bluuebunny/crossref_metadata_2025 huggingface dataset:
MESSAGE IN THE SKY
Authors: HSU S. , ZEE A.
Published: July 2006

We argue that the cosmic microwave background (CMB) provides a stupendous opportunity for the Creator of our universe (assuming one exists) to have sent a message to its occupants, using known physics. Our work does not support the Intelligent Design movement in any way whatsoever, but asks, and attempts to answer, the entirely scientific question of what the medium and message might be IF there was actually a message. The medium for the message is unique. We elaborate on this observation, noting that it requires only careful adjustment of the fundamental Lagrangian, but no direct intervention in the subsequent evolution of the universe.
GENERALIZED STRONG CURVATURE SINGULARITIES AND WEAK COSMIC CENSORSHIP IN COSMOLOGICAL SPACETIMES
Authors: RUDNICKI WIESŁAW , BUDZYŃSKI ROBERT J. , KONDRACKI WITOLD
Published: July 2006

This paper is a further development of the approach to weak cosmic censorship proposed by the authors in Ref. 5. We state and prove a modified version of that work's main result under significantly relaxed assumptions on the asymptotic structure of spacetime. The result, which imposes strong constraints on the occurrence of naked singularities of the strong curvature type, is in particular applicable to physically realistic cosmological models.
NON-BOLTZMANN STATISTICS AS AN ALTERNATIVE TO HOLOGRAPHY
Authors: CANTCHEFF MARCELO BOTTA , NOGALES JOSE A. C.
Published: July 2006

An intriguing question related to black hole thermodynamics is that the entropy of a region shall scale as the area rather than the volume. In this essay we propose that the microscopical degrees of freedom contained in a given region of space, are statistically related in such a way that obey a nonstandard statistics, in which case an holographic hypothesis would not be needed. This could provide us with some insight about the nature of degrees of freedom of the geometry and/or the way in which gravitation plays a role in the statistic correlation between the degrees of freedom of a system.
COSMOLOGICAL CONSTANT PROBING SHAPE MODULI THROUGH LARGE EXTRA DIMENSIONS
Authors: MATSUDA SATOSHI , SEKI SHIGENORI
Published: July 2006

We consider a compactification of extra dimensions and numerically calculate Casimir energy which is provided by the mass of Kaluza–Klein modes. For the extra space we consider a torus with shape moduli and show that the corresponding vacuum energy is represented as a function of the moduli parameter of the extra dimensions. By assuming that the Casimir energy may be identified with cosmological constant, we evaluate the size of extra dimensions in terms of the recent data given by the Wilkinson Microwave Anisotropy Probe (WMAP) measurement and the supernovae observations. We suggest that the observed cosmological constant may probe the shape moduli of the extra space by the study of the Casimir energy of the compactified extra dimensions.
EFFECT OF A CONSTANT UNIFORM MAGNETIC FIELD ON AN ELECTRON BOUND INTO A SINGULAR POTENTIAL
Authors: KHALILOV V. R. , KH. CHIBIROVA F.
Published: July 2006

The behavior of an electrically charged massive particle (an electron) is studied in a constant uniform magnetic field and a single attractive λδ(r) potential. A simple transcendental equation that determines the electron energy spectrum is derived. The approximate wave function of a loosely bound state is constructed in a very simple form. The model under consideration makes it possible to study the effect of magnetic fields on a loosely bound electron. It is shown that the sizes of the electron localization region change and the probability current density arises when the electron is in the loosely bound state in the presence of a constant uniform magnetic field. The above current must involve (and exercise influence on) the electron scattering. The probability current resembles a stack of "pancake vortices" whose circulating (around the z-axes) "currents" are mostly confined within the plane z = 0 in the weak magnetic field. The equation for determining the energy levels of the electron states is obtained for the model under study in two spatial dimensions and the energy of the loosely bound state is found for the two-dimensional model.
A THEOREM ON CYCLIC HARMONIC OSCILLATORS
Authors: KONISHI KENICHI , PAFFUTI GIAMPIERO
Published: July 2006

It is proven that the energy of a quantum mechanical harmonic oscillator with a generically time-dependent but cyclic frequency, ω(t0) = ω(0), cannot decrease on an average if the system is originally in a stationary state, after the system goes through a full cycle. The energy exchange always takes place in the direction from the macroscopic system (environment) to the quantum microscopic system.
STUDY OF THE ANOMALY PHENOMENA FOR THE HYBRID SUPERCONDUCTOR-SEMICONDUCTOR JUNCTIONS
Authors: ALY ARAFA H. , HONG J. , PHILLIPS A. H.
Published: July 2006

The conductance anomaly behavior for superconductor-semiconductor-superconductor junctions is investigated. We propose a potential profile at the interface which depends on the intrinsic parameters of the junctions, e.g. carrier concentration. The tunneling probability is derived by the WKB method and the corresponding conductance is expressed in terms of the tunneling probability through Landauer–Buttiker formula. The results show a zero-bias anomaly (ZBA) for the dependence of conductance on bias voltage. Also, the oscillatory behavior of the conductance with the magnetic field, due to the chaotic behavior of the junction.
HEAVY ELECTRONS: ELECTRON DROPLETS GENERATED BY PHOTOGALVANIC AND PYROELECTRIC EFFECTS
Authors: KRASNOHOLOVETS VOLODYMYR , KUKHTAREV NICOLAI , KUKHTAREVA TATIANA
Published: July 2006

Electron clusters, X-rays and nanosecond radio-frequency pulses are produced by 100 mW continuous-wave laser illuminating ferroelectric crystal of LiNbO 3. A long-living stable electron droplet with the size of about 100μ m has freely moved with the velocity ~0.5 cm/s in the air near the surface of the crystal experiencing the Earth gravitational field. The microscopic model of cluster stability, which is based on submicroscopic mechanics developed in the real physical space, is suggested. The role of a restraining force plays the inerton field, a substructure of the particles' matter waves, which a solitary one can elastically withstand the Coulomb repulsion of electrons. It is shown that electrons in the droplet are heavy electrons whose mass exceeds the rest mass of free electron at least 1 million of times. Application for X-ray imaging and lithography is discussed.
SUPPORTING DEVELOPMENT OF CONTEXT-AWARE APPLICATIONS USING SEMANTIC SPACE TOOLKIT
Authors: ZHANG DAQING , YU ZHIWEN , WANG XIAOHANG , MA MATTHEW Y.
Published: July 2006

In order to facilitate rapid development of context-aware applications, there is a need for architectural support in the entire context processing flow, and improved programming abstractions that ease the prototyping. In this paper, a toolkit called Semantic Space, is proposed to support rapid prototyping of context-aware applications via a set of programming abstractions on context processing. The functionality encapsulated in the toolkit handles the common, time-consuming and low-level details in context acquisition, aggregation, storage and inference. Architectural design and implementation issues of the Semantic Space toolkit are discussed in detail. Finally, a case study on building a mobile situation aware phone is described to illustrate the validity of our approach and usability of the toolkit.
SELECTIVE PRESENTATION OF PERCEPTUALLY IMPORTANT INFORMATION TO AID ORIENTATION AND NAVIGATION IN AN URBAN ENVIRONMENT
Authors: BESSA MAXIMINO , COELHO ANTONIO , CRUZ JOSE BULAS , CHALMERS ALAN
Published: July 2006

A map can be a major advantage when exploring unfamiliar environments. With the proliferation of mobile devices, such as PDAs and even mobile phones, the tourist industry is currently exploring the potential of new presentation strategies that will maximize the promotional appeal of tourism in their region. Mobile devices are capable of guiding a tourist when he/she is exploring a city. These mobile devices offer the potential for providing relevant 3D information to enable tourists to locate themselves within the city, rapidly navigate around the unfamiliar environment and explore it interactively. However, the computational resources of current mobile technology prevents the display of full complex 3D content in real-time, and thus selective rendering techniques must be adopted to ensure the viewer is provided with the perceptually most important information at interactive rates.

This paper presents a series of experiments which help to identify key features of a scene for users to orientate themselves in that environment. Knowledge of these salient key features enable them to be provided to a user at a high quality while the remainder of the scene can be rendered in a much lower quality, saving significant bandwidth and computing power, without the user being perceptually aware of this difference in quality within the image.
FAST WATERMARK DETECTION SCHEME FROM CAMERA-CAPTURED IMAGES ON MOBILE PHONES
Authors: NAKAMURA TAKAO , KATAYAMA ATSUSHI , YAMAMURO MASASHI , SONEHARA NOBORU
Published: July 2006

Digital watermarking technology would be very useful as part of a related service introduction system (RSIS); which links physical objects in the real world, such as printed photographs, to those in the cyber world. In this paper, we focus on a camera-equipped mobile phone as an RSIS terminal, and propose a fast watermark detection scheme for the captured images. The proposed scheme consists of two processes; to correct geometric distortion of the captured image, and to detect watermark information from the corrected image. For our scheme, we also propose a fast quadrangle detection algorithm and a robust watermarking algorithm. Moreover, we introduce a quantitative evaluation method for determining the reliability of watermark detection, which is essential for RSIS services. Finally, we show that the proposed scheme enables users to detect embedded information far less than one second, even when implemented as a Java application on a mobile phone with limited resources, and our experiments confirm the efficiency of our scheme.
BIOMETRIC WRITER IDENTIFICATION: FEATURE ANALYSIS AND CLASSIFICATION
Authors: CHAPRAN JOULIA
Published: July 2006

This paper describes an efficient biometric writer identification system that can be used in a resource contained embedded environment. Writer identification (personal identification by general handwriting) is a relatively new area of handwriting research when compared to the handwriting recognition or signature verification areas. This work is aimed at exploring only small-scale handwriting samples, especially single handwritten words. A database of such samples has been collected dynamically using a digital writing tablet and a force sensitive pen. The dynamic approach adapted in this area is largely new, and only a few papers exist on the subject. Mainly dynamic features of handwriting connected with the writing process itself are considered, although some static features are also used. It is also shown how simple parameters can be used in embedded writer identification devices, and whether they can perform adequately in this type of application. A new feature selection algorithm based on likeness coefficients is proposed. The classifiers used are Minimum-Distance Classifier, Bayes Classifier, and finally their serial combination. The efficiency of this approach and its high performance together show the reasons for employing it in embedded biometric identification devices.
WEAVING DEPLOYMENT ASPECTS INTO DOMAIN-SPECIFIC MODELS
Authors: BALASUBRAMANIAN KRISHNAKUMAR , GOKHALE ANIRUDDHA , LIN YUEHUA , ZHANG JING , GRAY JEFF
Published: July 2006

Domain-specific models increase the level of abstraction used to develop large-scale component-based systems. Model-driven development (MDD) approaches (e.g., Model-Integrated Computing and Model-Driven Architecture) emphasize the use of models at all stages of system development. Decomposing problems using MDD approaches may result in a separation of the artifacts in a way that impedes comprehension. For example, a single concern (such as deployment of a distributed system) may crosscut different orthogonal activities (such as component specification, interaction, packaging and planning). To keep track of all entities associated with a component, and to ensure that the constraints for the system as a whole are not violated, a purely model-driven approach imposes extra effort, thereby negating some of the benefits of MDD.

This paper provides three contributions to the study of applying aspect-oriented techniques to address the crosscutting challenges of model-driven component-based distributed systems development. First, we identify the sources of crosscutting concerns that typically arise in model-driven development of component-based systems. Second, we describe how aspect-oriented model weaving helps modularize these crosscutting concerns using model transformations. Third, we describe how we have applied model weaving using a tool called the Constraint-Specification Aspect Weaver (C-SAW) in the context of the Platform-Independent Component Modeling Language (PICML), which is a domain-specific modeling language for developing component-based systems. A case study of a joint-emergency response system is presented to express the challenges in modeling a typical distributed system. Our experience shows that model weaving is an effective and scalable technique for dealing with crosscutting aspects of component-based systems development.
JOIN POINT DESIGNATION DIAGRAMS: A GRAPHICAL REPRESENTATION OF JOIN POINT SELECTIONS
Authors: STEIN DOMINIK , HANENBERG STEFAN , UNLAND RAINER
Published: July 2006

The specification of join point selections (also known as "pointcuts") is a major design issue in Aspect-Oriented Software Development. Aspect-oriented systems generally provide specific language constructs (subsumed by the term "pointcut language") for specifying such a join point selection. Pointcut languages differ widely with respect to their syntax and semantics. Consequently, developers familiar with one specific language can hardly benefit from this knowledge when designing and implementing pointcuts in another language. This implies that developers working with different aspect-oriented languages can hardly communicate their design to each other, and knowledge about aspect-oriented design can hardly be transferred among developers developing in different languages. In order to overcome this problem, we present novel specification means based on the UML to represent diverse ways of join point selections — without relying on language-specific syntax and semantics. Instead, the proposed language constructs are able to express join point selections in a variety of different aspect-oriented programming languages.
MODELING SECURE SYSTEMS USING AN AGENT-ORIENTED APPROACH AND SECURITY PATTERNS
Authors: MOURATIDIS HARALAMBOS , WEISS MICHAEL , GIORGINI PAOLO
Published: July 2006

In this paper we describe an approach for modeling security issues in information systems. It is based on an agent-oriented approach, and extends it with the use of security patterns. Agent-oriented software engineering provides advantages when modeling security issues, since agents are often a natural way of conceptualizing an information system, in particular at the requirements stage, when the viewpoints of multiple stakeholders need to be considered. Our approach uses the Tropos methodology for modeling a system as a set of agents and their social dependencies, with specific extensions for representing security constraints. As an extension to the existing methodology we propose the use of security patterns. These patterns capture proven solutions to common security issues, and support the systematic and structured mapping of these constraints to an architectural model of the system, in particular for non-security specialists.
MODELING AND ANALYSIS OF PERFORMANCE ASPECTS FOR SOFTWARE ARCHITECTURE: A UML-BASED APPROACH
Authors: DAI LIRONG , COOPER KENDRA , WONG W. ERIC
Published: July 2006

Much attention has been focused on the problem of effectively designing software architecture to meet non-functional requirements (NFRs). The significant benefits of such work include detecting and removing defects earlier, which reduces development time and cost while improving the quality of the design; in turn the improved quality of the design makes it easier to maintain as the system evolves. The Formal Design Analysis Framework (FDAF) is an aspect-oriented approach proposed to support the design and analysis of multiple NFRs for distributed, concurrent, and real-time systems. In FDAF, non-functional requirements are realized and represented as reusable aspects in the repository; designs are captured in an extended version of the Unified Modeling Language (UML). FDAF supports the automated translation of extended UML designs into existing formal notations. Subsequently, the analysis of an aspect design is achieved using existing formal analysis tools, which leverages a large body of work in the research community. This paper focuses on the modeling and analysis of the response time performance aspect. The algorithms for translating extended UML diagrams into Rapide, the proofs of correctness for the algorithms, and an illustration of the FDAF approach using the Domain Name System are presented.
COMPOSITION OF ASPECTS BASED ON A RELATION MODEL: SYNERGY OF MULTIPLE PARADIGMS
Authors: HAN IKJOO , BAE DOO-HWAN
Published: July 2006

Software composition for timely and affordable software development and evolution is one of the oldest pursuits of software engineering. In current software composition techniques, Component-Based Software Development (CBSD) and Aspect-Oriented Software Development (AOSD) have attracted academic and industrial attention. Black box composition used in CBSD provides simple and safe modularization for its strong information hiding, which is, however, the main obstacle for a black box composite to evolve later. This implies that an application developed through black box composition cannot take advantage of Aspect-Oriented Programming (AOP) used in AOSD. On the contrary, AOP enhances maintainability and comprehensibility by modularizing concerns crosscutting multiple components but lacks the support for the hierarchical and external composition of aspects themselves and compromises the important software engineering principles such as encapsulation, which is almost perfectly supported in black box composition. The role and role model have been recognized to have many similarities with CBSD and AOP but have significant differences with those composition techniques as well. Although each composition paradigm has its own advantages and disadvantages, there is no substantial support to realize the synergy of these composition paradigms; the black box composition, AOP, and role model. In this paper, a new composition technique based on representational abstraction of the relationship between component instances is introduced. The model supports the simple, elegant, and dynamic composition of components with its declarative form and provides the hooks through which an aspect can evolve and a parallel developed aspect can be merged at the instance level.
NOTES ON FINITELY GENERATED SEMIGROUPS
Authors: PASKU ELTON
Published: July 2006

We show that analogues of results from [4, 5] can be obtained if the relation [Formula: see text] is replaced by [Formula: see text]. We also give an example of a semigroup S in which [Formula: see text] does not follow from S being finitely generated, periodic, inverse, E-unitary and not even from the finiteness of its maximal subgroups.
FAITHFULNESS OF CERTAIN MODULES AND RESIDUAL NILPOTENCE OF GROUPS
Authors: MIKHAILOV ROMAN , PASSI INDER BIR S.
Published: July 2006

Let F be a non-cyclic free group and R, S its normal subgroups. We study the abelian group [Formula: see text], viewed as a module over F/RS, via conjugation in F, and residual nilpotence of the group F/[R, S]. An application to the asphericity of finite presentations is given.
ON COMPLETING PARTIAL GROUPOIDS TO SEMIGROUPS
Authors: GORALČÍK P. , KOUBEK V.
Published: July 2006

Let [Formula: see text] be a class of semigroups containing all finite commutative bands, and let p(x) be a real polynomial. The [Formula: see text]-completion problem asks whether for a given partial groupoid G there exists a semigroup [Formula: see text] such that G ⊆ S, every product for (a, b) ∈ G2 defined in G coincides with that for (a, b) in S, and |S| ≤ p(|G|). We prove the problem to be ℕℙ-hard in general and ℕℙ-complete if the membership problem for [Formula: see text] is in ℙ.
EVALUATION PROPERTIES OF SYMMETRIC POLYNOMIALS
Authors: GAUDRY PIERRICK , SCHOST ÉRIC , THIÉRY NICOLAS M.
Published: July 2006

By the fundamental theorem of symmetric polynomials, if P ∈ ℚ[X1,…,Xn] is symmetric, then it can be written P = Q(σ1,…,σn), where σ1,…,σn are the elementary symmetric polynomials in n variables, and Q is in ℚ[S1,…,Sn].

We investigate the complexity properties of this construction in the straight-line program model, showing that the complexity of evaluation of Q depends only on n and on the complexity of evaluation of P.

Similar results are given for the decomposition of a general polynomial in a basis of ℚ[X1,…,Xn] seen as a module over the ring of symmetric polynomials, as well as for the computation of the Reynolds operator.
REACHABILITY PROBLEMS FOR PRODUCTS OF MATRICES IN SEMIRINGS
Authors: GAUBERT STÉPHANE , KATZ RICARDO D.
Published: July 2006

We consider the following matrix reachability problem: given r square matrices with entries in a semiring, is there a product of these matrices which attains a prescribed matrix? Similarly, we define the vector (resp. scalar) reachability problem, by requiring that the matrix product, acting by right multiplication on a prescribed row vector, gives another prescribed row vector (resp. when multiplied on the left and right by prescribed row and column vectors, gives a prescribed scalar). We show that over any semiring, scalar reachability reduces to vector reachability which is equivalent to matrix reachability, and that for any of these problems, the specialization to any r ≥ 2 is equivalent to the specialization to r = 2. As an application of these reductions and of a theorem of Krob, we show that when r = 2, the vector and matrix reachability problems are undecidable over the max-plus semiring (ℤ∪{-∞}, max ,+). These reductions also improve known results concerning the classical zero corner problem. Finally, we show that the matrix, vector, and scalar reachability problems are decidable over semirings whose elements are "positive", like the tropical semiring (ℤ∪{+∞}, min ,+).
EFFECT OF GAS PRESSURE ON THE BORON-DOPED HYDROGENATED AMORPHOUS CARBON THIN FILMS GROWN BY RADIO FREQUENCY PLASMA-ENHANCED CHEMICAL VAPOR DEPOSITION
Authors: RUSOP M. , ABDULLAH S. , PODDER J. , SOGA T. , JIMBO T.
Published: July 2006

Boron-doped hydrogenated amorphous carbon ( a-C:B:H ) thin films have been deposited by radio frequency plasma-enhanced chemical vapor deposition (r.f. PECVD) with a frequency of 13.56 MHz at room temperature using pure methane as a precursor of carbon source mixed with hydrogen ( H2) as a carrier gas. The films were prepared by varying the r.f. power, different gas flow rates of CH4, and partial pressure of mixed gas ( CH4/ H2) using boron as a solid target. The thickness, structural bonding, and optical properties of the as-deposited films were studied by Alpha-step surface profiler, Raman spectroscopy (Raman), Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy, and UV–visible spectroscopy. It was found that changing the deposition pressure in addition of using solid boron target in the r.f. PECVD process has a profound effect on the properties of the deposited films as evidenced from their Raman scattering and optical results. The grown a-C:B:H films were found to be smooth and their thicknesses were in the range of 200 to 400 nm for 1 h of deposition time. Films deposited at lower pressure appear brownish in color, whereas those deposited at higher pressure appear pale yellowish. The as-deposited film was found to be dominated by trigonal (sp2) rather than tetrahedral (sp3), which might be due to the formation of small crystallites. The optical band gap is found to be reduced from 2.60 to 1.62 eV as the partial pressure of CH4/ H2gas is reduced.
A NOVEL METHOD OF CALCULATING THE INTERACTION ENERGIES OF DOUBLE LAYERS
Authors: ZHANG SHIMIN
Published: July 2006

A novel, simple, and efficient method to calculate the interaction energies of double layers, λ parameter method, is presented by introducing a parameter λ in the elliptical integral. The interaction energies between two similar plane parallel double layers are expanded in the power series with such a method. The series converge very fast. When the dimensionless surface potential of double layers is less than or equal to 30, the number of the series terms required does not exceed 3 to obtain the interaction energies with six significant digits.
CHARACTERIZATION OF SOME METHODS OF PREPARATION FOR BIOACTIVE GLASS COATING ON IMPLANTS
Authors: MA JIE , CHEN CHUANZHONG , YAO LIANG , BAO QUANHE
Published: July 2006

Since the discovery of Bioglass® by Hench, bioactive glasses have been used in many medical applications, such as drug delivery systems, nonload-bearing implants, and bone cements because of their excellent bioactivity and biocompatibility. However, due to their poor mechanical properties, these glasses cannot be used in load-bearing applications, where the metallic alloys are still main materials. One useful approach to solving the mechanical limitations of bioactive glasses is to apply the glasses as the coating on mechanically tough substrates; it was also recognized early that bioactive glasses could be used as coatings for prosthetic metallic implants. In this paper, the mechanism, characterization, and current status of some methods of preparation for bioactive glass coating on implants are introduced. In the end, to get the homogeneous and compact coating with perfect bonding strength, some ideas of improving the performance of coatings are also presented.
ON THE STRUCTURE, ELECTRICAL AND OPTICAL PROPERTIES OF TiO2 SPUTTERED THIN FILMS
Authors: ASHOUR A.
Published: July 2006

Titanium oxide thin films were prepared by sputtering technique onto glass substrates at room temperature (RT). The structure of the films was confirmed using X-ray diffraction (XRD) and revealed the stoichiometry with an O and Ti ratio of 2. The deposited films at RT were found to be amorphous and the films annealed at 300 and 400°C for 2 h were crystalline with orthorhombic structure. The lattice constants and grain size of the film are calculated. The electrical resistivity was found to depend on the film thickness and decreased with increasing the film thicknesses. The optical constants of the films such as the refractive index, extinction coefficient, and absorption coefficient were also determined using the optical transmittance measurements, and the results were discussed. The optical band gap varies from 3.2 to 3.5 eV as a function of oxygen/argon ratios.
SUPERHYDROPHOBIC SURFACES PREPARED BY PLASMA FLUORINATION OF LOTUS-LEAF-LIKE AMORPHOUS CARBON FILMS
Authors: ZHOU YING , SONG XUEMEI , YU MUNAN , WANG BO , YAN HUI
Published: July 2006

Lotus-leaf-like amorphous carbon ( a-C ) films were fabricated on glass and Si substrates by a magnetron sputtering system and fluorinated in carbon tetrafluoride plasma. The fluorinated films ( a-C:F ) had a maximum contact angle (CA) of about 162°, which is much larger than that of the nonfluorinated films (105°). Furthermore, the geometric microstructure and chemical composition of the a-C:F films were investigated by scanning electron microscopy and Fourier transform infrared spectrometry, respectively. The characterization results indicated that the CA on the surfaces of the a-C:F films can be improved remarkably by the plasma-fluorinated process. Such a-C:F films that combine superhydrophobicity with other properties may have many potential applications.
IN VIVOEVALUATION OF THE HUMAN CAROTID ARTERY COMPLEX ELASTIC MODULUS
Authors: SEBASTIÁN GRAF , YANINA ZÓCALO , FRANCO PESSANA , DANIEL BIA , LUCAS GAMERO , RAMIRO SANCHEZ , RICARDO ARMENTANO
Published: July 2006

The arterial wall dynamics evaluation requires the assessment of its frequency-response. The aim was to apply an original methodology, to evaluate the arterial wall pressure-diameter frequency-response and elastic complex modulus, of human in vivo and in vitro common carotid arteries (CCA). CCA pressure, diameter and wall thickness were recorded. In vitro recordings were performed using pressure microtransducer (Konigsberg) and sonomicrometry, in 14 CCA segments (from donors). The in vivo recordings were obtained non-invasively by tonometry and mode-B echography in 10 normotensive patients, and in 10 hypertensive patients before and after 3 months of treatment with an ACE-inhibitor. A system modeling-identification approach was used to estimate the viscoelastic parameters: elastic, viscous and inertial indexes, and to perform an isofrequency analysis (up to 5Hz) of the incremental elastic modulus Einc(jω) of the arterial wall. The new approach, proposed to evaluate the frequency-dependence of arterial wall mechanics, was applied satisfactorily.
DATA MINING APPROACHES FOR KIDNEY DIALYSIS TREATMENT
Authors: SRIRAAM N. , NATASHA V. , KAUR H.
Published: July 2006

Data mining techniques has been used as a recent trend for achieving diagnostics results, especially in medical fields such as kidney dialysis, skin cancer and breast cancer detection, and also biological sequences classification. Due to its ability to discover the relationship and pattern of the medical database, early detection or prediction of pathological conditions through mining has become feasible. This paper discusses the data mining approach for parametric evaluation to improve the treatment of kidney dialysis patient. The experimental result shows that classification accuracy using Association mining between the ranges 50–97.7% is obtained based on the dialysis parameter combination. Such a decision-based approach helps the clinician to decide the level of dialysis required for individual patient.
STATISTICAL MEASURES OF THE STRUCTURE OF GENOMIC SEQUENCES: ENTROPY, COMPLEXITY, AND POSITION INFORMATION
Authors: ORLOV YURIY L. , TE BOEKHORST RENE , ABNIZOVA IRINA I.
Published: July 2006

Identifying regions of DNA with extreme statistical characteristics is an important aspect of the structural analysis of complete genomes. Linguistic methods, mainly based on estimating word frequency, can be used for this as they allow for the delineation of regions of low complexity. Low complexity may be due to biased nucleotide composition, by tandem- or dispersed repeats, by palindrome-hairpin structures, as well as by a combination of all these features. We developed software tools in which various numerical measures of text complexity are implemented, including combinatorial and linguistic ones. We also added Hurst exponent estimate to the software to measure dependencies in DNA sequences. By applying these tools to various functional genomic regions, we demonstrate that the complexity of introns and regulatory regions is lower than that of coding regions, whilst Hurst exponent is larger. Further analysis of promoter sequences revealed that the lower complexity of these regions is associated with long-range correlations caused by transcription factor binding sites.
THE NEW CLASSIFICATION SCHEME OF THE GENETIC CODE, ITS EARLY EVOLUTION, AND tRNA USAGE
Authors: NIKOLAJEWA SWETLANA , FRIEDEL MAIK , BEYER ANDREAS , WILHELM THOMAS
Published: July 2006

We present a new classification scheme of the genetic code. In contrast to the standard form it clearly shows five codon symmetries: codon-anticodon, codon-reverse codon, and sense-antisense symmetry, as well as symmetries with respect to purine-pyrimidine (A versus G, U versus C) and keto-aminobase (G versus U, A versus C) exchanges. We study the number of tRNA genes of 16 archaea, 81 bacteria and 7 eucaryotes to analyze whether these symmetries are reflected in the corresponding tRNA usage patterns. Two features are especially striking: reverse stop codons do not have their own tRNAs (just one exception in human), and A** anticodons are significantly suppressed. Our classification scheme of the genetic code and the identified tRNA usage patterns support recent speculations about the early evolution of the genetic code. In particular, pre-tRNAs might have had the ability to bind their codons in two directions to the corresponding codons.
ANTIBODY CDR H3 MODELING RULES: EXTENSION FOR THE CASE OF ABSENCE OF ARG H94 AND ASP H101
Authors: KOLIASNIKOV OLEG V. , KIRAL MIROSLAV O. , GRIGORENKO VITALY G. , EGOROV ALEXEY M.
Published: July 2006

The third complementary determining region of the immunoglobulin heavy chain (CDR H3) is one of the more difficult structures to model due to genetic reasons. However, the conformation of proximal to β-framework ("torso") part of the CDR H3 is very predictable. Current "CDR's canonical classes" theory is based on identifying the key positions, H94 and H101. We can determine the CDR H3 "torso" structure if arginine or lysine is present in the H94 position and/or aspartic acid in the H101 position. We target the case characterized by the absence of key residues in both the H94 and H101 positions. There has not been discussion on this case in the literature. 51 CDR H3 structures of this nature are analyzed and we established new sequence-structure rules. These rules contribute to more accurate modeling of the antibody's structure.
DECOMPOSITION OF OVERLAPPING PATTERNS BY CUMULATIVE LOCAL CROSS-CORRELATION
Authors: KOGAN SIMON B.
Published: July 2006

A large portion of the usual eukaryotic genome is comprised of repetitive sequences. A common situation, when several related but different repeat families share the same conserved motif, complicates repeat classification and repeat boundary definition. If the repeats are aligned by the motif position, then the sequence profile (pattern) resulting from the alignment will represent overlapping of the profiles (patterns) corresponding to the individual families. A novel algorithm for the decomposition of overlapping patterns is proposed. It can be used with both continuous and gapped patterns. The technique is based on accumulation of simultaneously occurring pattern features found by cross-correlation procedure with limited lag length; thus, the name is Cumulative Local Cross-Correlation (referred further as CLCC). Its sensitivity is tested on human genomic sequences. Software implementation of the algorithm is available on request from the author.
AUTOMATED VALIDATION OF POLYMERASE CHAIN REACTION AMPLICON MELTING CURVES
Authors: MANN TOBIAS P. , HUMBERT RICHARD , STAMATOYANNOPOLOUS JOHN A. , NOBLE WILLIAM STAFFORD
Published: July 2006

The polymerase chain reaction (PCR) is a fundamental tool of molecular biology. Quantitative PCR is the gold-standard methodology for determination of DNA copy numbers, quantitating transcription, and numerous other applications. A major barrier to large-scale application of PCR for quantitative genomic analyses is the current requirement for manual validation of individual PCRs to ensure generation of a single product. This typically requires visual inspection either of gel electrophoreses or temperature dissociation ("melting") curves of individual PCRs — a time-consuming and costly process.

Here we describe a robust computational solution to this fundamental problem. Using a training set of 10 080 reactions comprising multiple quantitative PCRs from each of 1728 unique human genomic amplicons, we developed a support vector machine classifier capable of discriminating single-product PCRs with better than 99% accuracy. This approach has broad utility, and eliminates a major bottleneck to widespread application of PCR for high-throughput genomic applications.
TREND OF AMINO ACID COMPOSITION OF PROTEINS OF DIFFERENT TAXA
Authors: BOGATYREVA NATALYA S. , FINKELSTEIN ALEXEI V. , GALZITSKAYA OXANA V.
Published: July 2006

Archaea, bacteria and eukaryotes represent the main kingdoms of life. Is there any trend for amino acid compositions of proteins found in full genomes of species of different kingdoms? What is the percentage of totally unstructured proteins in various proteomes? We obtained amino acid frequencies for different taxa using 195 known proteomes and all annotated sequences from the Swiss–Prot data base. Investigation of the two data bases (proteomes and Swiss–Prot) shows that the amino acid compositions of proteins differ substantially for different kingdoms of life, and this difference is larger between different proteomes than between different kingdoms of life. Our data demonstrate that there is a surprisingly small selection for the amino acid composition of proteins for higher organisms (eukaryotes) and their viruses in comparison with the "random" frequency following from a uniform usage of codons of the universal genetic code. On the contrary, lower organisms (bacteria and especially archaea) demonstrate an enhanced selection of amino acids. Moreover, according to our estimates, 12%, 3% and 2% of the proteins in eukaryotic, bacterial and archaean proteomes are totally disordered, and long (> 41 residues) disordered segments are found to occur in 16% of arhaean, 20% of eubacterial and 43% of eukaryotic proteins for 19 archaean, 159 bacterial and 17 eukaryotic proteomes, respectively. A correlation between amino acid compositions of proteins of various taxa, show that the highest correlation is observed between eukaryotes and their viruses (the correlation coefficient is 0.98), and bacteria and their viruses (the correlation coefficient is 0.96), while correlation between eukaryotes and archaea is 0.85 only.
EFFICIENT ALGORITHMS AND SOFTWARE FOR DETECTION OF FULL-LENGTH LTR RETROTRANSPOSONS
Authors: KALYANARAMAN ANANTHARAMAN , ALURU SRINIVAS
Published: July 2006

LTR retrotransposons constitute one of the most abundant classes of repetitive elements in eukaryotic genomes. In this paper, we present a new algorithm for detection of full-length LTR retrotransposons in genomic sequences. The algorithm identifies regions in a genomic sequence that show structural characteristics of LTR retrotransposons. Three key components distinguish our algorithm from that of current software — (i) a novel method that preprocesses the entire genomic sequence in linear time and produces high quality pairs of LTR candidates in run-time that is constant per pair, (ii) a thorough alignment-based evaluation of candidate pairs to ensure high quality prediction, and (iii) a robust parameter set encompassing both structural constraints and quality controls providing users with a high degree of flexibility. We implemented our algorithm into a software program called LTR_par, which can be run on both serial and parallel computers. Validation of our software against the yeast genome indicates superior results in both quality and performance when compared to existing software. Additional validations are presented on rice BACs and chimpanzee genome.
SELECTION OF CRYPTIC B-CELL EPITOPES USING INFORMATIONAL ANALYSIS OF PROTEIN SEQUENSES
Authors: SVIRSHCHEVSKAYA ELENA , ALEKSEEVA LUDMILA , MARCHENKO ALEXEI , BENEVOLENSKII SERGEI , BERZHEC VALENTINA M. , NEKRASOV ALEXEI
Published: July 2006

Sub-unit vaccines are synthetic or recombinant peptides representing T- or B-cell epitopes of major protein antigens from a particular pathogen. Epitope selection requires the synthesis of peptides that overlap the protein sequences and screening for the most effective ones. In this study a new method of immunogenic peptide selection based on the analysis of information structure of protein sequences is suggested. The analysis of known B-cell epitope location in the information structure of Aspergillus fumigatus proteins Asp f 2 and Asp f 3 has shown that epitopes are scattered along the sequences of proteins for the exception of sites with Increased Degree Information Coordination (IDIC). Based on these results peptides from different allergens such as Asp f 2, Der p 1, and Fel d 1 were selected and produced in a recombinant form in the context of yeast virus-like particles (VLPs). Immunization of mice with VLPs containing peptides form allergens has induced the production of IgG able to recognize full-length antigens. This result suggests that the analysis of information structure of proteins can be used for the selection of peptides possessing cryptic B-cell epitope activity.
SYMMETRIC AND ASYMMETRIC MULTI-MODALITY BICLUSTERING ANALYSIS FOR MICROARRAY DATA MATRIX
Authors: KUNG SUN-YUAN , MAK MAN-WAI , TAGKOPOULOS ILIAS
Published: July 2006

Machine learning techniques offer a viable approach to cluster discovery from microarray data, which involves identifying and classifying biologically relevant groups in genes and conditions. It has been recognized that genes (whether or not they belong to the same gene group) may be co-expressed via a variety of pathways. Therefore, they can be adequately described by a diversity of coherence models. In fact, it is known that a gene may participate in multiple pathways that may or may not be co-active under all conditions. It is therefore biologically meaningful to simultaneously divide genes into functional groups and conditions into co-active categories — leading to the so-called biclustering analysis. For this, we have proposed a comprehensive set of coherence models to cope with various plausible regulation processes. Furthermore, a multivariate biclustering analysis based on fusion of different coherence models appears to be promising because the expression level of genes from the same group may follow more than one coherence models. The simulation studies further confirm that the proposed framework enjoys the advantage of high prediction performance.
ELECTROSTATIC PROPERTIES OF PROMOTER RECOGNIZED BYE. COLIRNA POLYMERASE Eσ70
Authors: SOROKIN ANATOLY A. , OSYPOV ALEXANDR A. , DZHELYADIN TIMUR R. , BESKARAVAINY PETR M. , KAMZOLOVA SVETLANA G.
Published: July 2006

A comparative analysis of electrostatic patterns for 359 σ70-specific promoters and 359 nonpromoter regions on electrostatic map of Escherichia coli genome was carried out. It was found that DNA is not a uniformly charged molecule. There are some local inhomogeneities in its electrostatic profile which correlate with promoter sequences. Electrostatic patterns of promoter DNAs can be specified due to the presence of some distinctive motifs which differ for different promoter groups and may be involved as signal elements in differential recognition of various promoters by the enzyme. Some specific electrostatic elements which are responsible for modulating promoter activities due to ADP-ribosylation of RNA polymerase α-subunit were found in far upstream regions of T4 phage early promoters and E. coli ribosomal promoters.
DYNAMICS OF CONFLICT BETWEEN PRODUCTION AND MANUFACTURING ENGINEERING
Authors: LU QIANG , MAANI KAMBIZ
Published: July 2006

Based on a two-year in-depth case study in an electronics plant in Singapore, this paper examines the interaction between Production (P) and Manufacturing Engineering (ME). This interaction is rather hidden because the roles of P and ME are often consigned or executed within the manufacturing operation. P and ME are responsible for process execution and process development respectively, and for process smoothness jointly; their relationship is asymmetrical from various aspects. These factors, together with the complex market demand and associated multi-prong operational requirements, became the potential sources of short-sighted behaviors and resulting conflicts at the P-ME interface which are illustrated via a system dynamics model. Conflict management would be easier if long-term solutions (operational capability-building and technological innovation) were considered along with short-term solutions (management intervention). A key implication for management is that giving ME an equal bargaining voice and investment in process development can encourage ME to develop more advanced process technologies that enhance the performance of both P and ME.
CASE STUDIES OF ADVANCED MANUFACTURING TECHNOLOGY IMPLEMENTATION IN SMALL COMPANIES
Authors: WALTERS ANDREW T. , MILLWARD HUW , LEWIS ALAN
Published: July 2006

Issues of Advanced Manufacturing Technology (AMT) implementation have been extensively covered in the literature in regard to large companies; however, exclusive examination of the impact of AMT on small companies remains under researched. This examination of ten case study companies demonstrates the potential benefits of AMT use, as each of the companies achieved positive outcomes from AMT. However, the benefits achieved did not always meet the companies' expectations. Analysis of the experiences of the companies indicates the importance of considering the impact of AMT output on the manufacturing process, the levels of pre-existing AMT experience and the availability of external support mechanisms.
UNDERSTANDING REGIONAL INNOVATION IN THE MARITIME INDUSTRY: AN EMPIRICAL ANALYSIS
Authors: DOLOREUX DAVID
Published: July 2006

This paper discusses the findings of a study of innovation activities by maritime firms located in Quebec's coastal region. The aims of the study are to describe the characteristics of the maritime industry in the region, compare groups of firms in terms of their innovation activities and co-operation behavior, and examine the influence of business environment on innovation. The findings reveal that no single characteristic of Quebec's coastal maritime firms defines the way that the firms design their competitive strategies, conduct innovation activities, engage in collaborations, or perceive the importance of location factors in determining the success of their business activities.
BUSINESS IMPACT OF TECHNOLOGY PILOTING — MODEL FOR ANALYSIS IN DIFFERENT PHASES OF DEVELOPMENT CYCLE
Authors: SUIKKI RAIJA , HAAPASALO HARRI
Published: July 2006

The challenge of companies in today's turbulent business environment is to identify customers' requirements when technology platforms and products are still in development and customers lack experience with the products. This paper presents experiences from piloting new technologies in telecommunications industry and proposes piloting as a means to introduce new products and applications. To date, piloting has been mostly considered as black box; there is no general or facilitated description for piloting process. This study opens piloting up to a process embedded in new product development (NPD). This study validates the probe and learn process and shows the importance of customer involvement in providing new innovations and enhancement ideas in technologically advanced environment. This paper presents and facilitates the actual process of piloting in order to manage it. Benefits of piloting are verified.
A SIMPLE ADAPTIVE INTERPOLATION APPROACH BASED ON VARYING IMAGE LOCAL ACTIVITY LEVELS
Authors: EL-KHAMY SAID E. , HADHOUD MOHEY M. , DESSOUKY MOAWAD I. , SALAM BASSIOUNY M. , EL-SAMIE FATHI E. ABD
Published: July 2006

In this paper, a simple adaptive interpolation approach is proposed for image interpolation. It depends on modifying the warped distance technique for image interpolation considering the local activity levels in each region of the image. This is performed by weighting the pixels used in the interpolation process with different adaptive weights. The adaptation can be extended to different traditional interpolation techniques such as bilinear, bicubic and cubic spline techniques as well as the warped distance technique. Our study shows that the adaptive weighting of pixels in interpolation yields better results than that obtained using only traditional interpolation methods or by using the warped distance technique. The computation cost of the suggested interpolation approach is moderate and acceptable.