bluuebunny/crossref_metadata_2025_split huggingface dataset:
ModView, visualization of multiple protein sequences and
structures
Authors: Ilyin Valentin A. , Pieper Ursula , Stuart Ashley C. , Marti-Renom Marc A. , McMahan Linda , Sali Andrej 
Published: December 2002

Abstract
Summary: We describe ModView, a web application for visualization of multiple protein sequences and structures. ModView integrates a multiple structure viewer, a multiple sequence alignment editor, and a database querying engine. It is possible to interactively manipulate hundreds of proteins, to visualize conservative and variable residues, active and binding sites, fragments, and domains in protein families, as well as to display large macromolecular complexes such as ribosomes or viruses. As a Netscape plug-in, ModView can be included in HTML pages along with text and figures, which makes it useful for teaching and presentations. ModView is also suitable as a graphical interface to various databases because it can be controlled through JavaScript commands and called from CGI scripts.
Availability: ModView is available at http://guitar.rockefeller.edu/modview.
Contact: ilyin@neu.edu, sali@rockefeller.edu
* To whom correspondence should be addressed.
Representation of DNA sequences with virtual potentials and their
processing by (SEQREP) Kohonen self-organizing maps
Authors: Aires-de-Sousa João , Aires-de-Sousa Luisa 
Published: December 2002

Abstract
Motivation: We propose representing individual positions in DNA sequences by virtual potentials generated by other bases of the same sequence. This is a compact representation of the neighbourhood of a base. The distribution of the virtual potentials over the whole sequence can be used as a representation of the entire sequence (SEQREP code). It is a flexible code, with a length independent of the sequence size, does not require previous alignment, and is convenient for processing by neural networks or statistical techniques.
Results: To evaluate its biological significance, the SEQREP code was used for training Kohonen self-organizing maps (SOMs) in two applications: (a) detection of Alu sequences, and (b) classification of sequences encoding for HIV-1 envelope glycoprotein (env) into subtypes A-G. It was demonstrated that SOMs clustered sequences belonging to different classes into distinct regions. For independent test sets, very high rates of correct predictions were obtained (97% in the first application, 91% in the second). Possible areas of application of SEQREP codes include functional genomics, phylogenetic analysis, detection of repetitions, database retrieval, and automatic alignment.
Availability: Software for representing sequences by SEQREP code, and for training Kohonen SOMs is made freely available from http://www.dq.fct.unl.pt/qoa/jas/seqrep
Contact: jas@fct.unl.pt
Supplementary Information: Supplementary material is available at http://www.dq.fct.unl.pt/qoa/jas/seqrep/bioinf2002
* To whom correspondence should be addressed.
Evolutionary algorithms for finding optimal gene sets in microarray prediction
Authors: Deutsch J. M. 
Published: December 2002

Abstract
Motivation: Microarray data has been shown recently to be efficacious in distinguishing closely related cell types that often appear in different forms of cancer, but is not yet practical clinically. However, the data might be used to construct a minimal set of marker genes that could then be used clinically by making antibody assays to diagnose a specific type of cancer. Here a replication algorithm is used for this purpose. It evolves an ensemble of predictors, all using different combinations of genes to generate a set of optimal predictors.
Results: We apply this method to the leukemia data of the Whitehead/MIT group that attempts to differentially diagnose two kinds of leukemia, and also to data of Khan et al. to distinguish four different kinds of childhood cancers. In the latter case we were able to reduce the number of genes needed from 96 to less than 15, while at the same time being able to classify all of their test data perfectly. We also apply this method to two other cases, Diffuse large B-cell lymphoma data (Shipp et al., 2002), and data of Ramaswamy et al. on multiclass diagnosis of 14 common tumor types.
Availability: http://stravinsky.ucsc.edu/josh/gesses/
Contact: josh@physics.ucsc.edu
* To whom correspondence should be addressed.
Topology optimization of fluids in Stokes flow
Authors: Borrvall Thomas , Petersson Joakim 
Published: December 2002

AbstractWe consider topology optimization of fluids in Stokes flow. The design objective is to minimize a power function, which for the absence of body fluid forces is the dissipated power in the fluid, subject to a fluid volume constraint. A generalized Stokes problem is derived that is used as a base for introducing the design parameterization. Mathematical proofs of existence of optimal solutions and convergence of discretized solutions are given and it is concluded that no regularization of the optimization problem is needed. The discretized state problem is a mixed finite element problem that is solved by a preconditioned conjugate gradient method and the design optimization problem is solved using sequential separable and convex programming. Several numerical examples are presented that illustrate this new methodology and the results are compared to results obtained in the context of shape optimization of fluids. Copyright © 2003 John Wiley & Sons, Ltd.
Options on bond futures: Isolating the risk premium
Authors: Tompkins Robert G. 
Published: December 2002

AbstractThe introduction of unspanned sources of risk (and frictions) implies that option prices include a
risk premium. Prima facie evidence of the existence of risk premia in option prices is contained in the implied
volatility smile patterns reported in the literature. This article isolates the risk premium (defined as the
simple difference between estimated and observed option prices) on options on U.K. Gilts, German Bunds, and
U.S. Treasury bond futures using models that include price jumps and stochastic volatility. This study finds that
single and multi‐factor stochastic volatility models with jumps may explain the empirical regularities
observed in bond futures. © 2003 Wiley Periodicals, Inc. Jrl Fut Mark 23:169–215, 2003
The economic advantage of learners in a spot/futures market
Authors: Linn Scott C. , Stanhouse Bryan E. 
Published: December 2002

AbstractThis article examines the economic advantage of learners in a futures market. We develop a dynamic model of
learning in which a spot market and futures market both exist for a real good. The economy is composed of
producers who can engage in hedging activities, speculators who trade in the futures market, and consumers who are
described by an inverse demand function for the underlying commodity. Producers and speculators are heterogeneous
and are differentiated based upon the predictive equations they employ when formulating forecasts of next
period's spot price. We derive the dynamic rational‐expectations equilibrium of the model and show
that learners enjoy an economic advantage in the futures market. © 2003 Wiley Periodicals, Inc. Jrl Fut Mark
23:151–167, 2003
Adult day service use and reductions in caregiving hours: effects on stress and psychological well‐being for dementia caregivers
Authors: Gaugler Joseph E. , Jarrott Shannon E. , Zarit Steven H. , Stephens Mary‐Ann Parris , Townsend Aloen , Greene Rick 
Published: December 2002

AbstractBackgroundThe objective of this study was to determine whether adult day service use interacts with decreases in primary caregiving hours (i.e. the time caregivers spent on activities of daily living/instrumental activities of daily living, memory problems, and behavior problems for patients) to alleviate caregiver stress and negative mental health over time.MethodsThree‐month longitudinal data from the Adult Day Care Collaborative Study (n=400) were used.ResultsDecreases in memory problem hours among adult day service users were associated with reduced feelings of role overload; decreases in ADL hours among non‐users were associated with decreases in worry and strain over a three‐month period.ConclusionThe findings suggest that adult day services are potentially effective in restructuring caregiving time and providing respite to family members. Copyright © 2002 John Wiley & Sons, Ltd.
Vulnerability to neuroleptic side effects in frontotemporal lobar degeneration
Authors: Pijnenburg Y. A. L. , Sampson E. L. , Harvey R. J. , Fox N. C. , Rossor M. N. 
Published: December 2002

AbstractBackgroundFrontotemporal lobar degeneration (FTLD) is commonly associated with behavioural disturbances such as disinhibition and aggression; these often result in the use of neuroleptic medication.MethodsAll available case notes of patients attending a specialist cognitive disorders clinic with a diagnosis of FTLD were selected. This gave 100 subjects (62 male, 38 female).ResultsIn 61 patients significant behavioural disturbances were present. Of these patients, 24 had been prescribed neuroleptics. Significant extrapyramidal side effects were reported in eight patients (33%); in five patients these were severe enough to cause severe mobility problems and in one patient resulted in impaired consciousness. In some instances the extrapyramidal side effects took weeks to wear off.ConclusionThese results suggest that patients with FTLD may, as in Lewy body dementia, be particularly sensitive to the extrapyramidal side effects of neuroleptics. We suggest that neuroleptics should be used cautiously in FTLD and treatment should be started at low doses avoiding depot preparations until further prospective studies have been performed. Copyright © 2002 John Wiley & Sons, Ltd.
On the vibrations of a plate with a concentrated mass and very small thickness
Authors: Gómez D. , Lobo M. , Pérez E. 
Published: December 2002

AbstractWe consider the vibrations of an elastic plate that contains a small region whose size depends on a small parameter ε. The density is of order O(ε–m) in the small region, the concentrated mass, and it is of order O(1) outside; m is a positive parameter. The thickness plate h being fixed, we describe the asymptotic behaviour, as ε→O, of the eigenvalues and eigenfunctions of the corresponding spectral problem, depending on the value of m: Low‐ and high‐frequency vibrations are studied for m>2. We also consider the case where the thickness plate h depends on ε; then, different values of m are singled out. Copyright © 2003 John Wiley & Sons, Ltd.
Ab initio and experimental study on thermally degradable polycarbonates: Effect of structure on reactivity
Authors: Van Speybroeck V. , Waroquier M. , Martelé Y. , Schacht E. 
Published: December 2002

AbstractThe thermal degradation process of some new synthesized polycarbonates is studied both from theoretical and experimental points of view to obtain microscopic insight into the factors that govern the reaction rates. Ab initio density functional theory calculations are performed on a set of carbonates, which are model systems for the polycarbonates. Kinetic parameters are determined by transition‐state theory and compared with experimental‐derived degradation temperatures. The study as presented here gives evidence of the existence of a correlation between these degradation temperatures and the reaction rates resulting from static ab initio calculations on small model systems that are representative for the active area of the degradation process. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2003
Oligothiophene radical cations: Polaron structure in hybrid DFT and MP2 calculations
Authors: Geskin V. M. , Dkhissi A. , Brédas J. L. 
Published: December 2002

AbstractWe investigate the geometric and electronic structure of radical cations in oligothiophene chains by performing hybrid DFT (BHandHLYP) calculations on chains with up to 13 thiophene rings and ab initio MP2 calculations. The BHandHLYP‐optimized structures indicate a self‐localization of charge, spin, and geometric distortion around the middle of the chain, i.e., the formation of a polaron even in the case of the longer chains. This result contrasts with previous pure DFT findings that indicate complete delocalization of the radical cation over the whole chain. The MP2‐optimized structure of octathiophene, an oligomer long enough to allow for possible polaron formation, confirms the presence of a well‐localized polaron structure, similar to that obtained at the Hartree–Fock level. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002
Density functional study of nitroprusside: Mechanism of the photochemical formation and deactivation of the metastable states
Authors: Buchs M. , Daul C. A. , Manoharan P. T. , Schläpfer C. W. 
Published: December 2002

AbstractIn this article, we present a theoretical investigation about the mechanism of the photochemical formation and deactivation of the metastable states observed in nitroprusside ions. The quantum chemical calculations are based on density functional theory. The peculiar photochemical and photophysical behavior of this molecule has attracted chemists' interest for a while. Due to this interest, many details on the nature of nitroprusside's ground state and its two metastable states were known. However, a clear picture of the reaction pathways between the three minima on the ground‐state potential energy curve was still missing. By studying the excited states corresponding to all three minima, we could set up, in this work, a model explaining the photochemistry and photophysics responsible for the population of the three different states on the ground‐state potential energy curve. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2003
Breathing modes of 2‐D quantum dots with elliptical shape in magnetic fields
Authors: Serra Llorenç , Puente Antonio , Lipparini Enrico 
Published: December 2002

AbstractThe characteristics of the breathing modes of 2‐D dots are theoretically investigated as a function of the dot elliptical deformation and intensity of an applied perpendicular magnetic field. Analytic results obtained by neglecting the interelectron Coulomb interaction are compared with numerical results including interactions within the time‐dependent local spin density approximation. The existence of four characteristic E0 modes and the evolution of their oscillator strength with both deformation and magnetic field are discussed. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002
DFT analysis of fluctuations in electronegativity and hardness of a molecular oscillator
Authors: Komorowski Ludwik , Ordon Piotr 
Published: December 2002

AbstractThis work extends application of the density functional theory apparatus to the analysis of thermal fluctuations. It focuses on expectations concerning the role of molecular deformation in changing the global hardness and electronegativity (chemical potential), and hence, the affinity for an intermolecular electron exchange. Molecular harmonic oscillations, the most common molecular deformations, have been analyzed in detail to discover the circumstances, leading to significant modifications in electronegativity and hardness of the molecule. The mean fluctuations of electronegativity and global hardness have been analyzed for a harmonic oscillator. The nuclear reactivity and nuclear stiffness indices have been explored in calculation of thermal fluctuations for any system, harmonic as well as anharmonic. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2003
Ab initio electrical conductance of a molecular wire
Authors: Baer Roi , Neuhauser Daniel 
Published: December 2002

AbstractA method is developed for computing the direct current and alternating current conductance of molecular wires at small bias. The basic ingredients are: linear response theory, time‐dependent density functional theory, imaginary potentials, and a jellium model for the metallic leads. The theory is capable of incorporating the effect of realistic charge distributions in the system and electron–electron correlation. We demonstrate the method on the jellium–C3–jellium system. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2003
A non‐standard J‐spectral factorization of rational matrices via zero compensator approach
Authors: Kawamoto Atsushi , Katayama Tohru 
Published: December 2002

AbstractThis paper deals with a non‐standard J‐spectral factorization problem (NS‐J‐SFP) that arises in he non‐standard H∞ control problem for a descriptor system. We derive the solvability conditions for the NS‐J‐SFP by adapting the zero compensation technique due to Copeland and Safonov (Internat. J. Robust Nonlinear Control 1992; 2:139) to the descriptor system. It is also shown that the solvability conditions of the NS‐J‐SFP are equivalent to the existence of a semi‐stabilizing solution of a generalized algebraic Riccati equation. Copyright © 2002 John Wiley & Sons, Ltd.
Can Home Visitation Enhance Maternal Social Support?
Authors: McCurdy Karen 
Published: December 2002

AbstractThis study investigates the impacts of Healthy Start, a statewide, home visitation program, on the social support systems of 212 disadvantaged mothers in Oahu, Hawaii. Maternal support was assessed at the time these mothers gave birth and 12 months later with the Maternal Social Support Index. Comparisons of mothers randomly assigned to visited (n = 108) or nonvisited (n = 104) conditions uncover few differences on structural or affiliational aspects of support after 12 months. Visited mothers, however, are significantly less likely to report a decline in satisfaction with a close adult than nonvisited mothers do. The discussion examines the challenges of fostering social support and the ability of home visitation efforts to achieve this outcome.
The role of chaperone‐assisted folding and quality control in inborn errors of metabolism: Protein folding disorders
Authors: Gregersen N. , Bross P. , Andresen B. S. , Pedersen C. B. , Corydon T. J. , Bolund L. 
Published: December 2002

AbstractMolecular chaperones are present in the various compartments of the cell and assist the folding of newly synthesized proteins. Compared to wild‐type proteins, missense mutant proteins are generally synthesized in a normal fashion, but may be impaired in their folding. A broad array of diseases that are due to misfolding of mutant proteins may be labelled conformational diseases: aggregation diseases, such as Alzheimer disease; diseases caused by negative dominance from misfolded structural proteins, such as hypertrophic cardiomyopathy; and disorders where the misfolded protein is degraded by intracellular proteases. Many metabolic disorders belong to this last category, where the so‐called protein quality control systems, comprising chaperones and proteases, attempt to eliminate folding intermediates or misfolded proteins. On the basis of in vitro experiments with a limited number of missense mutations identified in patients with phenylalanine hydroxylase and fatty acid oxidation deficiencies, we discuss the cellular fate of missense mutant proteins. We find that the balance between folding to functional conformers, retention (holding) and degradation of folding intermediates or misfolded proteins is dependent on the nature of the mutation and on the efficiency of the quality control. For example, low temperature may promote formation of functional conformers, while elevated temperature usually promotes retention and degradation. We conclude that disorders caused by many missense mutations are complex diseases in which the mutation itself is a necessary major primary component, but that its effect may be modified by cellular conditions and possibly by genetic variations in the quality control systems. We suggest that this new knowledge about cell handling may open new avenues of understanding of the cell pathology and treatment of patients with metabolic disorders.
The Psychological Sense of Economic Hardship: Measurement Models, Validity, and Cross‐Ethnic Equivalence for Urban Families
Authors: Barrera Manuel , Caples Heather , Tein Jenn-Yun 
Published: December 2002

AbstractPoverty is a community stressor that disproportionally affects ethnic minority families. One aspect of programmatic research on poverty focuses on the psychological sense of economic hardship. In a study of 319 African American, European American, and Mexican American urban families, parents completed objective measures of economic status and scales of perceived economic hardship that were adapted from previous research. Measurement models identified a coherent construct of psychological sense of economic hardship that was essentially equivalent for mothers and fathers, English‐ and Spanish‐speaking Mexican Americans, and the 3 ethnic groups. In support of the validity of this construct, relations between objective indicators of economic status and perceived economic hardship showed equivalence across these same groups.
Diagnosis of mitochondrial disorders: Clinical and biochemical approach
Authors: Thorburn D. R. , Smeitink J. 
Published: December 2002

AbstractThe topic of Workshop W3‐1 was clinical and biochemical approaches to the diagnosis of mitochondrial respiratory chain disorders. Four main questions were addressed in an attempt to make some progress towards a consensus diagnostic approach: What are the major limitations in diagnosis of respiratory chain dysfunction? What is the ideal approach to investigating children with a suspected respiratory chain disorder? Can we begin to develop consensus diagnostic criteria? Can we develop a quality assurance (QA) scheme for respiratory chain enzyme assays? The workshop demonstrated strong consensus on recognizing the limitations of current diagnostic approaches, on the ideal diagnostic approach and on the desirability of an enzyme QA scheme. There was also support for the desirability of consensus diagnostic criteria, albeit with some concerns about the practicality of gaining consensus. Two potential approaches to developing consensus criteria were described.
Life Stressors, Social Support, and Depressive Symptoms Among First‐Time Welfare Recipients
Authors: Kalil Ariel , Born Catherine E. , Kunz James , Caudill Pamela J. 
Published: December 2002

AbstractThis paper examines the associations among stressful life events, social support, and depressive symptoms in a sample of 580 first‐time welfare recipients. Self‐reported number of depressive symptoms was greater than in corresponding community samples. Stressors and social supports made independent main effect contributions to depressive symptoms in a multiple regression analysis. Women with transportation barriers to employment, those experiencing greater numbers of stressful life events, and those who were less satisfied with their housing situation reported greater numbers of depressive symptoms. In contrast, women who were more satisfied with their social support and those with higher attendance at religious services reported fewer depressive symptoms. Implications for welfare reform policy and programs are discussed.