bluuebunny/crossref_metadata_2025 huggingface dataset:
Antigenicity and Immunogenicity of a Synthetic Oligosaccharide-Protein Conjugate Vaccine against
Haemophilus influenzae
Type b
Authors: Fernández-Santana V. , Cardoso Félix , Rodriguez Arlene , Carmenate Tania , Peña Luis , Valdés Yuri , Hardy Eugenio , Mawas Fatme , Heynngnezz Lazaro , Rodríguez Maria C. , Figueroa Ignacio , Chang Janoi , Toledo Maria E. , Musacchio Alexis , Hernández Ibis , Izquierdo Mabel , Cosme Karelia , Roy Rene , Verez-Bencomo V.
Published: November 2004

Polysaccharide-protein conjugates as vaccines have proven to be very effective in preventing
Haemophilus influenzae
type b infections in industrialized countries. However, cost-effective technologies need to be developed for increasing the availability of anti-
H. influenzae
type b vaccines in countries from the developing world. Consequently, vaccine production with partially synthetic antigens is a desirable goal for many reasons. They may be rigidly controlled for purity and effectiveness while at the same time being cheap enough that they may be made universally available. We describe here the antigenicity and immunogenicity of several
H. influenzae
type b synthetic oligosaccharide-protein conjugates in laboratory animals. The serum of
H. influenzae
type b-immunized animals recognized our synthetic
H. influenzae
type b antigens to the same extent as the native bacterial capsular polysaccharide. Compared to the anti-
H. influenzae
type b vaccine employed, these synthetic versions induced similar antibody response patterns in terms of titer, specificity, and functional capacity. The further development of synthetic vaccines will meet urgent needs in the less prosperous parts of the world and remains our major goal.
Diversity and Host Range of Shiga Toxin-Encoding Phage
Authors: Gamage Shantini D. , Patton Angela K. , Hanson James F. , Weiss Alison A.
Published: November 2004

Shiga toxin 2 (Stx2) from the foodborne pathogen
Escherichia coli
O157:H7 is encoded on a temperate bacteriophage. Toxin-encoding phages from C600::933W and from six clinical
E. coli
O157:H7 isolates were characterized for PCR polymorphisms, phage morphology, toxin production, and lytic and lysogenic infection profiles on O157 and non-O157 serotype
E. coli
. The phages were found to be highly variable, and even phages isolated from strains with identical pulsed-field gel electrophoresis profiles differed. Examination of cross-plaquing and lysogeny profiles further substantiated that each phage is distinct; reciprocal patterns of susceptibility and resistance were not observed and it was not possible to define immunity groups. The interaction between Shiga toxin-encoding phage and intestinal
E. coli
was examined. Lytic infection was assessed by examining Shiga toxin production following overnight incubation with phage. While not common, lytic infection was observed, with a more-than-1,000-fold increase in Stx2 seen in one case, demonstrating that commensal
E. coli
cells can amplify Shiga toxin if they are susceptible to infection by the Shiga toxin-encoding phages. Antibiotic-resistant derivatives of the Stx2-encoding phages were used to examine lysogeny. Different phages were found to lysogenize different strains of intestinal
E. coli
. Lysogeny was found to occur more commonly than lytic infection. The presence of a diverse population of Shiga toxin-encoding phages may increase the pathogenic fitness of
E. coli
O157:H7.
Characterization of a Defensin from the Sand Fly
Phlebotomus duboscqi
Induced by Challenge with Bacteria or the Protozoan Parasite
Leishmania major
Authors: Boulanger Nathalie , Lowenberger Carl , Volf Petr , Ursic Raul , Sigutova Lucie , Sabatier Laurence , Svobodova Milena , Beverley Stephen M. , Späth Gerald , Brun Reto , Pesson Bernard , Bulet Philippe
Published: November 2004

Antimicrobial peptides are major components of the innate immune response of epithelial cells. In insect vectors, these peptides may play a role in the control of gut pathogens. We have analyzed antimicrobial peptides produced by the sand fly
Phlebotomus duboscqi
, after challenge by injected bacteria or feeding with bacteria or the protozoan parasite
Leishmania major
. A new hemolymph peptide with antimicrobial activity was identified and shown to be a member of the insect defensin family. Interestingly, this defensin exhibits an antiparasitic activity against the promastigote forms of
L. major
, which reside normally within the sand fly midgut.
P. duboscqi
defensin could be induced by both hemolymph or gut infections. Defensin mRNA was induced following infection by wild-type
L. major
, and this induction was much less following infections with
L. major
knockout mutants that survive poorly in sand flies, due to specific deficiencies in abundant cell surface glycoconjugates containing phosphoglycans (including lipophosphoglycan). The ability of gut pathogens to induce gut as well as fat body expression of defensin raises the possibility that this antimicrobial peptide might play a key role in the development of parasitic infections.
BBE02 Disruption Mutants of
Borrelia burgdorferi
B31 Have a Highly Transformable, Infectious Phenotype
Authors: Kawabata Hiroki , Norris Steven J. , Watanabe Haruo
Published: November 2004

We constructed highly transformable and infectious
Borrelia burgdorferi
B31 by inactivating BBE02, a putative restriction-modification gene on the linear plasmid lp25. The low-passage-number B31 clones 5A4 (containing all plasmids) and 5A18 (lp28-4
−
lp56
−
) were used for this study, and BBE02 was disrupted by homologous recombination. The transformation efficiency with the shuttle vector pBSV2
C03
::
gntΔkan
was increased from <1 to ∼10 colonies per μg of DNA for 5A4 and 5A4 BBE02::Kan
r
and from 14 to approximately 600 colonies per μg of DNA for 5A18 and 5A18 BBE02::Kan
r
. lp25, which is required for infectivity in mice, was retained in BBE02 mutants transformed with pBSV2
C03
::
gntΔkan
, but lp25 was not detected in transformants of the parental clones 5A4 and 5A18. BBE02 disruptants and pBSV2
C03
::
gntΔkan
transformants of these clones remained infectious in C3H/HeN mice, and the 50% infective doses of the BBE02 disruptants were <10
2
organisms per mouse. The inactivation of BBE02 thus eliminates a transformation barrier for infectious
B. burgdorferi
B31 and will provide a valuable tool for studying the virulence factors of Lyme disease.
Distinct Roles of Reactive Nitrogen and Oxygen Species To Control Infection with the Facultative Intracellular BacteriumFrancisella tularensis
Authors: Lindgren Helena , Stenmark Stephan , Chen Wangxue , Tärnvik Arne , Sjöstedt Anders
Published: November 2004

Reactive nitrogen species (RNS) and reactive oxygen species (ROS) are important mediators of the bactericidal host response. We investigated the contribution of these two mediators to the control of infection with the facultative intracellular bacteriumFrancisella tularensis. When intradermally infected with the live vaccine strainF. tularensisLVS, mice deficient in production of RNS (iNOS−/−mice) or in production of ROS by the phagocyte oxidase (p47phox−/−mice) showed compromised resistance to infection. The 50% lethal dose (LD50) for iNOS−/−mice was <20 CFU, and the LD50for p47phox−/−mice was 4,400 CFU, compared to an LD50of >500,000 CFU for wild-type mice. The iNOS−/−mice survived for 26.4 ± 1.8 days, and the p47phox−/−mice survived for 10.1 ± 1.3 days. During the course of infection, the serum levels of gamma interferon (IFN-γ) and interleukin-6 were higher in iNOS−/−and p47phox−/−mice than in wild-type mice. Histological examination of livers of iNOS−/−mice revealed severe liver pathology. Splenocytes obtained 5 weeks after primary infection from antibiotic-treated iNOS−/−mice showed an in vitro recall response that was similar in magnitude and greater secretion of IFN-γ compared to cells obtained from wild-type mice. In summary, mice lacking expression of RNS or ROS showed extreme susceptibility to infection withF. tularensisLVS. The roles of RNS and ROS seemed to be distinct since mice deficient in production of ROS showed dissemination of infection and died during the early phase of infection, whereas RNS deficiency led to severe liver pathology and a contracted course of infection.
Synovial Fibroblasts Infected with
Salmonella enterica
Serovar Typhimurium Mediate Osteoclast Differentiation and Activation
Authors: Zhang Xiang , Aubin Jane E. , Kim Tae-Hwan , Payne Ursula , Chiu Basil , Inman Robert D.
Published: November 2004

The mechanisms whereby arthritogenic organisms may induce cartilage and bone erosions in infection-triggered arthritis remain unknown. In this study, we asked whether an arthritogenic organism could contribute to osteoclast differentiation and activation through regulation of the receptor activator of NF-κB ligand (RANKL) in synovial fibroblasts. Rat synovial fibroblasts were infected in vitro with
Salmonella enterica
serovar Typhimurium and monitored over time. The expression of RANKL in resting and infected synovial fibroblasts was quantified by reverse transcription-PCR and Western blotting. Osteoclast progenitors, isolated from femurs of 8-week-old rats and cultured in the presence of macrophage colony-stimulating factor, were cocultured with either infected or noninfected synovial fibroblasts for 2 to 4 days. Differentiation and maturation of osteoclasts were determined by morphology and tartrate-resistant acid phosphatase (TRAP) staining and by a bone resorption bioassay. RANKL expression was undetectable in resting synovial fibroblasts but was dose-dependently upregulated in cells after
Salmonella
infection. Osteoprotegerin was constitutively expressed by synovial fibroblasts and was not upregulated by infection. Further, we observed the formation of multinucleated TRAP-positive cells and formation of bone resorption pits in cocultures of bone marrow-derived osteoclast precursors with synovial fibroblasts infected with
Salmonella
but not with heat-killed
Salmonella
or noninfected cells. Arthritogenic bacteria may alter bone structure via synovial fibroblast intermediaries, since infected synovial fibroblasts (i) upregulate RANKL expression and (ii) enhance osteoclast precursor maturation into multinucleated, TRAP-positive, bone-resorbing, osteoclast-like cells. These data provide a link between infection and osteoclastogenesis. A better understanding of infection-mediated osteoclast differentiation and activation may provide new therapeutic strategies for inflammatory joint disease.
Intranasal Vaccination with Streptococcal Fibronectin Binding Protein Sfb1 Fails To Prevent Growth and Dissemination ofStreptococcus pyogenesin a Murine Skin Infection Model
Authors: McArthur J. , Medina E. , Mueller A. , Chin J. , Currie B. J. , Sriprakash K. S. , Talay S. R. , Chhatwal G. S. , Walker M. J.
Published: November 2004

Fibronectin binding protein F1 (Sfb1) ofStreptococcus pyogenes(group A streptococcus [GAS]) is a well-characterized adhesin that has been shown to induce protection in mice against a lethal intranasal GAS challenge after intranasal immunization with cholera toxin B subunit (CTB) as adjuvant. With a murine skin infection model, we have shown that Sfb1/CTB vaccination neither elicits opsonizing antibodies nor prevents systemic bacterial growth and dissemination to internal organs after a subcutaneous GAS challenge. These results indicate that an Sfb1-based vaccine should be complemented with additional protective antigens in order to be used in areas such as the tropical north of Australia, where the skin is the primary route of entry for invasive streptococcal diseases.
Lipid Raft-Mediated Entry Is Not Required for
Chlamydia trachomatis
Infection of Cultured Epithelial Cells
Authors: Gabel B. R. , Elwell C. , van Ijzendoorn S. C. D. , Engel J. N.
Published: November 2004

Using pharmacologic and biochemical criteria, we evaluated whether uptake of four different
Chlamydia trachomatis
serovars, D, E, K, and L2, was dependent upon lipid rafts. Our data suggest that lipid raft-mediated entry is not required for
C. trachomatis
infection of cultured epithelial cells.
Listeria monocytogenesσBContributes to Invasion of Human Intestinal Epithelial Cells
Authors: Kim Heesun , Boor Kathryn J. , Marquis Hélène
Published: November 2004

The role of σBinListeria monocytogenesinfection of human intestinal epithelial cells was investigated. Invasion defects associated with loss of σBparalleled those of a ΔinlAstrain independently of the σB-dependent P2prfApromoter. Concomitantly, amounts ofinlAtranscript and InlA protein were significantly decreased in the ΔsigBstrain.
Formulation of the classical and the relativistic Doppler effect by a systematic method
Authors: Huang Y -S , Lu K -H
Published: November 2004

The classical and the relativistic Doppler effect for both acoustic and light waves are formulated exactly by a systematic method. This method differs only in its usage of classical and relativistic transformation laws in the formulation of the classical and relativistic Doppler effect, respectively. The method is straightforward, and much more logically rigorous than the typical demonstrations using graphical illustration. In the formulation of the classical Doppler effect, as expected, no aberration and no transverse classical Doppler effect are found. In the formulation of the relativistic Doppler effect, one important discovery is that the transverse relativistic Doppler effect depends only on the speed of the source relative to the observer, irrespective of the nonskew velocities of the source and the observer relative to the medium. PACS No.: 03.30.+p
Atomic state interference with fast hydrogen-like helium
Authors: Pal'chikov V G , Yakovlev V P , Sokolov Yu L
Published: November 2004

We study the stationary interference of the 2S1/2 or 2P1/2 states due to the passage of metastable hydrogen-like helium ions 4He+ through static electric fields. The basic theory of atomic state interference is presented and experimental conditions allowing observation of the interference pattern with a beam of 4He+ ions are analyzed. We show that optimal conditions are within the reach of modern day experimental techniques. We present theoretical interference curves for two types of atomic interferometers and discuss in detail approaches for the precise measurement of the Lamb shift δn=2 = 2S1/2  2P1/2 in 4He+. PACS Nos.: 31.30.Jv, 32.70.Fw, 39.10.+j, 39.20.+q
Relativity in introductory physics
Authors: Baylis W E
Published: November 2004

A century after its formulation by Einstein, it is time to incorporate special relativity early in the physics curriculum. The approach advocated here employs a simple algebraic extension of vector formalism that generates Minkowski spacetime, displays covariant symmetries, and enables calculations of boosts and spatial rotations without matrices or tensors. The approach is part of a comprehensive geometric algebra with applications in many areas of physics, but only an intuitive subset is needed at the introductory level. The approach and some of its extensions are given here and illustrated with insights into the geometry of spacetime. PACS Nos.: 03.30.+p, 01.40.Gm, 03.50.De, 02.10.Hh
Exact normal forces and trajectories for a rotating tripod sliding on a smooth surface
Authors: Shegelski M R.A. , Goodvin G L , Booth R , Bagnall P , Reid M
Published: November 2004

We study the motion of a rotating tripod sliding over a smooth surface. The tripod is important and unique in that it is the only case where all aspects of the motion can be solved exactly. From the three constraint equations, we calculate the three normal forces and friction forces, which we then use to calculate the trajectory and other physical quantities of interest. We report novel results: the normal force has an interesting form when the sliding speed and the speed of rotation are almost equal; the tripod can execute serpentine trajectories; trajectories can have large lateral deflections; the translational kinetic energy can decrease and increase during a full rotation; the tripod can tip at a very late stage of its motion. The tripod trajectories are compared to trajectories of rotating, sliding cylinders that have continuous contact rings. We discuss significant implications of our results. PACS No.: 45.40.–f
Carbon stable isotopes: a tool for studying the mating, oviposition, and spatial distribution of races of European corn borer, Ostrinia nubilalis, among host plants in the field
Authors: Ponsard S , Bethenod M -T , Bontemps A , Pélozuelo L , Souqual M -C , Bourguet D
Published: November 2004

The European corn borer, Ostrinia nubilalis (Hübner, 1796) (Lepidoptera: Crambidae), is a polyphagous corn pest species that includes two host races: one feeding on corn (Zea mays L.) and one feeding on mugwort (Artemisia vulgaris L.) and hop (Humulus lupulus L.). Being able to determine the type of host plant on which field-caught moths fed as larvae would allow for the quantification of mating rates within and between races, as well as the quantification of the spatial distribution and oviposition of both races in the field. We found that stable carbon isotopes (δ;13C) are a reliable indicator of host-plant photosynthetic type (C3 or C4) regardless of adult food and intensity of metabolism; so even when food or metabolism had a significant effect on wing δ13C values, the magnitude of this effect was too small to obscure the signal characterizing host-plant type. Egg and spermatophore δ13C values similarly reflect female and male host-plant type, respectively, regardless of adult feeding. We found 224 host-plant species of O. nubilalis in the literature, including 19 species with C4-type photosynthesis. However, in temperate areas, corn is probably the only significant C4 source of adult moths. Accordingly, wing δ13C values were more variable in field-caught moths showing a typical C3-type δ13C value than in those showing a typical C4-type δ13C value.
Discrimination of airborne pheromones by mate-searching male western black widow spiders (Latrodectus hesperus): species- and population-specific responses
Authors: Kasumovic Michael M , Andrade Maydianne C.B
Published: November 2004

Males of many web-building spiders abandon their webs at maturity to search for a potential mate. Since wandering can be very risky, and females are often widely distributed, males should use any cues that might ensure rapid and accurate location of conspecific females. Although it has long been assumed that mate-searching male spiders locate females using species-specific airborne pheromones released from webs, few studies have experimentally examined this phenomenon in the field. Our results show that male western black widow spiders (Latrodectus hesperus Chamberlin and Ivie, 1935) are attracted to females' webs by an airborne cue released from the web, can distinguish between conspecific and heterospecific females, and can discriminate between webs produced by conspecific females from different geographical populations. The latter result demonstrates a partial premating block to fertilization between populations at the edges of the species range. Complementary interpopulation laboratory matings suggest that there may also be a postmating block to fertilization, as these copulations did not result in viable offspring. This study provides experimental field evidence of male attraction by airborne pheromones released from females' webs, shows the potential importance of these pheromones in species discrimination in black widow spiders, and suggests that northern and southern populations of L. hesperus may be incipient biological species.
Physiological tolerances of three sympatric riparian wolf spiders (Araneae: Lycosidae) correspond with microhabitat distributions
Authors: DeVito Jill , Meik Jesse M , Gerson Marina M , Formanowicz, Jr. Daniel R
Published: November 2004

Coexisting species from the same ecological guild often exhibit different adaptations to discontinuous, abiotic environmental factors. In the laboratory, we compared tolerance to thermal and desiccation stress among three sympatric wolf spiders (Pirata sedentarius Montgomery, 1904, Pardosa lapidicina Emerton, 1885, and Pardosa fuscula Thorell, 1875). In the field, we examined spatial structure across a microhabitat (moisture) gradient in a streamside cobble habitat where these three species are abundant. Female P. sedentarius succumbed more quickly to desiccation stress than females of either Pardosa species. In the absence of thermal stress, desiccation tolerance was high for both Pardosa species. However, P. fuscula appears to be more resistant to combined thermal and desiccation stress than P. lapidicina. These findings correspond with the results of the field survey; the distribution of P. sedentarius was the most restricted (by proximity to the shoreline) among the three species. Contingency analyses also revealed greater relative abundance of P. fuscula than P. lapidicina farther away from the creek. Further examination of spatial structure suggests that neither of these two species was restricted by proximity to the shoreline within the sampling grid.
General polynomial decomposition and the s-1-decomposition are NP-Hard
Authors: Dickerson Matthew T.
Published: November 2004

In the past few years, much work has been done on the functional decomposition of polynomials. Beginning with the first polynomial time algorithm of Kozen and Landau1 for the decomposition of a univariate polynomial in the “tame” case, significant progress has been made toward polynomial time algoithms for the more general cases: decomposition of multivariate polynomials, and decomposition in the “wild” case.2−8 However it has remained an open problem whether general multivariate decomposition is in P. In this paper, we present a basic form for the general polynomial decomposition problem which encompasses most forms of previously examined decomposition problems, and then prove that the problem is NP-Hard by proving that a sub-problem called the S-1-Decomposition problem is NP-Hard.
THE EQUALITY CONDITION FOR INFINITE CATENATIONS OF TWO SETS OF FINITE WORDS
Authors: MELNIKOV BORIS F.
Published: November 2004

Some special sets of ω-words, namely, the sets that can be obtained by catenating nonempty finite sets of words, an infinite number of times, are considered. A condition for the equality of two such sets of ω-words is obtained.
STRUCTURAL CONNECTIONIST LEARNING WITH COMPLEMENTARY CODING
Authors: NAMATAME AKIRA , TSUKAMOTO YOSHIAKI
Published: November 2004

We propose a new learning algorithm, structural learning with the complementary coding for concept learning problems. We introduce the new grouping measure that forms the similarity matrix over the training set and show this similarity matrix provides a sufficient condition for the linear separability of the set. Using the sufficient condition one should figure out a suitable composition of linearly separable threshold functions that classify exactly the set of labeled vectors. In the case of the nonlinear separability, the internal representation of connectionist networks, the number of the hidden units and value-space of these units, is pre-determined before learning based on the structure of the similarity matrix. A three-layer neural network is then constructed where each linearly separable threshold function is computed by a linear-threshold unit whose weights are determined by the one-shot learning algorithm that requires a single presentation of the training set. The structural learning algorithm proceeds to capture the connection weights so as to realize the pre-determined internal representation. The pre-structured internal representation, the activation value spaces at the hidden layer, defines intermediate-concepts. The target-concept is then learned as a combination of those intermediate-concepts. The ability to create the pre-structured internal representation based on the grouping measure distinguishes the structural learning from earlier methods such as backpropagation.
A CONNECTIONIST APPROACH TO VERTEX COVERING PROBLEMS
Authors: Peng Yun , Reggia James A. , Li Tao
Published: November 2004

This paper describes a connectionist approach to solving computationally difficult minimum vertex covering problems. This approach uses the graph representing the vertex covering problem as the connectionist network without any modifications (nodes of the connectionist network represent vertices and links represent edges of the given graph). The activation rule governing node behavior is derived by breaking down the global constraints on a solution into local constraints on individual nodes. The resulting model uses a competitive activation mechanism to carry out the computation where vertices compete not by explicit inhibitory links but through common resources (edges). Convergence and other properties of this model are formally established by introducing a monotonically non-increasing global energy function. Simulation results show that this model yields very high accuracy, significantly outperforming a well-known sequential approximation algorithm.
NEURAL NETWORK ANALYSIS OF THERMAL IMAGE DATA
Authors: Hejazi Shahram , Bauer Stephen M. , Spangler Robert A.
Published: November 2004

Thermal images of the human body, when obtained at different wavelengths of infrared radiation, offer a means of eliminating several sources of error which can occur in single-wavelength thermal imaging procedures. Algebraic treatment of image data, however, utilizing nonlinear functions derived from integration over Planck’s law of radiation distribution, proves to be extremely sensitive to experimental errors in measurement and truncation errors in computation. The neural network backpropagation algorithm has been applied to thermal data processing which has resulted in a more stable and error-tolerant method of data reduction. Trained on a computed ideal data set, this algorithm has been shown to more reliably process actual data.
SPOKEN LETTER RECOGNITION WITH NEURAL NETWORKS
Authors: REYNOLDS JAKE , TARASSENKO LIONEL
Published: November 2004

Neural networks have recently been applied to real-world speech recognition problems with a great deal of success. This paper develops a strategy for optimising a neural network known as the Radial Basis Function classifier (RBF) on a large spoken letter recognition problem designed by British Telecom Research Laboratories. The strategy developed can be viewed as a compromise between a fully adaptive approach involving prohibitively large amounts of computation and a heuristic approach resulting in poor generalisation. A value for the optimal number of kernel functions is suggested and methods for determining the positions of the centres and the values of the kernel function widths are provided. During the evolution of the optimisation strategy, it was demonstrated that spatial organisation of the centres does not adversely affect the ability of the classifier to generalise. An RBF employing the optimisation strategy achieved a lower error rate than Woodland’s multilayer perceptron26 and two traditional static pattern classifiers on the same problem. The error rate of the RBF was very close to the estimated minimum error rate obtainable with an optimal Bayesian classifier. An examination of the computational requirements of the classifiers illustrated a significant trade-off between the computational investment in training and level of generalisation achieved.
A MEASURE OF RELATIVE ROBUSTNESS FOR FEEDFORWARD NEURAL NETWORKS SUBJECT TO SMALL INPUT PERTURBATIONS
Authors: CHOW MO-YUEN , YEE SUE OI
Published: November 2004

The relative robustness of artificial neural networks subject to small input perturbations (e.g. measurement noises) is an important issue in real world applications. This paper uses the concept of input-output sensitivity analysis to derive a relative network robustness measure for different feedforward neural network configurations. For illustration purposes, this measure is used to compare different neural network configurations designed for detecting incipient faults in induction motors. Analytical and simulation results are presented to show that the relative network robustness measure derived in this paper is an effective indicator of the relative performance of different feedforward neural network configurations in noisy environments and that this measure should be considered in the design of neural networks for real time applications. The concept of input-output sensitivity analysis and relative network robustness measure presented can be extended to analyze other neural networks designed for on-line applications.
CLASSIFICATION AND PREDICTION OF PROTEIN SIDE-CHAINS BY NEURAL NETWORK TECHNIQUES
Authors: IRWIN J. , BOHR H. , MOCHIZUKI K. , WOLYNES P.G.
Published: November 2004

Neural Network methodology is used to classify and predict side-chain configurations in proteins on the basis of their sequence and in some cases also Cα-atomic distance information. In some of these methods, where Potts Associative Memories are employed, a mixed set of Potts systems each describe the various orientational states of a particular side-chain. The methods can find the correct side-chain orientations in proteins reasonably well after being trained on a data set of other proteins of known 3-dimensional structure.
PROTEINS AND RANDOM HETEROPOLYMERS: AN OVERVIEW
Authors: IORI GIULIA
Published: November 2004

We present a brief review of the main analytical and experimental results on the problem of protein folding. We will then discuss the conformational properties of the IMP model for an heteropolymeric chain at low and zero temperature. Finally we will analyze the dynamical relaxation of this system subject to the action of an external perturbation and we will discuss the localization of the normal oscillation modes around one stable configuration.
PATTERN RECOGNITION: INVARIANTS IN 3D
Authors: Proriol J.
Published: November 2004

We define invariants for 3D objects with a spherical symmetry. These new invariants are used to tag the number of jets in e+ e− events.
PIXE ANALYSIS OF TRACE ELEMENTS IN SERUM AND HAIR OF PATIENTS WITH BRAIN TUMORS
Authors: MA CHENGJUN , YIN ZHONGLI , HAO JIFANG , JIONG XINZHOU , SU QIONG , WU XIAOFENG , WANG KUI
Published: November 2004

This investigation describes results of measurements of trace element distributions in serum and hair obtained from 30 patients with brain tumors. The experimental procedure is also described in this article. The results show that the contents of Zn, Fe and Sr in serum are lower compared to those of healthy people (p<0.01, p<0.05 and p<0.05). The contents of Ca, Cu, Sr and Zn in hair are decreased compared to healthy people (p<0.01 and p<0.05), while the contents of Cr and Fe in hair are higher by 2 times and 1.8 times (p<0.01), respectively. The results above might be of clinical importance.
SURFACE EMITTING LASERS
Authors: IGA KENICHI
Published: November 2004

In this paper we review the progress and basic technology of vertical cavity surface emitting lasers together with related parallel surface operating optical devices. First, the concept of a vertical cavity surface emitting laser is presented, and then currently developed devices and their performances will be introduced. We will then feature some technical issues, such as multilayer structures, 2-dimensional arrays, photonic integration, etc. Lastly, future prospects for parallel lightwave subsystems using surface emitting lasers will be discussed.
A NEW EQUIAFFINE THEORY FOR SURFACES IN ℝ4
Authors: NOMIZU KATSUMI , VRANCKEN LUC
Published: November 2004

In this paper, we investigate the geometry of nondegenerate affine surfaces in ℝ4. The main idea is to introduce an equiaffine structure on the surface by constructing a canonical transversal plane field with the aid of the affine metric.

As an application, we then investigate surfaces with vanishing cubic forms. If the affine metric is positive-definite, such a surface can be locally described as a complex curve in [Formula: see text]. On the other hand, if the affine metric is indefinite, such a surface can be seen as the product of two planar curves.
SPECTRAL INVARIANCE OF DENSE SUBALGEBRAS OF OPERATOR ALGEBRAS
Authors: SCHWEITZER LARRY B.
Published: November 2004

We define the notion of strong spectral invariance for a dense Fréchet subalgebra A of a Banach algebra B. We show that if A is strongly spectral invariant in a C*-algebra B, and G is a compactly generated polynomial growth Type R Lie group, not necessarily connected, then the smooth crossed product G ⋊ A is spectral invariant in the C*-crossed product G ⋊ B. Examples of such groups are given by finitely generated polynomial growth discrete groups, compact or connected nilpotent Lie groups, the group of Euclidean motions on the plane, the Mautner group, or any closed subgroup of one of these. Our theorem gives the spectral invariance of G ⋊ A if A is the set of C∞-vectors for the action of G on B, or if B = C0 (M), and A is a set of G-differentiable Schwartz functions [Formula: see text] on M. This gives many examples of spectral invariant dense subalgebras for the C*-algebras associated with dynamical systems. We also obtain relevant results about exact sequences, subalgebras, tensoring by smooth compact operators, and strong spectral invariance in L1 (G, B).
HARMONIC MAPS FROM A CLOSED SURFACE OF HIGHER GENUS TO THE UNIT 2-SPHERE
Authors: WANG GUOFANG
Published: November 2004

We obtain the existence of harmonic maps of degree one from a closed Riemann surface of genus greater than 1 with a metric admitting a plane of symmetry to the unit 2-sphere.
REVIEW OF MATCHED FIELD PROCESSING FOR ENVIRONMENTAL INVERSE PROBLEMS
Authors: TOLSTOY A.
Published: November 2004

Matched Field Processing (MFP) is a signal processing technique that has enjoyed much recent success in the Underwater Acoustics community, mainly as a consequence of the high accuracy currently achievable in predictions of non-isotropic, non-planar ocean acoustic fields. MFP is applied to acoustic fields measured on arrays of hydrophones and has been used primarily to solve the inverse source problem, i.e., to determine the unknown range, depth, and bearing of acoustic sources in a known ocean environment. However, the MFP approach has also been applied to the environmental inverse problem, i.e., to determine the characteristics of an unknown ocean environment. This paper will review the work done in this latter area.
FUZZY NUMBER SUBTRACTION CONVOLUTION ON THE CM-2
Authors: PETKOV NIKOLAY
Published: November 2004

The running time of data-parallel algorithms can be reduced by avoiding global reduction operations. Using fuzzy number subtraction convolution as an example, this paper illustrates how data-parallel programs can be restructured to eliminate global reduction operations. This is done by using techniques from systolic array design. The algorithms are programmed in CM Fortran and have been run on a Connection Machine CM-2. The running time results show that advantages can be achieved in a considerable domain of the problem size space. At the same time the results show that for obtaining shortest running times different algorithms have to be used in different domains.
STUDY OF THE A + B → C REACTION-DIFFUSION PROCESS
Authors: CHOPARD BASTIEN , DROZ MICHEL
Published: November 2004

In low dimensions, reaction-diffusion phenomena may not be correctly described by the usual differential equations: fluctuations play an important role on the time behavior of these systems. We present a cellular automata model which simulate such processes, taking into account all the fluctuations and giving the correct dynamics. The implementation of this model on a Connection Machine CM-2 is discussed, as well as the results of the numerical simulations.
NONEQUILIBRIUM PHASE TRANSITIONS IN CATALYSIS AND POPULATION MODELS
Authors: DICKMAN RONALD
Published: November 2004

A wide variety of far-from-equilibrium models, arising in fields such as surface catalysis, autocatalytic chemical reactions, and epidemic or population models, exhibit phase transitions into an absorbing state. When continuous, these transitions typically belong to the universality class of directed percolation, but unusual phase diagrams and new kinds of critical behavior have also been identified.
SYMPLECTIC NUMERICAL METHODS FOR HAMILTONIAN PROBLEMS
Authors: SANZ-SERNA J. M. , CALVO M. P.
Published: November 2004

We consider symplectic methods for the numerical integration of Hamiltonian problems, i.e. methods that preserve the Poincaré integral invariants. Examples of symplectic methods are given and numerical experiments are reported.
HIGH PRECISION SIMULATION TECHNIQUES FOR LATTICE FIELD THEORY
Authors: Wolff Ulli
Published: November 2004

An overview is given over the recently developed and now widely used Monte Carlo algorithms with reduced or eliminated critical slowing down. The basic techniques are overrelaxation, cluster algorithms and multigrid methods. With these tools one is able to probe much closer than before the universal continuum behavior of field theories on the lattice. This is demonstrated by reviewing some applications.
A NUMERICAL IMPLEMENTATION OF THE DIRAC EQUATION ON A HYPERCUBE MULTICOMPUTER
Authors: WELLS J. C. , UMAR A. S. , OBERACKER V. E. , BOTTCHER C. , STRAYER M. R. , WU J.-S. , DRAKE J. , FLANERY R.
Published: November 2004

We describe the numerical methods used to solve the time-dependent Dirac equation on a three-dimensional Cartesian lattice. Efficient algorithms are required for computationally intensive studies of nonperturbative electromagnetic lepton-pair production in relativistic heavy-ion collisions. Discretization is achieved through the lattice basis-spline collocation method, in which quantum-state vectors and coordinate-space operators are expressed in terms of basis-spline functions on a spatial lattice. For relativistic lepton fields on a lattice, the fermion-doubling problem is central in the formulation of the numerical method. All numerical procedures reduce to a series of matrix-vector operations which we perform on the Intel iPSC/860 hypercube, making full use of parallelism. We discuss solutions to the problems of limited node memory and node-to-node communication overhead inherent in using distributed-memory, multiple-instruction, multiple-data stream parallel computers.
BHAGEN: AN EVENT GENERATOR OF BHABHA SCATTERING AT Z0 ENERGY, FOR SMALL AND LARGE SCATTERING ANGLES
Authors: CAFFO M. , CZYZ H. , REMIDDI E.
Published: November 2004

The event generator BHAGEN provides a realistic description of Bhabha scattering at Z0 energy, for both small and large scattering angles. The algorithms used to build it and the structure of the program are illustrated in detail. A user guide for handling the program is given and some results and computational characteristics are presented to show its behaviour in some cases of interest.
FIRST CLUSTER ALGORITHM SPECIAL PURPOSE PROCESSOR
Authors: TALAPOV A. L. , ANDREICHENKO V. B. , DOTSENKO VI. S. , SHCHUR L. N.
Published: November 2004

We describe the architecture of the special purpose processor built to realize in hardware cluster Wolff algorithm, which is not hampered by a critical slowing down. The processor simulates two-dimensional Ising-like spin systems. With minor changes the same very effective architecture, which can be defined as a Memory Machine, can be used to study phase transitions in a wide range of models in two or three dimensions.
A HYBRID NEURAL NETWORK ARCHITECTURE FOR THE CLASSIFICATION OF THE HADRONIC DECAYS OF THE Z0
Authors: COSMO G. , ANGELIS A. DE
Published: November 2004

Feed-Forward Neural Networks have shown to be a useful tool for the automatic classification of events in High Energy Physics. A shortcoming of the method is anyway given by the large value of simulated events to be used for training the classifier. In this paper, we describe an alternative Neural Network architecture that allows a substantial reduction of the CPU time spent in the training phase. This architecture has been tested on a complex problem, such as the classification of the hadronic decays of the Z0, and its performance has been compared with that of a Feed-Forward Neural Network.
PARALLEL COMPUTING AT CRS4
Authors: SCHEININE ALAN LOUIS
Published: November 2004

An overview is given of parallel computing work being done at CRS4 (Centro di Ricerca, Sviluppo e Studi Superiori in Sardegna). Parallel computation projects include: parallelization of a simulation of the interaction of high energy particles with matter (GEANT), domain decomposition for numerical solution of partial differential equations, seismic migration for oil prospecting, finite-element structural analysis, parallel molecular dynamics, a C++ library for distributed processing of specific functions, and real-time visualization of a computer simulation that runs as distributed processes.
REFINED MARK(S)-SET-BASED BACKTRACK LITERAL SELECTION FOR AND PARALLELISM IN LOGIC PROGRAMS
Authors: KIM DO-HYUNG , CHOE KWANG-MOO , HAN TAISOOK
Published: November 2004

Recently Conery proposed a backward execution algorithm for AND-parallel execution of logic programs, and Ng and Leung extended it. They adopt the same data structure called mark(s) set to store information about failure history during AND-parallel evaluation of clauses. Both of the two algorithms essentially have the same rationale with minor differences and have been considered correct, largely due to their intuitive persuasiveness. We closely re-examine those algorithms and find out that they are incorrect. Their incorrectness comes from oversimplification of failure situations. Our analyses focused on the mark(s)-set-based backtrack literal selection are presented. We also propose another backtrack literal selection method based on the mark(s) set, and prove its correctness.
SIMULATING ENHANCED MESHES, WITH APPLICATIONS
Authors: LIN RONG , OLARIU STEPHAN , SCHWING JAMES L. , ZHANG JINGYUAN
Published: November 2004

The purpose of this paper is to present non-trivial lower bounds for two classes of enhanced meshes. To achieve this goal we present efficient simulations of these two classes of enhanced meshes on the CREW-PRAM and Common-CRCW. From this, known computational lower bounds for the PRAM are transferred to the enhanced meshes. Our approach of transferring lower bounds from the PRAM to enhanced meshes is novel. Specifically, we show that any computation that takes O (t(n)) steps on an n-processor mesh with multiple broadcasting can be performed in O (t(n)) steps on an n-processor CREW-PRAM with O (n) extra memory. Similarly, with α standing for the inverse Ackermann function, we show that any computation that takes O (t(n)) computational steps on an n-processor basic reconfigurable mesh can be performed in O (α(n)t(n)) computational steps on an n-processor Common-CRCW with O (n) extra memory. We also show that some of the lower bounds that we derive are tight by providing matching upper bounds; as an example, we show that n items stored in one row of a mesh with multiple broadcasting can be sorted in O(log n) time and that this is time optimal. The best previously-known algorithm for this problem takes O(log2 n) time.
AN EFFICIENT CRASH-TOLERANT SEQUENTIAL TRAVERSAL
Authors: GASTIN PAUL , VILLAIN VINCENT
Published: November 2004

This paper presents a sequential traversal of a network in an environment with crash-failures. This communication primitive is basic and may be used to solve easily many problems like identification, termination detection, and agreement, etc. Contrary to a possible intuition, this primitive is non-trivial since crash-failures involve tricky problems. Moreover, the implementation proposed in this paper is optimistic in the sense that, in the absence of fault, it is as efficient as the underlying non-fault-tolerant one.
BREADTH-DEPTH SEARCH IS ${\mathcal P}$-COMPLETE
Authors: GREENLAW RAYMOND
Published: November 2004

The parallel complexity of a search strategy that combines attributes of both breadth-first search and depth-first search is studied. The search called breadth-depth search was defined by Horowitz and Sahni. The search technique has applications in branch-and-bound strategies. Kindervater and Lenstra posed the complexity of this type of search strategy as an open problem. We resolve their question by showing that a natural decision problem based on breadth-depth search is [Formula: see text]-complete. Specifically, we prove that if given a graph G=(V, E) either directed or undirected, a start vertex s∈V, and two designated vertices u and v in V, then the problem of deciding whether u is visited before v by a breadth-depth search originating from s is [Formula: see text]-complete. The search can be based either on vertex numbers or fixed ordered adjacency lists. Our reductions differ for directed/undirected graphs and depending on whether vertex numbers/fixed ordered adjacency lists are used. These results indicate breadth-depth search is highly sequential in nature and probably will not adapt to a fast parallel solution, unless [Formula: see text] equals [Formula: see text].
A UNIFIED APPROACH TO PARALLEL ALGORITHMS FOR THE DOMATIC PARTITION PROBLEM ON SPECIAL CLASSES OF PERFECT GRAPHS
Authors: RAMAN A. , PANDU RANGAN C.
Published: November 2004

A set of vertices D is a dominating set of a graph G=(V, E) if every vertex in V−D is adjacent to at least one vertex in D. The domatic partition of G is the partition of the vertex set V into a maximum number of dominating sets. In this paper, we present efficient parallel algorithms for finding the domatic partition of Interval graphs, Block graphs and K-trees.
OPTIMALITY OF A VLSI DECOMPOSITION SCHEME FOR THE DEBRUIJN GRAPH
Authors: SCHWABE ERIC J.
Published: November 2004

Collins, Dolinar, McEliece and Pollara recently gave a method for designing VLSI “building block” chips, based on structured subgraphs of the deBruijn graph, that can be wired together to construct arbitrarily large deBruijn graphs. In such a setting, it is clearly preferable to have as many deBruijn graph edges as possible residing on the individual chips, as opposed to being implemented as connections between chips. In this paper, we show that their method can be used to design building blocks that asymptotically require the smallest possible fraction of the deBruijn graph wires to be implemented as inter-chip connections, thus keeping the largest possible fraction of the wires internal to the chips.
ON THE COMPARATIVE POWERS OF THE 2D-PARBS AND THE CRCW-PRAM MODELS
Authors: FRAGOPOULOU PARASKEVI
Published: November 2004

This paper is a critique on some recently published results concerning the relative powers of the 2D-PARBS and the CRCW-PRAM models.
EFFICIENT GLOBAL COMBINE OPERATIONS IN MULTI-PORT MESSAGE-PASSING SYSTEMS
Authors: BRUCK JEHOSHUA , HO CHING-TIEN
Published: November 2004

We present a class of efficient algorithms for global combine operations in k-port message-passing systems. In the k-port communication model, in each communication round, a processor can send data to k other processors and simultaneously receive data from k other processors. We consider algorithms for global combine operations in n processors with respect to a commutative and associative reduction function. Initially, each processor holds a vector of m data items and finally the result of the reduction function over the n vectors of data items, which is also a vector of m data items, is known to all n processors. We present three efficient algorithms that employ various trade-offs between the number of communication rounds and the number of data items transferred in sequence. For the case m=1, we have an algorithm which is optimal in both the number of communication rounds and the number of data items transferred in sequence.
OPTIMAL GOSSIPING IN MESH-BUS COMPUTERS
Authors: FUJITA SATOSHI , YAMASHITA MASAFUMI
Published: November 2004

This paper considers the gossiping problem in mesh-bus computers, in which n2 nodes arranged on an n×n array are connected by n column-buses and n row-buses. The algorithm we propose in this paper completes the gossiping in [n/2]+[ log 2 n]+1 steps. Since a lower bound on the number of steps for this problem is shown to be [n/2]+[ log 2 n]−1, it takes at most only 2 more steps than an optimal algorithm.