bluuebunny/crossref_metadata_2025 huggingface dataset:
Identifying property based sequence motifs in protein
families and superfamilies: application to DNase-1 related
endonucleases
Authors: Mathura Venkatarajan S. , Schein Catherine H. , Braun Werner
Published: July 2003

Motivation: Identification of short conserved sequence motifs common to a protein family or superfamily can be more useful than overall sequence similarity in suggesting the function of novel gene products. Locating motifs still requires expert knowledge, as automated methods using stringent criteria may not differentiate subtle similarities from statistical noise.

Results: We have developed a novel automatic method, based on patterns of conservation of 237 physical–chemical properties of amino acids in aligned protein sequences, to find related motifs in proteins with little or no overall sequence similarity. As an application, our web-server MASIA identified 12 property-based motifs in the apurinic/apyrimidinic endonuclease (APE) family of DNA-repair enzymes of the DNase-I superfamily. Searching with these motifs located distantly related representatives of the DNase-I superfamily, such as Inositol 5′-polyphosphate phosphatases in the ASTRAL40 database, using a Bayesian scoring function. Other proteins containing APE motifs had no overall sequence or structural similarity. However, all were phosphatases and/or had a metal ion binding active site. Thus our automated method can identify discrete elements in distantly related proteins that define local structure and aspects of function. We anticipate that our method will complement existing ones to functionally annotate novel protein sequences from genomic projects.

Availability: MASIA WEB site: http://www.scsb.utmb.edu/masia/masia.html

Contact: werner@newton.utmb.edu

Supplementary information: The dendrogram of 42 APE sequences used to derive motifs is available on http://www.scsb.utmb.edu/comp_biol.html/DNA_repair/publication.html

* To whom correspondence should be addressed.
Exact significance levels for the maximumχ
2
method of detecting recombination
Authors: Spencer M.
Published: July 2003

Summary:Maynard Smith’s maximum χ2 method is a useful tool for detecting recombination. Significance testing is usually carried out by random permutation, which may require a large amount of computer time. I describe an exact algorithm.

Availability: Matlab source code from http://www.bioc.cam.ac.uk/UTOs/howe/

Contact: ms379@cam.ac.uk
Which genetic loci have greater population assignment power?
Authors: Banks Michael A. , Eichert Will , Olsen Jeffrey B.
Published: July 2003

Summary: WHICHLOCI is a program that determines the relative discriminatory power of alternate genetic loci and loci combinations for population assignment of individuals.

Availability: http://www.oregonstate.edu/dept/comes/genetics/software.htm

Contact: Michael.Banks@oregonstate.edu

* To whom correspondence should be addressed.
An adjustable-threshold algorithm for the identification of objects
in three-dimensional images
Authors: Ponomarev Artem L. , Davis Ronald L.
Published: July 2003

Motivation:To develop a highly accurate, practical and fast automated segmentation algorithm for three-dimensional images containing biological objects. To test the algorithm on images of the Drosophila brain, and identify, count and determine the locations of neurons in the images.

Results: A new adjustable-threshold algorithm was developed to efficiently segment fluorescently labeled objects contained within three-dimensional images obtained from laser scanning confocal microscopy, or two-photon microscopy. The result of the test segmentation with Drosophila brain images showed that the algorithm is extremely accurate and provided detailed information about the locations of neurons in the Drosophila brain. Centroids of each object (nucleus of each neuron) were also recorded into an algebraic matrix that describes the locations of the neurons.

Availability: Interested parties should send their request for the NeuronMapper™ program with the segmentation algorithm to artemp@bcm.tmc.edu.

Contact: artemp@bcm.tmc.edu

* To whom correspondence should be addressed.
Gene Prediction by Spectral Rotation Measure: A New Method for Identifying Protein-Coding Regions
Authors: Kotlar Daniel , Lavner Yizhar
Published: July 2003

A new measure for gene prediction in eukaryotes is presented. The measure is based on the Discrete Fourier Transform (DFT) phase at a frequency of 1/3, computed for the four binary sequences for A, T, C, and G. Analysis of all the experimental genes of S. cerevisiae revealed distribution of the phase in a bell-like curve around a central value, in all four nucleotides, whereas the distribution of the phase in the noncoding regions was found to be close to uniform. Similar findings were obtained for other organisms. Several measures based on the phase property are proposed. The measures are computed by clockwise rotation of the vectors, obtained by DFT for each analysis frame, by an angle equal to the corresponding central value. In protein coding regions, this rotation is assumed to closely align all vectors in the complex plane, thereby amplifying the magnitude of the vector sum. In noncoding regions, this operation does not significantly change this magnitude. Computing the measures with one chromosome and applying them on sequences of others reveals improved performance compared with other algorithms that use the 1/3 frequency feature, especially in short exons. The phase property is also used to find the reading frame of the sequence.
Biopipe: A Flexible Framework for Protocol-Based Bioinformatics Analysis
Authors: Hoon Shawn , Ratnapu Kiran Kumar , Chia Jer-ming , Kumarasamy Balamurugan , Juguang Xiao , Clamp Michele , Stabenau Arne , Potter Simon , Clarke Laura , Stupka Elia
Published: July 2003

We identify several challenges facing bioinformatics analysis today. Firstly, to fulfill the promise of comparative studies, bioinformatics analysis will need to accommodate different sources of data residing in a federation of databases that, in turn, come in different formats and modes of accessibility. Secondly, the tsunami of data to be handled will require robust systems that enable bioinformatics analysis to be carried out in a parallel fashion. Thirdly, the ever-evolving state of bioinformatics presents new algorithms and paradigms in conducting analysis. This means that any bioinformatics framework must be flexible and generic enough to accommodate such changes. In addition, we identify the need for introducing an explicit protocol-based approach to bioinformatics analysis that will lend rigorousness to the analysis. This makes it easier for experimentation and replication of results by external parties. Biopipe is designed in an effort to meet these goals. It aims to allow researchers to focus on protocol design. At the same time, it is designed to work over a compute farm and thus provides high-throughput performance. A common exchange format that encapsulates the entire protocol in terms of the analysis modules, parameters, and data versions has been developed to provide a powerful way in which to distribute and reproduce results. This will enable researchers to discuss and interpret the data better as the once implicit assumptions are now explicitly defined within the Biopipe framework.
Sequence Divergence Within Transposable Element Families in the Drosophila melanogaster Genome
Authors: Lerat Emmanuelle , Rizzon Carène , Biémont Christian
Published: July 2003

The availability of the sequenced Drosophila melanogaster genome provides an opportunity to study sequence variation between copies within transposable element families. In this study,we analyzed the 624 copies of 22 transposable element (TE) families (14 LTR retrotransposons, five non-LTR retrotransposons, and three transposons). LTR and non-LTR retrotransposons possessed far fewer divergent elements than the transposons,suggesting that the difference depends on the transposition mechanism. However,there was not a continuous range of divergence of the copies in each class,which were either very similar to the canonical elements,or very divergent from them. This sequence homogeneity among TE family copies matches the theoretical models of the dynamics of these repeated sequences. The sequenced Drosophila genome thus appears to be composed of a mixture of TEs that are still active and of ancient relics that have degenerated and the distribution of which along the chromosomes results from natural selection. This clearly demonstrates that the TEs are highly active within the genome,suggesting that the genetic variability of the Drosophila genome is still being renewed by the action of TEs.
Dragon Gene Start Finder: An Advanced System for Finding Approximate Locations of the Start of Gene Transcriptional Units
Authors: Bajic Vladimir B. , Seah Seng Hong
Published: July 2003

We present an advanced system for recognition of gene starts in mammalian genomes. The system makes predictions of gene start location by combining information about CpG islands, transcription start sites (TSSs), and signals downstream of the predicted TSSs. The system aims at predicting a region that contains the gene start or is in its proximity. Evaluation on human chromosomes 4, 21, and 22 resulted in Se of over 65% and in a ppv of ∼78%. The system makes on average one prediction per 177,000 nucleotides on the human genome, as judged by the results on chromosome 21. Comparison of abilities to predict TSS with the two other systems on human chromosomes 4, 21, and 22 reveals that our system has superior accuracy and overall provides the most confident predictions.
Structure of magnetic poly(oxyethylene)–siloxane nanohybrids doped with FeIIand FeIII
Authors: Silva N. J. O. , Dahmouche K. , Santilli C. V. , Amaral V. S. , Carlos L. D. , Bermudez V. de Zea , Craievich A. F.
Published: July 2003

Hybrid organic–inorganic nanocomposites doped with FeIIand FeIIIions and exhibiting interesting magnetic properties have been obtained by the sol–gel process. The hybrid matrix of these ormosils (organically modified silicates), classed as di-ureasils and termed U(2000), is composed of poly(oxyethylene) chains of variable length grafted to siloxane groups by means of urea crosslinkages. Iron perchlorate and iron nitrate were incorporated in the di-ureasil matrices, leading to compositions within the range 80 ≥n≥ 10,nbeing the molar ratio of ether-type O atoms per cation. The structure of the doped di-ureasils was investigated by small-angle X-ray scattering (SAXS). For FeII-doped samples, SAXS results suggest the existence of a two-level hierarchical structure. The primary level is composed of spatially correlated siloxane clusters embedded in the polymeric matrix and the secondary, coarser level consists of domains where the siloxane clusters are segregated. The structure of FeIII-doped hybrids is different, revealing the existence of iron oxide based nanoclusters, identified as ferrihydrite by wide-angle X-ray diffraction, dispersed in the hybrid matrix. The magnetic susceptibility of these materials was determined by zero-field-cooling and field-cooling procedures as functions of both temperature and field. The different magnetic features between FeII- and FeIII-doped samples are consistent with the structural differences revealed by SAXS. While FeII-doped composites exhibit a paramagnetic Curie-type behaviour, hybrids containing FeIIIions show thermal and field irreversibilities.
Determination of compaction and surface in mesostructured materials using SAXS
Authors: Né Frédéric , Zemb Thomas
Published: July 2003

An experimental method to determine simultaneously the compaction and the total specific area between an inorganic oxide network and a material of low electronic density (organic surfactant or air) is presented. This method is applicable when both the Porod limit and the invariant can be extracted from the small-angle X-ray scattering pattern on an absolute scale. An example is given using a hybrid precipitate of zirconium oxide and a cationic surfactant (CTAB). In such a mesostructured material, the total measured interface and the geometrically modelled one differ by a factor of 4, while compaction is about 0.4, well below 1. This is attributed to the presence of microporosity, in addition to the mesoporosity. The validity of the method is demonstrated using goethite as a reference inorganic material of known compaction equal to 1.
NeedleHaystack: a program for the rapid recognition of local structures in large sets of atomic coordinates
Authors: Hoppe Andreas , Frömmel Cornelius
Published: July 2003

A program that computes molecular superpositions is presented. A possible large molecule (target =haystack) is scanned for the occurrence of a given molecular motif (model =needle) within tolerances. The advance over other methods is that it can handle very large atom sets,e.g.targets of up to 100000 atoms, and does not necessarily require any chemical information and connectivity between atoms: chemical constraints to restrict the solution space are not used to relate non-obvious superpositions based on a geometric fit. The specialization to a needle-in-a-haystack problem allows a very fast algorithm. Trade-offs between run time and tolerance levels are possible. The program is fast enough to screen large databases in an acceptable time. An executable for Linux on Pentium-compatible machines is available free of charge at http://www.charite.de/bioinf/haystack. It is a command-line executable well suited for scripts and distributed computing. A Web interface for immediate testing is also available at this address.
PSILAM: a program for the calculation and graphical representation of multiple-diffraction peak location plots
Authors: Rossmanith Elisabeth
Published: July 2003

PSILAM, a derivative of the programUMWEG, makes possible the calculation and graphical representation of multiple-diffraction intensity-independent as well as intensity-dependent ψ−λ peak location plots and can be applied to X-rays as well as to neutrons. The program is written in Lahey Fortran 95. The program runs without further commercial subroutine libraries; consequently it can be used without licence problems. It is distributed for Windows 2000viahttp://www.rrz.uni-hamburg.de/mpi/rossmanith. Executable (binary files) are available free of charge for academic use only.
Identification of aggregates of magnetic nanoparticles in ferrofluids at low concentrations
Authors: Eberbeck D. , Lange A. , Hentschel M.
Published: July 2003

Different very dilute suspensions of magnetic nanoparticles (magnetite surrounded by an organic shell) in water (ferrofluids) were investigated using small-angle X-ray scattering. It is shown that the scattering originates not only from noncorrelated core–shell nanoparticles, but also from larger structures. By modelling, these structures can be identified as close-packed clusters consisting of core–shell particles (core diameter ∼10 nm). The analysis of the radial distance distribution function, obtained by Fourier transformation of the scattered intensity, reveals a lower bound of the mean cluster size of about 40 nm. The formation of clusters is persistent, even in very dilute suspensions.
A small-angle neutron scattering investigation of rigid polyelectrolytes under shear
Authors: Mendes E. , Viale S. , Santin O. , Heinrich M. , Picken S. J.
Published: July 2003

Solutions of a rigid polyelectrolyte molecule, sulfo-poly(phenyleneterephthalamide) (SPTTA), in deuterated water have been investigated using small-angle neutron scattering. At low concentrations (1 wt%) the scattering spectrum presents a soft maximum similar to that of the interaction of rod-like objects. Two counterions are used, H+and Li+, and it is shown that aggregation is favoured as the proportion of Li+counterions increases. When kept at rest at room temperature, the solutions exhibit spontaneous birefringence. A 1 wt% solution was investigated under shear and it is shown that a very small shear rate is needed to produce a very strong alignment of rod-like objects. Such alignment saturates at high shear rates. Upon cessation of shear, a very long relaxation time is observed. The set of results strongly suggest aggregation of rigid polyelectrolyte molecules into long needles exhibiting very small cross sections.
Investigating personal safety at railway stations using “virtual reality” technology
Authors: Cozens Paul , Neale Richard , Whitaker Jeremy , Hillier David
Published: July 2003

Understanding fear of crime is a crucial dimension to the “designing out crime” debate, particularly in view of the “dark figure” of crime which remains largely unknown due to under‐reporting and under recording of incidents. On the railways, customer satisfaction surveys have consistently reported that although recorded incidents of crime and nuisance are relatively low, customers perceive their personal risks to be significantly higher, discouraging many from using rail transport. This study of a representative sample of railway stations on a network in South Wales, focuses on personal safety issues as explained using the theory of crime prevention through environmental design (CPTED). The research project innovatively utilises interactive virtual reality scenes as the environmental stimuli to elucidate rich sources of data in terms of where passengers’ fears were located in and around the station and how service providers can make stations safer. Some basic design changes are briefly evaluated and recommendations for those who design and manage built environment facilities are discussed.
The effect of consumer‐based brand equity on firms’ financial performance
Authors: Kim Hong‐bumm , Gon Kim Woo , An Jeong A.
Published: July 2003

Examines the underlying dimensions of brand equity and how they affect financial performance of hotel firms. The results of this empirical study, using data collected from 12 luxury hotels, indicate that brand loyalty, perceived quality, and brand image are important components of consumer‐based brand equity. The result implies that hotel firms should seriously consider brand loyalty, perceived quality, and brand image when attempting to establish definite brand equity from the customers’ viewpoint. A review of detailed measures constituting these three variables, brand loyalty, brand awareness, and brand image, shows that most measures affect financial performances of hotels. Nonparametric correlation analysis provides fairly convincing evidence of the effect that consumer‐based brand equity has on a firm’s financial performance in the hotel industry
Orchestrating debate: a multimodal analysis of classroom interaction
Authors: Bourne Jill , Jewitt Carey
Published: July 2003

This paper examines the ways in which the interpretation of a literary text is constructed through social interaction in a multi‐ethnic urban secondary school English classroom. The focus is on the literacy experiences of Year 10 students (age 14 to 15 years). We take a multimodal approach to understanding social interaction around texts and show that higher‐order literacy skills are realised and constructed through the configuration of talk and writing with a range of other representational and communicational modes, such as gesture, gaze, movement, and posture. We suggest that despite the exhaustive regulation of literacy and school English, some English teachers, while still curriculum and examination focused, have found strategies that give them space to make connections between texts and the experiences of their particular student intake. They do so in ways that link to wider social and moral issues, drawing on their own and their students' life experiences, to make cultural connections with the texts studied. The paper shows how a multimodal analysis of social interaction facilitates and extends understanding of the teaching that is taking place.
Silicon Literacies – Communication, Innovation and Education in the Electronic Age
Authors: Merchant Guy
Published: July 2003

Ilana Snyder (Ed.) (2002) London: Routledge ISBN 0‐415‐27668‐3 (Pbk) £16.99
Unequal Plurality: Towards an Asymmetric Power Model of British Politics
Authors: Marsh David , Richards David , Smith Martin
Published: July 2003

Until recently, Rhodes's ‘Differentiate Polity Model’ (DPM) has been the most analytically-developed model of the British political system, but it is not without its problems. Here, we argue that the DPM over-stresses the diffuse nature of power in Britain and the extent to which the state has been hollowed out. Instead, we contend that the British political system is more closed and elitist than the DPM acknowledges; rather than being hollowed-out, the state has been reconstituted and the core executive still remains the most powerful actor in the policy process. These themes are reflected in our own ‘Asymmetric Power model’.
The Slovak Parliamentary Election of September 2002: Its Systemic Importance
Authors: Pridham Geoffrey
Published: July 2003

The Concept of ‘Critical Elections’ is Justifiably Used in Two eventualities: when there is a significant turning-point arising from a particular election, such as dramatic changes in party strengths which are subsequently consolidated and affect the structure of the party system (e.g. the replacement of one party by another as major opposition or government party); and, when in new democracies an election has a decisive effect in confirming or diverting from the democratization path. It may of course be that the latter incorporates the former.
Detection of Sweet and Umami Taste in the Absence of Taste Receptor T1r3
Authors: Damak Sami , Rong Minqing , Yasumatsu Keiko , Kokrashvili Zaza , Varadarajan Vijaya , Zou Shiying , Jiang Peihua , Ninomiya Yuzo , Margolskee Robert F.
Published: July 2003

The tastes of sugars (sweet) and glutamate (umami) are thought to be detected by T1r receptors expressed in taste cells. Molecular genetics and heterologous expression implicate T1r2 plus T1r3 as a sweet-responsive receptor,and T1r1 plus T1r3,as well as a truncated form of the type 4 metabotropic glutamate receptor (taste-mGluR4),as umami-responsive receptors. Here,we show that mice lacking T1r3 showed no preference for artificial sweeteners and had diminished but not abolished behavioral and nerve responses to sugars and umami compounds. These results indicate that T1r3-independent sweet- and umami-responsive receptors and/or pathways exist in taste cells.
Temperature Effect on Cirac and Zoller Model Using Two-Time Green's Function
Authors: Li Wei , Zhao Hong-Min , Lin Jia-Tih
Published: July 2003

Using the two-time Green's function method, we analyze the temperature effect on the famous Cirac and Zoller model. Formulas for the average number of different mode phonons and the deviation of its internal state from its ground state are derived. The influence of the internal state energy and trap frequency on the number of phonons is also discussed. The upper limit of temperature for regular quantum computation in the Cirac and Zoller model is obtained.
New Developments in Theory of Vortex States in Type-II Superconductors
Authors: Hu Xiao
Published: July 2003

Theoretical understanding of the vortex states of type II superconductors is reviewed, with a focus on thermodynamic phases and phase transitions. Results derived from computer simulations by our group are summarized. A new phase diagram for inter-layer Josephson vortices in layered superconductors is proposed.
An Output-Sensitive Convex Hull Algorithm for Planar Objects
Authors: Nielsen Franck , Yvinec Mariette
Published: July 2003

A set of planar objects is said to be of type m if the convex hull of any two objects has its size bounded by 2m. In this paper, we present an algorithm based on the marriage-before-conquest paradigm to compute the convex hull of a set of n planar convex objects of fixed type m. The algorithm is output-sensitive, i.e. its time complexity depends on the size h of the computed convex hull. The main ingredient of this algorithm is a linear method to find a bridge, i.e. a facet of the convex hull intersected by a given line. We obtain an O(nβ(h,m log h)-time convex hull algorithm for planar objects. Here β(h,2)=O(1) and β(h,m) is an extremely slowly growing function. As a direct consequence, we can compute in optimal Θ(n log h) time the convex hull of disks, convex homothets, non-overlapping objects. The method described in this paper also applies to compute lower envelopes of functions. In particular, we obtain an optimal Θ(n log h)-time algorithm to compute the upper envelope of line segments.
Evaluation of Range Searching Methods for Contact Searching in Mechanical Engineering
Authors: Fjällström Per-Olof , Petersson Jan , Nilsson Larsgunnar , Zhong Zhi-Hua
Published: July 2003

Contact searching is an important and time-consuming part of computer simulation of certain deformation processes. Contact searching can be facilitated by orthogonal range searching. We have experimentally evaluated four methods for orthogonal range searching: the projection method, the cell method, the k-d tree method, and the range tree method.

The results of our experiments indicate that two of these methods, the cell and k-d tree methods, have practical significance. The cell method is in most cases faster than the k-d tree method.
A Computational Geometric Approach to Visual Hulls
Authors: Petitjean Sylvain
Published: July 2003

Recognizing 3D objects from their 2D silhouettes is a popular topic in computer vision. Object reconstruction can be performed using the volume intersection approach. The visual hull of an object is the best approximation of an object that can be obtained by volume intersection. From the point of view of recognition from silhouettes, the visual hull can not be distinguished from the original object. In this paper, we present efficient algorithms for computing visual hulls. We start with the case of planar figures (polygons and curved objects) and base our approach on an efficient algorithm for computing the visibility graph of planar figures. We present and tackle many topics related to the query of visual hulls and to the recognition of objects equal to their visual hulls. We then move on to the 3-dimensional case and give a flavor of how it may be approached.
Polygon Area Decomposition for Multiple-Robot Workspace Division
Authors: Hert Susan , Lumelsky Vladimir
Published: July 2003

A new polygon decomposition problem, the anchored area partition problem, which has applications to a multiple-robot terrain-covering problem is presented. This problem concerns dividing a given polygon P into n polygonal pieces, each of a specified area and each containing a certain point (site) on its boundary or in its interior. First the algorithm for the case when P is convex and contains no holes is presented. Then the generalized version that handles nonconvex and nonsimply connected polygons is presented. The algorithm uses sweep-line and divide-and-conquer techniques to construct the polygon partition. The input polygon P is assumed to have been divided into a set of p convex pieces (p = 1 when P is convex), which can be done in O(vPlog log vP) time, where vPis the number of vertices of P and p = O(vP), using algorithms presented elsewhere in the literature. Assuming this convex decomposition, the running time of the algorithm presented here is O(pn2+vn), where v is the sum of the number of vertices of the convex pieces.
Stable Computation of the 2D Medial Axis Transform
Authors: Evans Guy , Middleditch Alan , Miles Nick
Published: July 2003

The medial axis transform of a 2D region was introduced by Blum in the 1960's as an aid to the description of biological shape. It is an alternative representation of a region which is often more amenable to analysis. This property has led to its use in diverse fields including pattern recognition and automatic finite element mesh generation. There are two widely agreed mathematical definitions for the medial axis transform which are closely related. It is shown that these definitions are not in general equivalent, despite being so far many types of region.

In this paper, precise mathematical definitions of the medial axis transform and its key points (atoms) are given, and an O(n2) algorithm for its computation via those atoms presented. This algorithm is described in terms of simple polygons whose sole boundary consists of circular arcs and straight line segments, then extended to polygons with holes. It is shown how more complex edges could be accommodated. In comparison with existing algorithms it is simple to implement and stable in the presence of geometric degeneracy.
DCEL
Authors: Barequet Gill
Published: July 2003

In this paper we describe the DCEL system: a geometric software package which implements a polyhedral programming environment. This package enables fast prototyping of geometric algorithms for polyhedra or for polyhedral surfaces. We provide an overview of the system's functionality and demonstrate its use in several applications.
Computational Geometry Column 34
Authors: Agarwal Pankaj K. , O'Rourke Joseph
Published: July 2003

Problems presented at the open-problem session of the 14th Annual ACM Symposium on Computational Geometry are listed.
THEORETICAL CONCEPTS FOR FRACTAL GROWTH AND SELF-ORGANIZED CRITICALITY
Authors: PIETRONERO L.
Published: July 2003

We discuss the properties of irreversible growth models that lead to self-organized fractal structures or to scale invariant distributions. In particular we compare these models with the usual critical phenomena and point out that the irreversible dynamics represents the major conceptual difference with respect to phase transition. This situation requires the introduction of new theoretical concepts which focus on this particular feature. We discuss how the Fixed Scale Transformation method allows us to deal with these properties, to understand the self-organized nature of these systems, and to compute analytically their fractal dimensions or critical exponents. We also outline the main open problems and the possible lines of development.
CLUSTERS AND FRACTALS IN THE ISING SPIN GLASS
Authors: JAN N. , GLOTZER S.C. , POOLE P.H. , CONIGLIO A.
Published: July 2003

We define clusters in the Ising ±J spin glass model, and present evidence for a percolation transition of these correlated clusters coincident with the thermodynamic transition. At the transition temperature Tsg, we search for the appropriate clusters of quasifrozen spins which will percolate with exponents in the Ising spin glass universality class. These clusters should provide the dominant contribution to the nonlinear susceptibility, which diverges at Tsg, and result from the interference of clusters of parallel and antiparallel spins, as predicted by the Frustrated Percolation model.
FRACTAL ASPECTS IN POLYMER SCIENCE
Authors: SCHIESSEL H. , BLUMEN A.
Published: July 2003

Scaling aspects are of common occurrence in polymer science. Here we concentrate on the fractal behavior of dynamical systems. As examples we focus on the sol-gel transition and on the patterns of motion displayed by polyampholytes (polymers containing positive and negative charges).
LÉVY FLIGHTS: CHAOTIC, TURBULENT, AND RELATIVISTIC
Authors: SHLESINGER MICHAEL F. , KLAFTER JOSEPH , ZUMOFEN GERT
Published: July 2003

Lévy flights were introduced through the mathematical investigation of the algebra of random variables with infinite moments. For many years Lévy flights remained an abstract topic in mathematics. Mandelbrot recognized that the Lévy flight prescription had a deep connection to scale-invariant fractal random walk trajectories. We review the utility of Lévy flights in several physics topics involving chaotic and turbulent diffusion and introduce the scaling to describe trajectories in relativistic turbulence.
DEPOSITION PROBLEMS
Authors: EDWARDS S.F.
Published: July 2003

The paper discusses the problem of the surface structure of a powder solid created by ballistic deposition in the cases of: (i) uniform spheres; (ii) deposition with preferential growth at high points (KPZ); (iii) deposition via DLA. A result of particular interest is the direct evaluation of the correlation function index in case (ii).
FRACTALS AND THE UNIVERSE
Authors: COLEMAN PAUL H.
Published: July 2003

Many examples of fractal geometry are seen in the field of Astronomy, from nearby objects such as our Sun, to phenomena at intermediate length scales in our Galaxy such as the distribution of masers. This paper will give many examples of various length scales and finally concentrates on the largest scales which can be probed in our universe, with analyses of locations of galaxies. It has been known for some twenty years that the distribution of galaxies on small scales is fractal. This is seen in analyses which indicate that both galaxies and their clusters are power law correlated (a signature of fractal behavior). At larger length scales the distribution is supposed to exhibit a so-called correlation length and was thought to then become homogeneous—except for occasional fluctuations. More data and subsequent analysis have shown that these fluctuations are anything but occasional, as structures are seen to exist on length scales up to the maximum scales which can be probed with the new data. By reanalyzing the data, with methods that are particularly suited to fractal distributions, one finds no correlation length at all—indicating that the fractal structure may extend up to perhaps the largest length scales possible. Analysis also indicates that when galaxy masses are considered, the distribution may be multifractal. These conclusions have serious implications for many subfields in astrophysics today, from galaxy formation to the Robertson-Walker metric of spacetime.
MANDELBROT’S ECONOMICS AFTER A QUARTER CENTURY
Authors: MIROWSKI PHILIP
Published: July 2003

A quarter century has passed since the bulk of Benoit Mandelbrot’s articles on economics were published. This paper outlines the broad reactions to Mandelbrot’s theses within the economics profession. There are two separate literatures which have responded skeptically to his innovations: that which considers the empirical possibility that economic time series are best described as stochastic processes based upon Levy stable distributions; and that which considers the possible evidence for chaotic dynamics in economic time series. The paper concludes that much of the skepticism in orthodox economics is founded upon inadequate empirical premises, especially when compared to the approach of physicists to similar issues.
BUSINESS INTERRUPTION INSURANCE, A RISKY BUSINESS: A STUDY ON SOME PARETIAN RISK PHENOMENA
Authors: ZAJDENWEBER DANIEL
Published: July 2003

Both the size-distribution or yearly claims in the French business interruption insurance branch and the claim size-distribution per firm have a Pareto tail. It is so long that the theoretical law has an infinite expectation. This paper analyzes the data and investigates the consequences of that Paretian behavior on the actuarial value of the business interruption insurance policies.
FROM FLATLAND TO FRACTALAND: NEW GEOMETRIES IN RELATIONSHIP TO ARTISTIC AND SCIENTIFIC REVOLUTIONS
Authors: SHEARER RHONDA ROLAND
Published: July 2003

Abbott’s 19th century book, Flatland, continues to be popularly interpreted as both a social commentary and a way of visualizing the 4th-dimension by analogy. I attempt here to integrate these two seemingly disparate readings. Flatland is better interpreted as a story with a central theme that social, perceptual, and conceptual innovations are linked to changes in geometry.

In such cases as the shift from the two-dimensional world of Flatland to a three-dimensional Spaceland, the taxonomic restructuring of human importance from Linnaeaus to Darwin, or the part/whole proportional shift from Ptolemy’s earth as the center of the universe to Copernicus’s sun, new geometries have changed our thinking, seeing, and social values, and lie at the heart of innovations in both art and science. For example, the two greatest innovations in art — the Renaissance with geometric perspective, and the birth of modern art at the beginning of this century with n-dimensional and non-Euclidean geometries — were developed by artists who were thinking within new geometries.

When we view the history of scientific revolutions as new geometries, rather than only as new ideas, we gain direct access to potential manipulations of the structures of human innovation itself. I will discuss the seven historical markers of scientific revolutions (suggested by Kuhn, Cohen, and Popper), and how these seven traits correlate and can now be seen within the new paradigm of fractals and nonlinear sciences.
Differential Effects of Oral and Transdermal Estrogen/Progesterone Regimens on Sensitivity to Activated Protein C Among Postmenopausal Women
Authors: Oger Emmanuel , Alhenc-Gelas Martine , Lacut Karine , Blouch Marie-Thérèse , Roudaut Nathalie , Kerlan Véronique , Collet Michel , Abgrall Jean-François , Aiach Martine , Scarabin Pierre-Yves , Mottier Dominique
Published: July 2003

Objective—

Activated protein C (APC) resistance not related to the factor V Leiden mutation is a risk factor for venous thrombosis. Oral estrogen replacement therapy (ERT) has been reported to induce APC resistance. Little is known about the effect of transdermal estrogen.

Methods and Results—

We enrolled 196 postmenopausal women who were randomly allocated to receive either 1 mg 17β-estradiol orally (n=63) or 50 μg 17β-estradiol transdermally per day (n=68), both associated with 100 mg progesterone daily or placebo (n=65) for 6 months. An activated partial thromboplastin time (APTT)–based test and the effect of APC on thrombin potential (ETP) were used. Oral ERT induced an ETP-based APC resistance compared with both placebo (
P
=0.006) and transdermal ERT (
P
<0.001), but there was no significant effect of transdermal ERT compared with placebo (
P
=0.191). There was no significant effect of ERT on the APTT-based APC sensitivity ratio. Prothrombin fragment 1+2 plasma levels were significantly higher after 6 months of treatment in women allocated to oral ERT compared with those on placebo and transdermal ERT and were positively and significantly correlated with changes in ETP-based APC sensitivity ratio.

Conclusions—

Our data show that oral, unlike transdermal, estrogen induces APC resistance and activates blood coagulation. These results emphasize the importance of the route of estrogen administration.
Effect of Different Intensities of Exercise on Endothelium-Dependent Vasodilation in Humans
Authors: Goto Chikara , Higashi Yukihito , Kimura Masashi , Noma Kensuke , Hara Keiko , Nakagawa Keigo , Kawamura Mitsutoshi , Chayama Kazuaki , Yoshizumi Masao , Nara Isao
Published: July 2003

Background—

Aerobic exercise enhances endothelium-dependent vasodilation in hypertensive patients, patients with chronic heart failure, and healthy individuals. However, it is unclear how the intensity of exercise affects endothelial function in humans. The purpose of the present study was to determine the effects of different intensities of exercise on endothelium-dependent vasodilation in humans.

Methods and Results—

We evaluated the forearm blood flow responses to acetylcholine, an endothelium-dependent vasodilator, and isosorbide dinitrate, an endothelium-independent vasodilator, before and after different intensities of exercise (mild, 25% V̇
o
2
max; moderate, 50% V̇
o
2
max; and high, 75% V̇
o
2
max; bicycle ergometers, 30 minutes, 5 to 7 times per week for 12 weeks) in 26 healthy young men. Forearm blood flow was measured using a mercury-filled Silastic strain-gauge plethysmograph. Twelve weeks of moderate-intensity exercise, but not mild- or high-intensity exercise, significantly augmented acetylcholine-induced vasodilation (7.5±2.4 to 11.4±5.8 mL/min per 100 mL tissue;
P
<0.05). No intensity of aerobic exercise altered isosorbide dinitrate–induced vasodilation. The administration of N
G
-monomethyl-
l
-arginine, a nitric oxide synthase inhibitor, abolished the moderate-intensity exercise-induced augmentation of the forearm blood flow response to acetylcholine. High-intensity exercise increases plasma concentrations of 8-hydroxy-2′-deoxyguanosine (from 6.7±1.1 to 9.2±2.3 ng/mL;
P
<0.05) and serum concentrations of malondialdehyde-modified low-density lipoprotein (from 69.0±19.5 to 82.4±21.5 U/L;
P
<0.05), whereas moderate exercise tended to decrease both indices of oxidative stress.

Conclusions—

These findings suggest that moderate-intensity aerobic exercise augments endothelium-dependent vasodilation in humans through the increased production of nitric oxide and that high-intensity exercise possibly increases oxidative stress.
Platelet Glycoprotein IIb/IIIa Receptor Blockade Improves Vascular Nitric Oxide Bioavailability in Patients With Coronary Artery Disease
Authors: Heitzer Thomas , Ollmann Isabel , Köke Katharina , Meinertz Thomas , Munzel Thomas
Published: July 2003

Background—

Platelet glycoprotein IIb/IIIa receptor blockade not only enhances epicardial flow but also improves microvascular perfusion. Inhibition of abnormal platelet–endothelial interactions may contribute to this beneficial effect. The present study was designed to determine whether glycoprotein IIb/IIIa receptor blockade influences endothelial vasomotor function and NO bioactivity in patients with coronary artery disease.

Methods and Results—

Forty patients with symptomatic coronary artery stenosis were studied before planned percutaneous coronary intervention. By using venous occlusion plethysmography, endothelium-dependent and -independent vasodilation was determined by measuring forearm blood flow responses to acetylcholine with and without
N
G
-monomethyl-
l
-arginine (L-NMMA) and sodium nitroprusside. Vascular function tests were repeated during glycoprotein IIb/IIIa receptor blockade by tirofiban in 27 patients and by eptifibatide in 13 patients. A subgroup of 10 patients was retested 6 hours after stopping infusion of tirofiban. Glycoprotein IIb/IIIa receptor blockade by both substances improved acetylcholine-induced vasodilation and L-NMMA responses. Six hours after withdrawal of tirofiban infusion, the beneficial effects were not evident. Sodium nitroprusside–induced vasodilation was not changed by glycoprotein IIb/IIIa receptor blockade.

Conclusions—

These findings support the concept that abnormal platelet-endothelial interactions contribute to endothelial dysfunction and impaired NO bioactivity in patients with symptomatic coronary artery disease.
Randomized, Double-Blind, Placebo-Controlled, International Trial of the Oral IIb/IIIa Antagonist Lotrafiban in Coronary and Cerebrovascular Disease
Authors: Topol Eric J. , Easton Donald , Harrington Robert A. , Amarenco Pierre , Califf Robert M. , Graffagnino Carmen , Davis Stephen , Diener Hans-Christophe , Ferguson James , Fitzgerald Desmond , Granett Jeffrey , Shuaib Ashfaq , Koudstaal Peter J. , Theroux Pierre , Van de Werf Frans , Sigmon Kristina , Pieper Karen , Vallee Marc , Willerson James T.
Published: July 2003

Background—

This is the primary report of the large-scale evaluation of lotrafiban, an orally administered IIb/IIIa receptor antagonist, a unique trial with respect to the platelet antagonist, protocol design, and inclusion of cerebrovascular disease in a significant proportion of patients.

Methods and Results—

Patients with vascular disease were randomized to lotrafiban 30 or 50 mg BID on the basis of age and predicted creatinine clearance or placebo in addition to aspirin at a dose ranging from 75 to 325 mg/d at the discretion of the physician-investigator. Follow-up was for up to 2 years. The primary end point was the composite of all-cause mortality, myocardial infarction, stroke, recurrent ischemia requiring hospitalization, and urgent revascularization. Of 9190 patients enrolled from 23 countries and 690 hospitals, 41% had cerebrovascular disease at the time of entry, and 59% had coronary artery disease. Death occurred in 2.3% of placebo-assigned patients and 3.0% of lotrafiban-group patients (hazard ratio 1.33, 95% CI 1.03 to 1.72,
P
=0.026), and the cause of excess death was vascular related. There was no significant difference in the primary end point (17.5% compared with 16.4%, respectively; hazard ratio 0.94, 95% CI 0.85 to 1.03,
P
=0.19). Serious bleeding was more frequent in the lotrafiban group (8.0% compared with 2.8%;
P
<0.001). Serious bleeding was more common among patients who received higher doses of aspirin (>162 mg/d), with or without lotrafiban.

Conclusions—

Lotrafiban, an orally administered platelet glycoprotein IIb/IIIa blocker, induced a 33% increase in death rate, which was vascular in origin and not affected by the type of atherosclerotic involvement at entry to the trial. Although the dose of aspirin was not randomly assigned, the finding of increased bleeding with doses >162 mg/d is noteworthy.
Deficiency of Interleukin-1 Receptor Antagonist Promotes Neointimal Formation After Injury
Authors: Isoda Kikuo , Shiigai Masaru , Ishigami Norio , Matsuki Taizo , Horai Reiko , Nishikawa Kenichirou , Kusuhara Masatoshi , Nishida Yasuhiro , Iwakura Yoichiro , Ohsuzu Fumitaka
Published: July 2003

Background—

The cytokine interleukin (IL)-1 is an important mediator of inflammation and cardiovascular disease. Activity of this cytokine is modulated endogenously via the IL-1 receptor antagonist (IL-1Ra). The role of IL-1Ra in neointima formation after injury, however, is poorly understood.

Methods and Results—

Using IL-1Ra–deficient (IL-1Ra
−/−
; backcrossed 8 generations into the C57BL/6J background) and wild-type (IL-1Ra
+/+
) mice, we investigated neointimal formation 3 weeks after femoral artery injury induced by an external vascular cuff model. Intima and media thicknesses were measured, and the intima/media ratio was calculated. The mean intimal thickness and the intima/media ratio of IL-1Ra
−/−
mice increased by 249% (31.8±2.9 μm [n=10] versus 9.1±0.7 μm [n=10];
P
<0.0001) and 257% (2.5±0.2 versus 0.7±0.1;
P
<0.0001), respectively, compared with IL-1Ra
+/+
mice. No significant differences were observed in the medial thickness. Control immunostaining for IL-1Ra in injured vessels localized IL-1β and the endogenous inhibitor in the endothelium and inflammatory cells of the adventitia in IL-1Ra
+/+
but not IL-1Ra
−/−
mice.

Conclusions—

The absence of IL-1Ra promotes neointimal formation in mice after injury. These results suggest that endogenous IL-1Ra may suppress other occlusive vascular responses to injury, such as atherosclerosis and restenosis after angioplasty.
Responses to GABA
A
Receptor Activation Are Altered in NTS Neurons Isolated From Renal-Wrap Hypertensive Rats
Authors: Tolstykh Gleb , Belugin Sergei , Tolstykh Olga , Mifflin Steve
Published: July 2003

The inhibitory amino acid GABA is a potent modulator of the spontaneous discharge and the responses to afferent inputs of neurons in the nucleus of the solitary tract (NTS). To determine if responses to activation of GABA
A
receptors are altered in hypertension, GABA
A
receptor–evoked whole cell currents were measured in enzymatically dispersed NTS neurons from 33 normotensive (NT, 109±4 mm Hg, n=7) and 24 hypertensive (HT, 167±5 mm Hg, n=24) rats. GABA
A
receptor–evoked currents reversed at the calculated equilibrium potential for chloride and were blocked by bicuculline (n=6). Membrane capacitance was the same in neurons from NT (7.5±0.6 pF, n=62) and HT (6.8±0.6 pF, n=51) rats. The EC
50
for peak GABA-evoked currents cells was significantly greater in neurons from HT (21.0±2.6 μmol/L, n=16) compared with NT rats (13.0±1.8 μmol/L, n=14,
P
=0.01). The EC
50
of neurons exhibiting DiA labeling of presumptive aortic nerve terminals was no different than that observed in the nonlabeled cells (19.0±4.9 μmol/L, n=4). The time constant for desensitization of GABA
A
-evoked currents was the same in neurons from HT (4.5±0.3 seconds, n=17) and NT rats (3.8±0.3 seconds, n=17,
P
>0.05). Repetitive pulse application of GABA revealed a more rapid decline in the evoked current in neurons from HT compared with NT rats. The amplitude of the 5th pulse of GABA (5-second duration, 2-second interval) was 21±2% the amplitude of the 1st pulse in NT rats (n=10) and 14±2% in HT rats (n=11,
P
<0.05). These alterations in GABA
A
-receptor evoked currents could render the neurons less sensitive to GABA
A
receptor inhibition and influence afferent integration by NTS neurons in HT.