are therefore all physiologically relevant and of interest as targets for inhibition of both coagulation and cell‐signaling pathways that are important in cardiovascular disease and inflammation. We therefore present a model of the TF/fVIIa/fXa complex, built with the use of the available structures of the TF/fVIIa complex and fXa by protein–protein docking calculations with the program Surfdock. The fXa model has an extended conformation, similar to that of fVIIa in the TF/fVIIa complex, with extensive interactions with TF and the protease domain of fVIIa. All four domains of fXa are involved in the interaction. The gamma‐carboxyglutamate (Gla) and epithelial growth factor (EGF1 and EGF2) domains of fVIIa are not significantly involved in the interaction. Docking of the Gla domain of fXa to TF/fVIIa has been reported previously. The docking results identify potential interface residues, allowing rational selection of target residues for site‐directed mutagenesis. This combination of docking and mutagenesis confirms that residues Glu51 and Asn57 in the EGF1 domain, Asp92 and Asp95 in the EGF2 domain, and Asp 185a, Lys 186, and Lys134 in the protease domain of factor Xa are involved in the interaction with TF/fVIIa. Other fX protease domain residues predicted to be involved in the interaction come from the 160s loop and the N‐terminus of the fX protease domain, which is oriented in such a way that activation of both fVII by fXa, and the reciprocal fX activation by fVIIa, is possible. Proteins 2003;53:000–000. © 2003 Wiley‐Liss, Inc.
Automatic annotation of protein function based on family identification
Authors: Abascal Federico , Valencia Alfonso 
Published: October 2003

AbstractAlthough genomes are being sequenced at an impressive rate, the information generated tells us little about protein function, which is slow to characterize by traditional methods. Automatic protein function annotation based on computational methods has alleviated this imbalance. The most powerful current approach for inferring the function of new proteins is by studying the annotations of their homologues, since their common origin is assumed to be reflected in their structure and function. Unfortunately, as proteins evolve they acquire new functions, so annotation based on homology must be carried out in the context of orthologues or subfamilies. Evolution adds new complications through domain shuffling: homology (or orthology) frequently corresponds to domains rather than complete proteins. Moreover, the function of a protein may be seen as the result of combining the functions of its domains. Additionally, automatic annotation has to deal with problems related to the annotations in the databases: errors (which are likely to be propagated), inconsistencies, or different degrees of function specification. We describe a method that addresses these difficulties for the annotation of protein function. Sequence relationships are detected and measured to obtain a map of the sequence space, which is searched for differentiated groups of proteins (similar to islands on the map), which are expected to have a common function and correspond to groups of orthologues or subfamilies. This mapmaking is done by applying a clustering algorithm based on Normalized cuts in graphs. The domain problem is addressed in a simple way: pairwise local alignments are analyzed to determine the extent to which they cover the entire sequence lengths of the two proteins. This analysis determines both what homologues are preferred for functional inheritance and the level of confidence of the annotation. To alleviate the problems associated with database annotations, the information on all the homologues that are grouped together with the query protein are taken into account to select the most representative functional descriptors. This method has been applied for the annotation of the genome of Buchnera aphidicola (specific host Baizongia pistaciae). Human inspection of the annotations allowed an estimation of accuracy of 94%; the different kinds of error that may appear when using this approach are described. Results can be accessed at http://www.pdg.cnb.uam.es/funcut.html. The programs are available upon request, although installation in other systems may be complicated. Proteins 2003;53:000–000. © 2003 Wiley‐Liss, Inc.
Characterization of the active site of DNA polymerase β by molecular dynamics and quantum chemical calculation
Authors: Rittenhouse Robert C. , Apostoluk Wlodzimierz K. , Miller John H. , Straatsma T. P. 
Published: October 2003

AbstractIt is well established that the fully formed polymerase active site of the DNA repair enzyme, polymerase β (pol β), including two bound Mg2+ cations and the nucleoside triphosphate (dNTP) substrate, exists at only one point in the catalytic cycle just prior to the chemical nucleotidyl transfer step. The structure of the active conformation has been the subject of much interest as it relates to the mechanism of the chemical step and also to the question of fidelity assurance. Although crystal structures of ternary pol β–(primer‐template) DNA–dNTP complexes have provided the main structural features of the active site, they are necessarily incomplete due to intentional alterations (e.g., removal of the 3′OH groups from primer and substrate) needed to obtain a structure from midcycle. Working from the crystal structure closest to the fully formed active site [Protein Data Bank (PDB) code: 1bpy], two molecular dynamics (MD) simulations of the solvated ternary complex were performed: one with the missing 3′OHs restored, via modeling, to the primer and substrate, and the other without restoration of the 3′OHs. The results of the simulations, together with ab initio optimizations on simplified active‐site models, indicate that the missing primer 3′OH in the crystal structure is responsible for a significant perturbation in the coordination sphere of the catalytic cation and allow us to suggest several corrections and additions to the active‐site structure as observed by crystallography. In addition, the calculations help to resolve questions raised regarding the protonation states of coordinating ligands. Proteins 2003;53:000–000. © 2003 Wiley‐Liss, Inc.