bluuebunny/crossref_metadata_2025_split huggingface dataset:
Heterotachy and Functional Shift in Protein Evolution
Authors: Philippe Hervé , Casane Didier , Gribaldo Simonetta , Lopez Philippe , Meunier Julien 
Published: July 2003

AbstractStudy of structure/function relationships constitutes an important field of research, especially for modification of protein function and drug design. However, the fact that rational design (i.e. the modification of amino acid sequences by means of directed mutagenesis, based on knowledge of the three‐dimensional structure) appears to be much less efficient than irrational design (i.e. random mutagenesis followed by in vitro selection) clearly indicates that we understand little about the relationships between primary sequence, three‐dimensional structure and function. The use of evolutionary approaches and concepts will bring insights to this difficult question. The increasing availability of multigene family sequences that has resulted from genome projects has inspired the creation of novel in silico evolutionary methods to predict details of protein function in duplicated (paralogous) proteins. The underlying principle of all such approaches is to compare the evolutionary properties of homologous sequence positions in paralogs. It has been proposed that the positions that show switches in substitution rate over time‐‐i.e., 'heterotachous sites'‐‐are good indicators of functional divergence. However, it appears that heterotachy is a much more general process, since most variable sites of homologous proteins with no evidence of functional shift are heterotachous. Similarly, it appears that switches in substitution rate are as frequent when paralogous sequences are compared as when orthologous sequences are compared. Heterotachy, instead of being indicative of functional shift, may more generally reflect a less specific process related to the many intra‐ and inter‐molecular interactions compatible with a range of more or less equally viable protein conformations. These interactions will lead to different constraints on the nature of the primary sequences, consistently with theories suggesting the non‐independence of substitutions in proteins. However, a specific type of amino acid variation might constitute a good indicator of functional divergence: substitutions occurring at positions that are generally slowly evolving. Such substitutions at constrained sites are indeed much more frequent soon after gene duplication. The identification and analysis of these sites by complementing structural information with evolutionary data may represent a promising direction to future studies dealing with the functional characterization of an ever increasing number of multi‐gene families identified by complete genome analysis. IUBMB Life, 55: 257‐265, 2003
Medical Diagnosis by High Resolution NMR of Human Specimens
Authors: Smith Ian , Baert Racquel 
Published: July 2003

AbstractNMR has progressed relatively recently from a technique used almost exclusively by chemists and physicists to a viable tool for medical diagnosis. NMR applications have developed from analysis of cells, tissues, and biological fluids, to in vivo analysis. We discuss some examples of its clinical successes, as well as some of the challenges encountered along the way. IUBMB Life, 55: 273‐277, 2003
4D Bioinformatics: A New Look at the Ribosome as an Example
Authors: Quon Gerald , Gordon Paul , Sensen Christoph 
Published: July 2003

AbstractWe have adapted the Java Molecular Viewer (JMV) to virtual reality display environments, through a number of extensions to the Java 3D code. Phylogenetic information derived from multiple alignments (temporal information) can be overlaid onto molecule structures (spatial information). The number of sequences included in the underlying multiple alignment can be changed instantaneously, resulting in dynamical updates of the displayed information. JMV was also extended to handle an infinite number of objects (molecules) in the same display. The objects can be manipulated in six degrees of freedom simultaneously or independently. We have used the small subunit ribosomal RNA to demonstrate the system (http://cave.ucalgary.ca), which can be used for any molecule with a resolved structure. IUBMB Life, 55: 279‐283, 2003
Two-dimensional magic numbers in mass abundances of photofragmented bimetallic clusters
Authors: Janssens Ewald , Tanaka Hiromasa , Neukermans Sven , Silverans Roger E , Lievens Peter 
Published: July 2003

The stability of cationic gold clusters doped with one transition metal atom was investigated by a mass spectrometric analysis of fragments resulting from high fluence irradiation of a cluster beam. Strongly enhanced abundances are found for Au5X+, X = V, Mn, Cr, Fe, Co, Zn, which implies that these species are far more stable towards fragmentation than their neighbouring cluster sizes. Here we interpret the enhanced stability of these clusters within a shell model approach for two-dimensional (2D) systems: the number of delocalized electrons in Au5X+is six, which is a magic number for 2D systems. Quantum chemical calculations for AuNZn+(N= 2-6) predict planar structures that are stabilized by the influence of the dopant atom. Also, the main features of the calculated molecular orbitals are well reproduced by a simple electron-in-a-box model. The present report constitutes the first observation of 2D magic numbers in size dependent properties of metal clusters.
Welfare Effects of Transparency in Foreign Exchange Markets: the Role of Hedging Opportunities
Authors: Drees Burkhard , Eckwert Bernhard 
Published: July 2003

AbstractThe paper studies the impact of more transparency on the risk‐sharing opportunities in the foreign exchange market and the associated implications on ex ante welfare. Transparency is measured in this model by the informational content of publicly observable signals about exchange rate developments. The authors find that in this model more transparency improves welfare in economies that are poorly endowed with capital and/or where investors are not very risk‐averse, while welfare is reduced in economies with large capital endowments and/or where investors are highly risk‐averse.
Growing Trade in Intermediate Goods: Outsourcing, Global Sourcing, or Increasing Importance of MNE Networks?
Authors: Kleinert Jörn 
Published: July 2003

AbstractGrowth in trade is often seen to have played a dominant role in integrating national economies. Analyses of this role have, however, almost exclusively been based on trade in final goods. This paper attempts to address this problem by analyzing recent growth in intermediate goods. Three possible causes are posited for this growth: outsourcing, global sourcing, and the increasing importance of MNE networks. These are examined in two analytical frameworks: one using OECD input–output table data and one using German time‐series data. Results from both frameworks give strong support to the hypothesis that international production plays a great role in explaining the strong increase in intermediate inputs imports of developed countries. The evidence for the hypothesis that the increasing importance of the MNE network causes the growing trade in intermediate goods is especially strong. The outsourcing hypothesis receives also some support.
Market Size and Economic Integration when Labor Markets are Unionized
Authors: Piperakis Andromachi S. , Hine Robert C. , Wright Peter W. 
Published: July 2003

AbstractThe paper explores the effects of economic integration on trade, wages, and welfare when market sizes differ. A duopoly model with two‐way intraindustry trade in similar products and with unionized labor markets is employed. It is confirmed that, for a wide range of different relative market sizes, integration leads to higher wages, employment, and welfare. However, where market sizes differ widely, the reduction of trade barriers leads to a reduction of wages, employment, and—in some circumstances—welfare in the country with the large market.
Strategic Environmental Policies when Waste Products are Tradable
Authors: Cassing James , Kuhn Thomas 
Published: July 2003

AbstractThe paper deals with international trade in hazardous waste products when there is an international oligopoly market for waste, and both waste‐importing and waste‐exporting countries act strategically to utilize national environmental policies to attach rents arising from trade in waste. The authors model a multiple‐stage game where waste is generated in an industrialized country as a byproduct of production, and potentially is exported to some less‐developed countries, if not abated locally, or imposed on local residents at a cost of an environmental tax. In the market for waste, an oligopolistic supply is assumed. The demand for waste is perfectly competitive, with waste‐processing firms guided by marginal disposal costs and environmental taxes levied by foreign countries. With each country playing Nash, the analysis finds domestic and foreign taxes to be distorted from the Pigouvian taxes in such a way that the domestic (waste‐exporter) tax rate is set below, and the foreign tax rate is set above, the Pigouvian taxes. However, a global welfare optimum requires tax distortions in the opposite direction, in the sense that foreign environmental taxes must be set below the Pigouvian tax rate.
Economic Integration and Regional Income Inequalities: Competing Dynamics of Regional Wages and Innovative Capabilities
Authors: Bellone Flora , Maupertuis Marie‐Antoinette 
Published: July 2003

AbstractA factor‐price difference scenario has recently been used by Krugman and Venables and by Puga to explain why, in the absence of labor migrations, economic integration should first produce and then dissolve regional income inequalities. The authors question this scenario in a dynamic analysis framework that extends the Baldwin, Martin, and Ottaviano ones to allow for regional wage differences. In this context, wage flexibility is no more a sufficient condition to induce long‐run convergence. Indeed, when regions are equally sized, the innovative capability advantage of the “core” outweighs the wage cost advantage of the “periphery” even for very low transport costs, and regional wage gaps are likely to persist in the long run.
European Sector Returns and Capital Market Integration
Authors: Oh Yonghyup 
Published: July 2003

AbstractThe paper tests European capital market integration at the sector level. It examines the recent trend of sector‐level returns for four European countries, France, Germany, Italy, and the UK, using “return on assets” of a panel of listed firms of these countries for the period 1988–95. Initial findings suggest that sector returns have converged across countries over time. However, when integration is tested within a capital‐asset pricing model framework, the country effect remains strong. The overall results support the view that European capital market integration is under way, but is far from complete.
Emigration and the Optimal Speed of Transition
Authors: Papapanagos Harry , Sanfey Peter 
Published: July 2003

AbstractThe paper presents a model of labor reallocation in a transition economy and analyzes the determinants of the optimal speed of transition. The model is extended to consider the effect of emigration flows from the transition country. In general, a rapid rather than slow pace of restructuring is preferable in the long run, but an initial period of gradualism may be optimal. The authors conclude that emigration, by improving the rate of job creation in the private sector and by reducing the burden of unemployment on the government, may lead to an earlier switch to rapid adjustment of labor, and hence to a faster transition to a market economy.
International Tax Competition: There is No Need for Cooperation in Information Sharing
Authors: Makris Miltiadis 
Published: July 2003

AbstractA model is investigated in which small open economies choose the degree of information exchange among tax authorities and an unrestricted set of capital income taxes. The author shows that cooperation in information sharing does not matter in equilibrium outcomes. This comes in striking contrast to existing results and the common belief among policy practitioners. The reason for this result is that if the set of distortionary taxes is unrestricted then, depending on the characteristics of the economy, either information sharing becomes redundant or the non‐cooperative equilibrium is characterized by zero information exchange and overprovision of information.
Book Reviews
Authors: Aksoy Yunus , Hoffmeyer Erik , Faini Riccardo , Eckel Carsten 
Published: July 2003

Books reviewed in this article:Richard Friberg, Exchange Rates and the Firm: Strategies to Manage Exposure and the Impact of EMUStephen Cecchetti, Hans Genberg, John Lipsky, and Sunil Wadhwani, Asset Prices and Central Bank PolicyMichael J. Greenwood and John M. McDowell, Legal U.S. Immigration: Influences on Gender, Age, and Skill CompositionPontus Braunerhjelm, Riccardo Faini, Victor Norman, Frances Ruane, and Paul Seabright, Integration and the Regions of Europe: How the Right Policies Can Prevent Polarization
A Theory of Statistical Models for Monte Carlo Integration
Authors: Kong A. , McCullagh P. , Meng X.-L. , Nicolae D. , Tan Z. 
Published: July 2003

SummaryThe task of estimating an integral by Monte Carlo methods is formulated as a statistical model using simulated observations as data. The difficulty in this exercise is that we ordinarily have at our disposal all of the information required to compute integrals exactly by calculus or numerical integration, but we choose to ignore some of the information for simplicity or computational feasibility. Our proposal is to use a semiparametric statistical model that makes explicit what information is ignored and what information is retained. The parameter space in this model is a set of measures on the sample space, which is ordinarily an infinite dimensional object. None-the-less, from simulated data the base-line measure can be estimated by maximum likelihood, and the required integrals computed by a simple formula previously derived by Vardi and by Lindsay in a closely related model for biased sampling. The same formula was also suggested by Geyer and by Meng and Wong using entirely different arguments. By contrast with Geyer's retrospective likelihood, a correct estimate of simulation error is available directly from the Fisher information. The principal advantage of the semiparametric model is that variance reduction techniques are associated with submodels in which the maximum likelihood estimator in the submodel may have substantially smaller variance than the traditional estimator. The method is applicable to Markov chain and more general Monte Carlo sampling schemes with multiple samplers.
Bayesian Inversion of Geoelectrical Resistivity Data
Authors: Andersen Kim E. , Brooks Stephen P. , Hansen Martin B. 
Published: July 2003

SummaryEnormous quantities of geoelectrical data are produced daily and often used for large scale reservoir modelling. To interpret these data requires reliable and efficient inversion methods which adequately incorporate prior information and use realistically complex modelling structures. We use models based on random coloured polygonal graphs as a powerful and flexible modelling framework for the layered composition of the Earth and we contrast our approach with earlier methods based on smooth Gaussian fields. We demonstrate how the reconstruction algorithm may be efficiently implemented through the use of multigrid Metropolis–coupled Markov chain Monte Carlo methods and illustrate the method on a set of field data.
Estimation of Dependence Between Paired Correlated Failure Times in the Presence of Covariate Measurement Error
Authors: Gorfine Malka , Hsu Li , Prentice Ross L. 
Published: July 2003

SummaryIn many biomedical studies, covariates are subject to measurement error. Although it is well known that the regression coefficients estimators can be substantially biased if the measurement error is not accommodated, there has been little study of the effect of covariate measurement error on the estimation of the dependence between bivariate failure times. We show that the dependence parameter estimator in the Clayton–Oakes model can be considerably biased if the measurement error in the covariate is not accommodated. In contrast with the typical bias towards the null for marginal regression coefficients, the dependence parameter can be biased in either direction. We introduce a bias reduction technique for the bivariate survival function in copula models while assuming an additive measurement error model and replicated measurement for the covariates, and we study the large and small sample properties of the dependence parameter estimator proposed.
An Empirical Likelihood Goodness-of-Fit Test for Time Series
Authors: Chen Song Xi , Härdle Wolfgang , Li Ming 
Published: July 2003

SummaryStandard goodness-of-fit tests for a parametric regression model against a series of nonparametric alternatives are based on residuals arising from a fitted model. When a parametric regression model is compared with a nonparametric model, goodness-of-fit testing can be naturally approached by evaluating the likelihood of the parametric model within a nonparametric framework. We employ the empirical likelihood for an α-mixing process to formulate a test statistic that measures the goodness of fit of a parametric regression model. The technique is based on a comparison with kernel smoothing estimators. The empirical likelihood formulation of the test has two attractive features. One is its automatic consideration of the variation that is associated with the nonparametric fit due to empirical likelihood's ability to Studentize internally. The other is that the asymptotic distribution of the test statistic is free of unknown parameters, avoiding plug-in estimation. We apply the test to a discretized diffusion model which has recently been considered in financial market analysis.
Reversible Jump, Birth-and-Death and More General Continuous Time Markov Chain Monte Carlo Samplers
Authors: Cappé Olivier , Robert Christian P. , Rydén Tobias 
Published: July 2003

SummaryReversible jump methods are the most commonly used Markov chain Monte Carlo tool for exploring variable dimension statistical models. Recently, however, an alternative approach based on birth-and-death processes has been proposed by Stephens for mixtures of distributions. We show that the birth-and-death setting can be generalized to include other types of continuous time jumps like split-and-combine moves in the spirit of Richardson and Green. We illustrate these extensions both for mixtures of distributions and for hidden Markov models. We demonstrate the strong similarity of reversible jump and continuous time methodologies by showing that, on appropriate rescaling of time, the reversible jump chain converges to a limiting continuous time birth-and-death process. A numerical comparison in the setting of mixtures of distributions highlights this similarity.
The Identifiability of the Mixed Proportional Hazards Competing Risks Model
Authors: Abbring Jaap H. , Van Den Berg Gerard J. 
Published: July 2003

SummaryWe prove identification of dependent competing risks models in which each risk has a mixed proportional hazard specification with regressors, and the risks are dependent by way of the unobserved heterogeneity, or frailty, components. We show that the conditions for identification given by Heckman and Honoré can be relaxed. We extend the results to the case in which multiple spells are observed for each subject.
Likelihood Methods for Missing Covariate Data in Highly Stratified Studies
Authors: Rathouz Paul J. 
Published: July 2003

SummaryThe paper considers canonical link generalized linear models with stratum-specific nuisance intercepts and missing covariate data. This family includes the conditional logistic regression model. Existing methods for this problem, each of which uses a conditioning argu- ment to eliminate the nuisance intercept, model either the missing covariate data or the missingness process. The paper compares these methods under a common likelihood framework. The semiparametric efficient estimator is identified, and a new estimator, which reduces dependence on the model for the missing covariate, is proposed. A simulation study compares the methods with respect to efficiency and robustness to model misspecification.
Efficient Design of Experiments in the Monod Model
Authors: Dette Holger , Melas Viatcheslav B. , Pepelyshev Andrey , Strigul Nikolai 
Published: July 2003

SummaryEstimation and experimental design in a non-linear regression model that is used in microbiology are studied. The Monod model is defined implicitly by a differential equation and has numerous applications in microbial growth kinetics, water research, pharmacokinetics and plant physiology. It is proved that least squares estimates are asymptotically unbiased and normally distributed. The asymptotic covariance matrix of the estimator is the basis for the construction of efficient designs of experiments. In particular locally D-, E- and c-optimal designs are determined and their properties are studied theoretically and by simulation. If certain intervals for the non-linear parameters can be specified, locally optimal designs can be constructed which are robust with respect to a misspecification of the initial parameters and which allow efficient parameter estimation. Parameter variances can be decreased by a factor of 2 by simply sampling at optimal times during the experiment.
Bayesian Inference for Non-Stationary Spatial Covariance Structure via Spatial Deformations
Authors: Schmidt Alexandra M. , O'Hagan Anthony 
Published: July 2003

SummaryIn geostatistics it is common practice to assume that the underlying spatial process is stationary and isotropic, i.e. the spatial distribution is unchanged when the origin of the index set is translated and under rotation about the origin. However, in environmental problems, such assumptions are not realistic since local influences in the correlation structure of the spatial process may be found in the data. The paper proposes a Bayesian model to address the anisot- ropy problem. Following Sampson and Guttorp, we define the correlation function of the spatial process by reference to a latent space, denoted by D, where stationarity and isotropy hold. The space where the gauged monitoring sites lie is denoted by G. We adopt a Bayesian approach in which the mapping between G and D is represented by an unknown function d(·). A Gaussian process prior distribution is defined for d(·). Unlike the Sampson–Guttorp approach, the mapping of both gauged and ungauged sites is handled in a single framework, and predictive inferences take explicit account of uncertainty in the mapping. Markov chain Monte Carlo methods are used to obtain samples from the posterior distributions. Two examples are discussed: a simulated data set and the solar radiation data set that also was analysed by Sampson and Guttorp.