bluuebunny/crossref_metadata_2025_split huggingface dataset:
High performance liquid chromatographic separation of dipeptide and tripeptide enantiomers using a chiral crown ether stationary phase
Authors: Conrad Uwe , Chankvetadze Bezhan , Scriba Gerhard K. E. 
Published: October 2005

AbstractA chiral stationary phase (CSP) based on (–)‐(18‐crown‐6)‐2,3,11,12‐tetracarboxylic acid was evaluated for the direct resolution of the enantiomers of dipeptides and tripeptides. The type and concentration of the acid and the methanol content were optimized with regard to retention time and resolution using Ala‐Phe as model peptide. A mobile phase consisting of 10 mM sulfuric acid in 70% aqueous methanol was applied to the separation of a set of 16 structurally diverse dipeptides and tripeptides. Generally, the configuration of the amino acid at the N‐terminus determined the enantiomer elution order. With a few exceptions the LL‐ and LD‐enantiomers interacted stronger with the CSP compared to the corresponding DD‐ or DL‐enantiomers. The experimental conditions also allowed the simultaneous separation of all four stereoisomers of Ala‐Phe. Addition of ammonium sulfate generally reduced retention times and enantiomer resolution. Addition of triethylamine as modifier led to an overall increase of the retention times while the resolution did not show a general trend, increasing in the case of Ala‐Ala but decreasing in the case of Ala‐Phe.
Boundary elements for cracks and notches in three dimensions
Authors: Watson J. O. 
Published: October 2005

AbstractPlane and curved cracks are modelled by boundary elements, of geometry defined by conforming quadratic and hybrid quadratic‐Hermitian cubic shape functions. Displacement and traction are interpolated by the quadratic functions, supplemented by singular functions by which are multiplied stress intensity factors corresponding to each of the three modes of crack opening displacement, for the first three eigenvalues of the Williams eigenfunction expansion and its equivalent for antiplane strain. Singular and hypersingular boundary integral equations are taken at nodes of elements and auxiliary collocation points. Singular and hypersingular components of integrals are evaluated by consideration of trial displacement fields (simple solutions) for subdomains lying to either side of the crack.Examples are shown of buried and surface cracks, and computed results compared with those obtained by other methods. For surface cracks, the computed results reveal the cause of significant discrepancies between values given by well established empirical and other formulae. The modelling of notches is demonstrated by an analysis of stress in rock near a tunnel intersection. Computational efficiency is discussed, and improvements and extensions of the analysis are proposed. Copyright © 2005 John Wiley & Sons, Ltd.
Performance of time‐stepping schemes for discrete models in fracture dynamic analysis
Authors: Delaplace Arnaud , Ibrahimbegovic Adnan 
Published: October 2005

AbstractIn this work we present a critical evaluation of different time integration schemes within the setting of non‐linear dynamic analysis of brittle fracture problem represented by a discrete model. The discrete model of this kind consists of Voronoi cells representing the grains of a heterogeneous structure, which are interconnected by cohesive forces modelled by beam‐like links capable of taking properly into account both brittle dynamic fracture and large displacement of a still connected pack of grains that might split from the structure. The brittle behaviour of cohesive links requires that the dynamic analysis of such a model be treated with care, and the best possible integration scheme be selected. Four different schemes are explored and compared in application to a dynamic traction test, including Newmark explicit and implicit schemes, HHT‐α scheme and energy‐decaying scheme. Copyright © 2005 John Wiley & Sons, Ltd.
Localized Jacobian ILU preconditioners for hydraulic fractures
Authors: Peirce A. P. 
Published: October 2005

AbstractWe discuss the properties of a class of sparse localized approximations to the Jacobian operator that arises in modelling the evolution of a hydraulically driven fracture in a multi‐layered elastic medium. The governing equations involve a highly non‐linear coupled system of integro‐partial differential equations along with the fracture front free boundary problem. We demonstrate that an incomplete LU factorization of these localized Jacobians yields an efficient preconditioner for the fully populated, stiff, non‐symmetric system of algebraic equations that need to be solved multiple times for every growth increment of the fracture. The performance characteristics of this class of preconditioners is explored via spectral analysis and numerical experiment. Copyright © 2005 John Wiley & Sons, Ltd.
A meshless method with enriched weight functions for three‐dimensional crack propagation
Authors: Duflot Marc 
Published: October 2005

AbstractThe propagation of cracks in three dimensions is analysed by a meshless method. The cracks are modelled by a set of triangles that are added when the propagation occurs. Since the method is meshless, no remeshing of the domain is necessary during the propagation. To avoid using a large number of degrees of freedom, the stress singularity along the front of the cracks is taken into account by an enrichment of the shape functions of the meshless method by means of appropriate weight functions. This enrichment technique is an extension of the technique that proved to be successful in two dimensions in a previous paper. Several algorithms for efficiently implementing the meshless method in three dimensions are detailed. The accuracy of the enrichment is first assessed on simple examples and some results of non‐planar propagation of multiple cracks are then presented. Copyright © 2005 John Wiley & Sons, Ltd.
Crush dynamics of square honeycomb sandwich cores
Authors: Xue Zhenyu , Hutchinson John W. 
Published: October 2005

AbstractSquare honeycombs are effective as cores for all‐metal sandwich plates in that they combine excellent crushing strength and energy absorption with good stiffness and strength in out‐of‐plane shear and in‐plane stretch. In applications where sandwich plates must absorb significant energy in crushing under intense impulsive loads, dynamic effects play a significant role in the behaviour of the core. Three distinct dynamic effects can be identified: (i) inertial resistance, (ii) inertial stabilization of webs against buckling, and (iii) material strain‐rate dependence. Each contributes to dynamic strengthening of the core. These effects are illustrated and quantified with the aid of detailed numerical calculations for rates of deformation characteristic of shock loads in air and water. A continuum model for high rate deformation of square honeycomb cores is introduced that can be used to simulate core behaviour in large structural calculations when it is not feasible to mesh the detailed core geometry. The performance of the continuum model is demonstrated for crushing deformations. Copyright © 2005 John Wiley & Sons, Ltd.
Effect of temperature and solvent on the structure and transport of a tethered membrane: Monte Carlo simulation
Authors: Pandey R. B. , Anderson Kelly L. , Farmer B. L. 
Published: October 2005

AbstractAn extended bond‐fluctuation model, introduced previously to study the conformation and dynamics of a self‐avoiding sheet (SAS), is further used to understand the temperature dependence on the conformation and dynamics of a tethered membrane (i.e., nodes tethered by fluctuating bonds with excluded volume constraints) in an effective solvent media on a cubic lattice by Monte Carlo simulations. The node–node (nn) and node–solvent (ns) interactions and temperature orchestrate the stochastic motion of each membrane node, and therefore describe the morphology of the membrane. With increasing temperature, the radius of gyration (Rg) of the membrane decreases with repulsive node–node interactions in an attractive solvent medium (ns < 0). The inverse effect is seen in a repulsive medium. Changes in the membrane'sRgshow that the membrane contracts (stretches) with the range of attractive (repulsive) node–node interaction with more pronounced effects on lowering the temperature. The variations ofRgwithT, which are affected by wrinkles and crumpling, are complex (with the possibility of stretched exponential functions) depending on the type of membrane, quality of the solvent, and the temperature. Likewise, the segmental dynamics exhibits a range of power‐laws, different from that of a SAS, while the global membrane reaches its asymptotic diffusive behavior. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 43: 3478–3486, 2005
Charged polypeptide diffusion at a very high ionic strength
Authors: Hong Liang , Granick Steve 
Published: October 2005

AbstractTwo charged polypeptides of opposite charge, poly(glutamic acid) (negative charge) and polylysine (positive charge), were end‐labeled with Alexa fluorescent dyes, and their translational diffusion coefficient (D) values in dilute solutions (∼10−4 mg mL−1) were studied at the biological pH with fluorescence correlation spectroscopy as a function of the ionic strength (Cs) mediated by the addition of NaCl. At a moderate ionic strength, D increased consistently with expected chain contraction because of electrostatic screening. At a very high ionic strength, D of poly(glutamic acid) increased more rapidly, following the empirical power law RH ∼ Cs−1/2 over a limited range of Cs, where the changes in D were interpreted as changes in the hydrodynamic radius, RH. However, D of polylysine at first decreased but eventually passed through a maximum followed by a decrease. These large increases implied that RH decreased considerably, in turn implying a strong contraction of the chain conformations even though the polymer remained soluble and showed no evidence of aggregation. For polylysine, the unexpected minimum RH value may be related to the salting‐in phenomenon. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 43: 3497–3502, 2005
Knowledge‐based voting algorithm for automated protein functional annotation†
Authors: Yu G.X. , Glass E.M. , Karonis N.T. , Maltsev N. 
Published: October 2005

AbstractAutomated annotation of high‐throughput genome sequences is one of the earliest steps toward a comprehensive understanding of the dynamic behavior of living organisms. However, the step is often error‐prone because of its underlying algorithms, which rely mainly on a simple similarity analysis, and lack of guidance from biological rules. We present herein a knowledge‐based protein annotation algorithm. Our objectives are to reduce errors and to improve annotation confidences. This algorithm consists of two major components: a knowledge system, called “RuleMiner,” and a voting procedure. The knowledge system, which includes biological rules and functional profiles for each function, provides a platform for seamless integration of multiple sequence analysis tools and guidance for function annotation. The voting procedure, which relies on the knowledge system, is designed to make (possibly) unbiased judgments in functional assignments among complicated, sometimes conflicting, information. We have applied this algorithm to 10 prokaryotic bacterial genomes and observed a significant improvement in annotation confidences. We also discuss the current limitations of the algorithm and the potential for future improvement. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Modelling age‐dependent force of infection from prevalence data using fractional polynomials
Authors: Shkedy Z. , Aerts M. , Molenberghs G. , Beutels Ph. , Van Damme P. 
Published: October 2005

AbstractThe force of infection is one of the primary epidemiological parameters of infectious diseases. For many infectious diseases it is assumed that the force of infection is age‐dependent. Although the force of infection can be estimated directly from a follow up study, it is much more common to have cross‐sectional seroprevalence data from which the prevalence and the force of infection can be estimated. In this paper, we propose to model the force of infection within the framework of fractional polynomials. We discuss several parametric examples from the literature and show that all of these examples can be expressed as special cases of fractional polynomial models. We illustrate the method on five seroprevalence samples, two of Hepatitis A, and one of Rubella, Mumps and Varicella. Copyright © 2005 John Wiley & Sons, Ltd.
Correcting for selection using frailty models
Authors: Olesen Anne Vingaard , Parner Erik Thorlund 
Published: October 2005

AbstractChronic diseases are roughly speaking lifelong transitions between the states: relapse and recovery. The long‐term pattern of recurrent times‐to‐relapse can be investigated with routine register data on hospital admissions. The relapses become readmissions to hospital, and the time spent in hospital are gaps between subsequent times‐at‐risk. However, problems of selection and dependent censoring arise because the calendar period of observation is limited and the study population likely to be heterogeneous. We will theoretically verify that an assumption of conditional independence of all times‐at‐risk and gaps, given the latent individual frailty level, allows for consistent inference in the shared frailty model. Using simulation studies, we also investigate cases where gaps (and/or staggered entry) are informative for the individual frailty. We found that the use of the shared frailty model can be extended to situations, where gaps are dependent on the frailty, but short compared to the distribution of the times‐to‐relapse. Our motivating example deals with the course of schizophrenia. We analysed routine register data on readmissions in almost 9000 persons with the disorder. Marginal survival curves of time‐to‐first‐readmission, time‐to‐second‐readmission, etc. were estimated in the shared frailty model. Based on the schizophrenia literature, the conclusion of our analysis was rather surprising: one of a stable course of disorder. Copyright © 2005 John Wiley & Sons, Ltd.
Confidence intervals for an effect size measure based on the Mann–Whitney statistic. Part 1: general issues and tail‐area‐based methods
Authors: Newcombe Robert G. 
Published: October 2005

AbstractFor two random variables X and Y, θ=Pr[Y>X] + ½Pr[Y=X] is advocated as a general measure of effect size to characterize the degree of separation of their distributions. It is estimated by U/mn, a generalization of the Mann–Whitney U statistic, derived by dividing U by the product of the two sample sizes. It is equivalent to the area under the receiver operating characteristic curve. It is readily visualized in terms of two Gaussian distributions with appropriately separated peaks. The effect of discretization of a continuous variable is explored. Tail‐area‐based confidence interval methods are developed which can be applied to very small samples or extreme outcomes. Copyright © 2005 John Wiley & Sons, Ltd.
Reduced models of doubly fed induction generator system for wind turbine simulations
Authors: Sørensen P. , Hansen A. D. , Lund T. , Bindner H. 
Published: October 2005

AbstractThis article compares three reduced models with a detailed model of a doubly fed induction generator system for wind turbine applications. The comparisons are based on simulations only. The main idea is to provide reduced generator models which are appropriate to simulate normal wind turbine operation in aeroelastic wind turbine models, e.g. for control system design or structural design of the wind turbine. The electrical behaviour such as grid influence will therefore not be considered. The work presented in this article shows that with an ideal, undisturbed grid the dynamics of the doubly fed induction generator system is very well represented by the dynamics due to the generator inertia and the generator control system, whereas the electromagnetic characteristics of the generator can be represented by the steady state relations. The parameters for the proposed models are derived from parameters typically available from the generator data sheet and from the controller settings. Thus the models are simple to apply in any case where the generator data sheet is available. Copyright © 2005 John Wiley & Sons, Ltd.
The combined effect of transport and temperature on distribution and growth of larvae and pelagic juveniles of Arcto-Norwegian cod
Authors: Vikebø Frode , Sundby Svein , Ådlandsvik Bjørn , Fiksen Øyvind 
Published: October 2005

Abstract
Temperature has been identified in field studies as the physical parameter most influential on growth and recruitment of Arcto-Norwegian cod. However, it has been pointed out by many authors that temperature in this context has not only direct effects on the cod, but also indirect effects through lower trophic levels. Moreover, it has been said that temperature might also be a proxy for other climatic parameters. The present paper analyses the direct quantitative effects of temperature on larval and pelagic juvenile growth from spawning in Lofoten until the 0-group fish settle in the Barents Sea. The approach taken is that of a modelling study, supported by analysis of existing data on fish stocks and climate. It is shown that transport and temperature alone can reproduce key features of the 0-group weight distribution and concentration in the Barents Sea for two consecutive years. The extent of the dispersion of the larvae and pelagic juveniles, as well as the ambient temperature they experience on their route, are shown to depend upon their depth in the water column and, to a lesser degree, the time of spawning.
Mullahs, Migrants and Murids: New Developments in the Study of Pakistan A Review Article
Authors: MARSDEN MAGNUS 
Published: October 2005

The Ulama in Contemporary Islam: Custodians of Change. By MUHAMMAD QASIM ZAMAN. Princeton, N.J. and Oxford: Princeton University Press.Migrants and Militants: Fun and Urban Violence in Pakistan. By OSKAR VERKAAIK. Princeton, N.J.: Princeton University Press.Pilgrims of Love: The Anthropology of a Global Sufi Cult. By PNINA WERBNER. London: Hurst and Company.
Global flows: Terror, oil & strategic philanthropy
Authors: Barnes Sandra T. 
Published: October 2005

US involvement in Africa is growing following threats of terrorism and interruptions in oil production and because of desires by foreign corporations to expand their activities on the continent. The response of American policymakers has been to establish a stronger military presence that will engage in counterterrorism initiatives and police oil installations. The goals and extent of this buildup, and the ideology legitimating it, are new. They are departures from Cold War policies. Similarly, the response of American business leaders to weaknesses in the infrastructure and political order of African states leads them to establish their own forms of community development, known as strategic philanthropy, in order to protect and expand local markets. Despite these major developments, the media are not informing the public. This article examines the implications of these military and business initiatives for African nations and the reasons for lack of information about them.
Editor's Note: This article was delivered as the presidential address to the African Studies Association, New Orleans, 12 November 2004. It first appeared in the African Studies Review, Vol. 47, No. 5, April 2005:1–22, the principal scholarly journal of that Association. On the role of the US in Africa, also see Daniel Volman, ‘US Military Involvement in Africa’ and Michel Chossudovsky, ‘New Undeclared Arms Race: America's Agenda for Global Military Domination’ in ROAPE 103, March 2005.
ConFind: a robust tool for conserved sequence identification
Authors: Smagala James A. , Dawson Erica D. , Mehlmann Martin , Townsend Michael B. , Kuchta Robert D. , Rowlen Kathy L. 
Published: October 2005

Abstract
Summary: ConFind (conserved region finder) identifies regions of conservation in multiple sequence alignments that can serve as diagnostic targets. Designed to work with a large number of closely related, highly variable sequences, ConFind provides robust handling of alignments containing partial sequences and ambiguous characters. Conserved regions are defined in terms of minimum region length, maximum informational entropy (variability) per position, number of exceptions allowed to the maximum entropy criterion and the minimum number of sequences that must contain a non-ambiguous character at a position to be considered for inclusion in a conserved region. Comparison of the calculated entropy for an alignment of 95 influenza A hemagglutinin sequences with random deletions results in a 98% reduction in the average error in ConFind relative to the ‘Find Conserved Regions’ option in BioEdit.
Requirements: ConFind requires Python 2.3, but Python 2.4 or an upgrade of the optparse module to Optik 1.5 is suggested. The program is known to run under Linux and DOS.
Availability: ConFind is licensed under the GNU General Public License (GPL). Source code, documentation, and a precompiled DOS executable are available for download at
Contact: rowlen@colorado.edu
OligoFaktory: a visual tool for interactive oligonucleotide design
Authors: Schretter Colas , Milinkovitch Michel C. 
Published: October 2005

Abstract
Summary: The OligoFaktory is a set of tools for the design, on an arbitrary number of target sequences, of high-quality long oligonucleotide for micro-array, of primer pair for PCR, of siRNA and more. The user-centered interface exists in two flavours: a web portal and a standalone software for Mac OS X Tiger. A unified presentation of results provides overviews with distribution charts and relative location bar graphs, as well as detailed features for each oligonucleotide. Input and output files conform to a common XML interchange file format to allow both automatic generation of input data, archiving, and post-processing of results. The design pipeline can use BLAST servers to evaluate specificity of selected oligonucleotides.
Availability: The web portal ; the software for Macintosh:
Contact: cschrett@ulb.ac.be
The baryonic mass function of galaxies
Authors: Read J.I , Trentham Neil 
Published: October 2005

In the Big Bang about 5% of the mass that was created was in the form of normal baryonic matter (neutrons and protons). Of this about 10% ended up in galaxies in the form of stars or of gas (that can be in molecules, can be atomic, or can be ionized).In this work, we measure the baryonic mass function of galaxies, which describes how the baryonic mass is distributedwithingalaxies of different types (e.g. spiral or elliptical) and of different sizes. This can provide useful constraints on our current cosmology, convolved with our understanding of how galaxies form. This work relies on various large astronomical surveys, e.g. the optical Sloan Digital Sky Survey (to observe stars) and the HIPASS radio survey (to observe atomic gas). We then perform an integral over our mass function to determine the cosmological density of baryons in galaxies:Ωb,gal=0.0035. Most of these baryons are in stars:Ω*=0.0028. Only about 20% are in gas. The error on the quantities, as determined from the range obtained between different methods, isca10%; systematic errors may be much larger.Most (ca90%) of the baryons in the Universe are not in galaxies. They probably exist in a warm/hot intergalactic medium. Searching for direct observational evidence and deeper theoretical understanding for this will form one of the major challenges for astronomy in the next decade.