bluuebunny/crossref_metadata_2025 huggingface dataset:
Herpes Simplex Virus Type 1 UL51 Protein Is Involved in Maturation and Egress of Virus Particles
Authors: Nozawa Naoki , Kawaguchi Yasushi , Tanaka Michiko , Kato Akihisa , Kato Ai , Kimura Hiroshi , Nishiyama Yukihiro
Published: May 2005

The
UL51
gene of herpes simplex virus type 1 (HSV-1) encodes a phosphoprotein whose homologs are conserved throughout the herpes virus family. Recently, we reported that UL51 protein colocalizes with Golgi marker proteins in transfected cells and that targeting of UL51 protein to the Golgi apparatus depends on palmitoylation of its N-terminal cysteine at position 9 (N. Nozawa, T. Daikoku, T. Koshizuka, Y. Yamauchi, T. Yoshikawa, and Y. Nishiyama, J. Virol. 77:3204-3216, 2003). However, its role in the HSV replication cycle was unknown. Here, we generated UL51-null mutants (FDL51) in HSV-1 to uncover the function of UL51 protein. We show that the mutant plaques were much smaller in size and that maximal titers were reduced nearly 100-fold compared to wild-type virus. Electron microscopy indicated that the formation of nucleocapsids was not affected by the deletion of UL51 but that viral egress from the perinuclear space was severely compromised. In FDL51-infected cells, a large number of enveloped nucleocapsids were observed in the perinuclear space, but enveloped mature virions in the cytoplasm, as well as extracellular mature virions, were rarely detected. These defects were fully rescued by reinsertion of the
UL51
gene. These results indicate that UL51 protein is involved in the maturation and egress of HSV-1 virus particles downstream of the initial envelopment step.
RNA and Protein Requirements for Incorporation of the Pol Protein into Foamy Virus Particles
Authors: Peters Katrin , Wiktorowicz Tatiana , Heinkelein Martin , Rethwilm Axel
Published: May 2005

Foamy viruses (FVs) generate their Pol protein precursor molecule independently of the Gag protein from a spliced mRNA. This mode of expression raises the question of the mechanism of Pol protein incorporation into the viral particle (capsid). We previously showed that the packaging of (pre)genomic RNA is essential for Pol encapsidation (M. Heinkelein, C. Leurs, M. Rammling, K. Peters, H. Hanenberg, and A. Rethwilm, J. Virol.
76:
10069-10073, 2002). Here, we demonstrate that distinct sequences in the RNA, which we termed Pol encapsidation sequences (PES), are required to incorporate Pol protein into the FV capsid. Two PES were found, which are contained in the previously identified
cis
-acting sequences necessary to transfer an FV vector. One PES is located in the U5 region of the 5′ long terminal repeat and one at the 3′ end of the
pol
gene region. Neither element has any significant effect on RNA packaging. However, deletion of either PES resulted in a significant reduction in Pol encapsidation. On the protein level, we show that only the Pol precursor, but not the individual reverse transcriptase (RT) and integrase (IN) subunits, is incorporated into FV particles. However, enzymatic activities of the protease (PR), RT, or IN are not required. Our results strengthen the view that in FVs, (pre)genomic RNA functions as a bridging molecule between Gag and Pol precursor proteins.
Diversifying Selection in Human Papillomavirus Type 16 Lineages Based on Complete Genome Analyses
Authors: Chen Zigui , Terai Masanori , Fu Leiping , Herrero Rolando , DeSalle Rob , Burk Robert D.
Published: May 2005

Human
papillomavirus type 16 (HPV16) is the primary etiological
agent of cervical cancer, the second most common cancer in women
worldwide. Complete genomes of 12 isolates representing the major
lineages of HPV16 were cloned and sequenced from cervicovaginal cells.
The sequence variations within the open reading frames (ORFs) and
noncoding regions were identified and compared with the HPV16R
reference sequence (50).
This whole-genome approach gives us unprecedented precision in
detailing sequence-level changes that are under selection on a
whole-viral-genome scale. Of 7,908 base pair nucleotide positions, 313
(4.0%) were variable. Within the 2,452 amino acids
(aa) comprising 8 ORFs, 243 (9.9%) amino acid positions were
variable. In order to investigate the molecular evolution of HPV16
variants, maximum likelihood models of codon substitution were
used to identify lineages and amino acid sites under selective
pressure. Five codon sites in the E5 (aa 48, 65) and E6 (aa
10, 14, 83) ORFs were demonstrated to be under diversifying selective
pressure. The E5 ORF had the overall highest nonsynonymous/synonymous
substitution rate (ω) ratio (M3 = 0.7965). The E2 gene
had the next-highest ω ratio (M3 = 0.5611); however, no
specific codons were under positive selection. These data
indicate that the E6 and E5 ORFs are evolving under positive Darwinian
selection and have done so in a relatively short time period. Whether
response to selective pressure upon the E5 and E6 ORFs
contributes to the biological success of HPV16, its specific biological
niche, and/or its oncogenic potential remains to be
established.
Pseudotypes of Vesicular Stomatitis Virus with CD4 Formed by Clustering of Membrane Microdomains during Budding
Authors: Brown Erica L. , Lyles Douglas S.
Published: May 2005

Many plasma membrane components are organized into detergent-resistant membrane microdomains referred to as lipid rafts. However, there is much less information about the organization of membrane components into microdomains outside of lipid rafts. Furthermore, there are few approaches to determine whether different membrane components are colocalized in microdomains as small as lipid rafts. We have previously described a new method of determining the extent of organization of proteins into membrane microdomains by analyzing the distribution of pairwise distances between immunogold particles in immunoelectron micrographs. We used this method to analyze the microdomains involved in the incorporation of the T-cell antigen CD4 into the envelope of vesicular stomatitis virus (VSV). In cells infected with a recombinant virus that expresses CD4 from the viral genome, both CD4 and the VSV envelope glycoprotein (G protein) were found in detergent-soluble (nonraft) membrane fractions. However, analysis of the distribution of CD4 and G protein in plasma membranes by immunoelectron microscopy showed that both were organized into membrane microdomains of similar sizes, approximately 100 to 150 nm. In regions of plasma membrane outside of virus budding sites, CD4 and G protein were present in separate membrane microdomains, as shown by double-label immunoelectron microscopy data. However, virus budding occurred from membrane microdomains that contained both G protein and CD4, and extended to approximately 300 nm, indicating that VSV pseudotype formation with CD4 occurs by clustering of G protein- and CD4-containing microdomains.
Cinanserin Is an Inhibitor of the 3C-Like Proteinase of Severe Acute Respiratory Syndrome Coronavirus and Strongly Reduces Virus Replication In Vitro
Authors: Chen Lili , Gui Chunshan , Luo Xiaomin , Yang Qingang , Günther Stephan , Scandella Elke , Drosten Christian , Bai Donglu , He Xichang , Ludewig Burkhard , Chen Jing , Luo Haibin , Yang Yiming , Yang Yifu , Zou Jianping , Thiel Volker , Chen Kaixian , Shen Jianhua , Shen Xu , Jiang Hualiang
Published: May 2005

The 3C-like proteinase (3CLpro) of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) is one of the most promising targets for anti-SARS-CoV drugs due to its crucial role in the viral life cycle. In this study, a database containing structural information of more than 8,000 existing drugs was virtually screened by a docking approach to identify potential binding molecules of SARS-CoV 3CLpro. As a target for screening, both a homology model and the crystallographic structure of the binding pocket of the enzyme were used. Cinanserin (SQ 10,643), a well-characterized serotonin antagonist that has undergone preliminary clinical testing in humans in the 1960s, showed a high score in the screening and was chosen for further experimental evaluation. Binding of both cinanserin and its hydrochloride to bacterially expressed 3CLproof SARS-CoV and the related human coronavirus 229E (HCoV-229E) was demonstrated by surface plasmon resonance technology. The catalytic activity of both enzymes was inhibited with 50% inhibitory concentration (IC50) values of 5 μM, as tested with a fluorogenic substrate. The antiviral activity of cinanserin was further evaluated in tissue culture assays, namely, a replicon system based on HCoV-229E and quantitative test assays with infectious SARS-CoV and HCoV-229E. All assays revealed a strong inhibition of coronavirus replication at nontoxic drug concentrations. The level of virus RNA and infectious particles was reduced by up to 4 log units, with IC50values ranging from 19 to 34 μM. These findings demonstrate that the old drug cinanserin is an inhibitor of SARS-CoV replication, acting most likely via inhibition of the 3CL proteinase.
Characterization of Human Immunodeficiency Virus Gag-Specific Gamma Interferon-Expressing Cells following Protective Mucosal Immunization with Alphavirus Replicon Particles
Authors: Gupta Soumi , Janani Ramesh , Bin Qian , Luciw Paul , Greer Catherine , Perri Silvia , Legg Harold , Donnelly John , Barnett Susan , O'Hagan Derek , Polo John M. , Vajdy Michael
Published: May 2005

A safe, replication-defective viral vector that can induce mucosal and systemic immune responses and confer protection against many infectious pathogens, such as human immunodeficiency virus type 1 (HIV-1), may be an ideal vaccine platform. Accordingly, we have generated and tested alphavirus replicon particles encoding HIV-1 Gag from Sindbis virus (SIN-Gag) and Venezuelan equine encephalitis virus (VEE-Gag), as well as chimeras between the two (VEE/SIN-Gag). Following intramuscular (i.m.), intranasal (i.n.), or intravaginal (IVAG) immunization with VEE/SIN-Gag and an IVAG challenge with vaccinia virus encoding HIV Gag (VV-Gag), a larger number of Gag-specific CD8+intracellular gamma interferon-expressing cells (iIFNEC) were detected in iliac lymph nodes (ILN), which drain the vaginal/uterine mucosa (VUM), than were observed after immunizations with SIN-Gag. Moreover, a single i.n. or IVAG immunization with VEE/SIN-Gag induced a larger number of cells expressing HIV Gag in ILN, and immunizations with VEE/SIN-Gag through any route induced better protective responses than immunizations with SIN-Gag. In VUM, a larger percentage of iIFNEC expressed α4β7 or αEβ7 integrin than expressed CD62L integrin. However, in spleens (SP), a larger percentage of iIFNEC expressed α4β7 or CD62L than expressed αEβ7. Moreover, a larger percentage of iIFNEC expressed the chemokine receptor CCR5 in VUM and ILN than in SP. These results demonstrate a better induction of cellular and protective responses following immunizations with VEE/SIN-Gag than that following immunizations with SIN-Gag and also indicate a differential expression of homing and chemokine receptors on iIFNEC in mucosal effector and inductive sites versus systemic lymphoid tissues.
Elimination of
ie
1 Significantly Attenuates Murine Cytomegalovirus Virulence but Does Not Alter Replicative Capacity in Cell Culture
Authors: Ghazal Peter , Visser Astrid E. , Gustems Montse , García Rosalía , Borst Eva Maria , Sullivan Kevin , Messerle Martin , Angulo Ana
Published: May 2005

The major immediate-early (MIE) genes of cytomegaloviruses (CMV) are broadly thought to be decisive regulators of lytic replication and reactivation from latency. To directly assess the role of the MIE protein IE1 during the infection of murine CMV (MCMV), we constructed an MCMV with exon 4 of the
ie
1 gene deleted. We found that, independent of the multiplicity of infection, the resulting recombinant virus, MCMVdie1, which fails to express the IE1 protein, was fully competent for early gene expression and replicated in different cultured cell types with identical kinetics to those of parental or revertant virus. Immunofluorescence microscopy studies revealed that MCMVdie1 was greatly impaired in its capacity to disrupt promyelocytic leukemia bodies in NIH 3T3 cells early after infection, a process that has been proposed to increase viral transcription efficiency. We examined MCMVdie1 in the murine model using both immunocompetent BALB/c and severe combined immunodeficient (SCID) mice. When MCMVdie1 was inoculated into these two types of mice, significantly lower viral titers were detected in infected organs than in those of the wild-type virus-infected animals. Moreover, the
ie
1-deficient MCMV exhibited a markedly reduced virulence. While all animals infected with 5 × 10
4
PFU of parental virus died by 30 days postinfection, SCID mice infected with a similar dose of MCMVdie1 did not succumb before 60 days postinfection. The in vivo defective growth phenotype of MCMVdie1 was abrogated upon rescue of
ie
1. These results demonstrate the significance of the
ie
1 gene for promoting an acute MCMV infection and virulence yet indicate that MCMV is able to grow in vivo, although impaired, in the absence of the
ie
1 gene.
Aureusvirus P14 Is an Efficient RNA Silencing Suppressor That Binds Double-Stranded RNAs without Size Specificity
Authors: Mérai Zsuzsanna , Kerényi Zoltán , Molnár Attila , Barta Endre , Válóczi Anna , Bisztray György , Havelda Zoltán , Burgyán József , Silhavy Dániel
Published: May 2005

RNA silencing is a conserved eukaryotic gene regulatory system in which sequence specificity is determined by small RNAs. Plant RNA silencing also acts as an antiviral mechanism; therefore, viral infection requires expression of a silencing suppressor. The mechanism and the evolution of silencing suppression are still poorly understood. Tombusvirus open reading frame (ORF) 5-encoded P19 is a size-selective double-stranded RNA (dsRNA) binding protein that suppresses silencing by sequestering double-stranded small interfering RNAs (siRNAs), the specificity determinant of the antiviral silencing system. To better understand the evolution of silencing suppression, we characterized the suppressor of the type member of Aureusviruses, the closest relatives of the genus
Tombusvirus
. We show that the
Pothos latent virus
(PoLV) ORF 5-encoded P14 is an efficient suppressor of both virus- and transgene-induced silencing. Findings that in vitro P14 binds dsRNAs and double-stranded siRNAs without obvious size selection suggest that P14, unlike P19, can suppress silencing by sequestering both long dsRNA and double-stranded siRNA components of the silencing machinery. Indeed, P14 prevents the accumulation of hairpin transcript-derived siRNAs, indicating that P14 inhibits inverted repeat-induced silencing by binding the long dsRNA precursors of siRNAs. However, viral siRNAs accumulate to high levels in PoLV-infected plants; therefore, P14 might inhibit virus-induced silencing by sequestering double-stranded siRNAs. Finally, sequence analyses suggest that P14 and P19 suppressors diverged from an ancient dsRNA binding suppressor that evolved as a nested protein within the common ancestor of aureusvirus-tombusvirus movement proteins.
Loss of Interferon Regulatory Factor 3 in Cells Infected with Classical Swine Fever Virus Involves the N-Terminal Protease, N
pro
Authors: La Rocca S. Anna , Herbert Rebecca J. , Crooke Helen , Drew Trevor W. , Wileman Thomas E. , Powell Penny P.
Published: May 2005

We show that cells infected with the pestivirus classical swine fever virus (CSFV) fail to produce alpha/beta interferon not only following treatment with double-stranded RNA but also after superinfection with a heterologous virus, the alphavirus Sindbis virus, a virus shown to normally induce interferon. We investigated whether the inhibition of interferon synthesis by CSFV involved a block in interferon regulatory factor 3 (IRF3) activity. Cells infected with CSFV exhibited a lack of translocation of green fluorescent protein-IRF3 to the nucleus; however, constitutive shuttling of IRF3 was not blocked, since it could still accumulate in the nucleus in the presence of leptomycin B. Interestingly subcellular fractionation analysis showed that IRF3 was lost from the cytoplasm of infected cells from 18 h postinfection onwards. Using IRF3 promoter-luciferase reporter constructs, we demonstrate that loss of IRF3 was due to an inhibition of transcription of the IRF3 gene in CSFV-infected cells. Further, we investigated which viral protein may be responsible for the inhibition of interferon and loss of IRF3. We used cell lines expressing the CSFV N-terminal protease (N
pro
) to show that this single viral protein, unique to pestiviruses, inhibited interferon production in response to Sindbis virus. In addition to being lost from CSFV-infected cells, IRF3 was lost from N
pro
-expressing cells. The results demonstrate a novel viral evasion of innate host defenses, where interferon synthesis is prevented by inhibiting transcription of IRF3 in CSFV-infected cells.
Heat Shock Protein 90 Expression in Epstein-Barr Virus-Infected B Cells Promotes γδ T-Cell Proliferation In Vitro
Authors: Kotsiopriftis Maria , Tanner Jerome E. , Alfieri Caroline
Published: May 2005

The aim of this study was to elucidate the in vitro response of γδ T cells to Epstein-Barr virus (EBV)-infected B cells and to determine whether EBV-induced heat shock proteins (HSPs) might serve as γδ T-cell stimulants. Cytofluorometric analysis revealed HSP90 cell surface expression in 12% of the EBV-immortalized B-cell population in all four of the B-cell lines tested. HSP27, HSP60, and HSP70 were not detected on the cell surface by cytofluorometry in these same B-cell lines. HSP90 and HSP60, but not HSP70 or HSP27, were detected on the cell surface after125I cell surface labeling and immunoprecipitation with anti-human HSP monoclonal antibodies. In vitro kinetic studies indicated that γδ T cells increased at least twofold by day 11 postinfection in cultures of EBV-seronegative peripheral blood lymphocytes infected with EBV, whereas percentages of αβ T cells in these same cultures either decreased slightly or remained relatively unchanged in response to EBV infection. Addition of anti-human HSP90 monoclonal antibody to the EBV-infected lymphocyte cultures inhibited γδ T-cell expansion by 92%. The inhibition of γδ T-cell expansion by anti-HSP90 antibody was reversed upon treatment with exogenous HSP90. Taken together, these results indicate that HSP90 played an important role in the stimulation of γδ T cells during EBV infection of B cells in vitro and may serve as an important immunomodulator of γδ T cells during acute EBV infection.
Genetic and Biochemical Evidence for an Oligomeric Structure of the Functional L Polymerase of the Prototypic Arenavirus Lymphocytic Choriomeningitis Virus
Authors: Sánchez Ana B. , de la Torre Juan C.
Published: May 2005

The arenavirus L protein has the characteristic sequence motifs conserved among the RNA-dependent RNA polymerase L proteins of negative-strand (NS) RNA viruses. Studies based on the use of reverse-genetics approaches have provided direct experimental evidence of the key role played by the arenavirus L protein in viral-RNA synthesis. Sequence alignment shows six conserved domains among L proteins of NS RNA viruses. The proposed polymerase module of L is located within its domain III, which contains highly conserved amino acids within motifs designated A and C. We have examined the role of these conserved residues in the polymerase activity of the L protein of the prototypic arenavirus, lymphocytic choriomeningitis virus (LCMV), in vivo using a minigenome rescue assay. We show here that the presence of sequence SDD, a characteristic of motif C of segmented NS RNA viruses, as well as the presence of the highly conserved D residue within motif A of L proteins, is strictly required for the polymerase activity of the LCMV L protein. The strong dominant negative phenotype associated with many of the mutants examined and results from coimmunoprecipitation studies provided genetic and biochemical evidence, respectively, for the requirement of the L-L interaction for the polymerase activity of the LCMV L protein.
A Computer Method for Validating Traditional Chinese Medicine Herbal Prescriptions
Authors: Wang J. F. , Cai C. Z. , Kong C. Y. , Cao Z. W. , Chen Y. Z.
Published: May 2005

Traditional Chinese medicine (TCM) has been widely practiced and is considered as an alternative to conventional medicine. TCM herbal prescriptions contain a mixture of herbs that collectively exert therapeutic actions and modulating effects. Traditionally defined herbal properties, related to the pharmacodynamic, pharmacokinetic and toxicological, as well as physicochemical properties of their principal ingredients, have been used as the basis for formulating TCM multi-herb prescriptions. These properties are used in this work to develop a computer program for predicting whether a multi-herb recipe is a valid TCM prescription. This program is based on a statistical learning method, support vector machine (SVM), and it is trained by using 575 well-known TCM prescriptions and 1961 non-TCM recipes generated by random combination of TCM herbs. Testing results by using 72 well-known TCM prescriptions and 5039 non-TCM recipes showed that 73.6% of the TCM prescriptions and 99.9% of non-TCM recipes are correctly classified by this system. A further test by using 48 TCM prescriptions published in recent years found that 68.7% of these are correctly classified. These accuracies are comparable to those of SVM classification of other biological systems. Our study indicates the potential of SVM for facilitating the analysis of TCM prescriptions.
A Medical Qigong Methodology for Early Intervention in Autism Spectrum Disorder: A Case Series
Authors: Silva Louisa M. T. , Cignolini Anita
Published: May 2005

A medical Qigong protocol was applied to a group of eight autistic children under the age of six. The children received medical Qigong massage twice weekly from the physician and daily Qigong massage from the parents for a five-week period, followed by daily parent massage for an additional four weeks. Standardized tests showed a decrease in autistic behaviors and increase in language development in all the children, as well as improvement in motor skills, sensory function and general health.
A Survey of Attitudes to Traditional Chinese Medicine Among Chinese Medical Students
Authors: Hon Kam-Lun Ellis , Leung Ting-Fan , Tse Hio-Meng , Lam Lai-Na , Tam Kwok-Cheong , Chu Ka-Man , Wong Yin , Fok Tai-Fai
Published: May 2005

We studied the attitudes and personal experiences with traditional Chinese Medicine (TCM) use in Chinese medical students. Medical students at the Chinese University of Hong Kong were asked 13 questions according to an anonymous survey. Six hundred and eleven of 780 medical students (47% males, 52% females) returned the questionnaire; 199 (33%) of the participants used TCM at least once in the past year, and 85% had ever tried various TCM. The attitude was positive in 41%, neutral in 52% and negative in only 6%. The majority (70%) reported no change in attitudes towards TCM after studying Western medicine (WM). Of the 199 participants who had used TCM in the past year, upper respiratory infections were the most common circumstance leading to TCM usage, with 31% immediately using TCM without any TCM practitioner consultation. The most common modality of TCM used by 85% of participants was herbal decoction, and nearly one-quarter had used over-the-counter Chinese medicine. Although 78% reported they knew of the TCM practitioner or treatment from family members or friends, 14% stated they randomly selected the practitioner. "Effectiveness of TCM," "fewer side effects than WM," "illness not completely treated by WM" and "recommendation from family/friends" were common beliefs held by participants for TCM usage. Forty-five percent reported that they had not been told of any side effects of TCM. Pre-clinical students had more positive attitudes towards TCM and consulted TCM practitioners more often in the past 12 months (OR 9.1, CI 3.16–28.18; p <0.001) compared to students in clinical years, who tended to become more negative towards TCM after studying WM. TCM usage is common among medical students in Hong Kong. It is important to note that nearly half of the students were not aware of any possible side effects from TCM. Students appear to become more negative towards TCM after studying WM.
SECOND HARMONIC GENERATION IN TWO-DIMENSIONAL PHOTONIC CRYSTAL CONSISTING OF CENTRO-SYMMETRIC DIELECTRIC
Authors: SHI JIANPING , CHEN XIANZHONG , CHEN XUNAN , YAO HANMIN , YANG GAIRONG , SUN JUNQI
Published: May 2005

We report optical second harmonic generation (OSHG) in a two dimension photonic crystal of centro-symmetric dielectric based on finite difference time domain (FDTD) algorithm. The electromagnetic field distribution in the structure and the intensity of second harmonic (SH) from electric quadrupole polarization along the waveguide are analyzed. The results show that the acute spatial variation of electromagnetic field results in the radiation of SH, and the intensity is proportional to the square of waveguide length. When the beam intensity of the pumping wave is 1.3 MW/mm2, which has wavelength of 10.6 μm, the conversion efficiency of power is 0.307% for a photonic crystal of Silicon with a length of 40 μm.
HAMILTONIAN DYNAMICS OF THE COMPLEX FROEHLICH DIMER
Authors: BURIĆ N. , RISTOVSKI LJ. , TODOROVIC K.
Published: May 2005

A classical Hamiltonian system modelling dynamics of dipole momenta of the complex Froehlich dimer is proposed and analyzed. Formally, the classical system is a system of two quartic oscillators with three different coupling constants, and all formal parameters in the Hamiltonian's function are expressed via only two parameters with microscopic physical interpretation. The classification of stable configurations of the dimer in terms of stationary states of its classical model is given. Their stability, in the linear approximation as well as for the full nonlinear dynamics, is analyzed with respect to the variations of the physical parameters. For example, it is shown that for the medium values of the parameter related to the rate of the energy supplied to the dimer, the stable stationary state is not with the minimal energy, but corresponds to the deformed dimer, with parallel dipole momenta of the monomers.
CLASSICAL OPTICAL TRANSFORMS STUDIED IN THE CONTEXT OF QUANTUM OPTICS VIA THE ROUTE OF DEVELOPING DIRAC'S SYMBOLIC METHOD
Authors: FAN HONG-YI , LU HAI-LIANG
Published: May 2005

Via the route of developing Dirac's symbolic method and following Dirac's assertion: "⋯ for a quantum dynamic system that has a classical analogue, unitary transformation in the quantum theory is the analogue of contact transformation in the classical theory", we find the generalized Fresnel operator (GFO) corresponding to the generalized Fresnel transform (GFT) in classical optics. We derive GFO's normal product form and its canonical coherent state representation and find that GFO is the loyal representation of symplectic group multiplication rule. We show that GFT is just the transformation matrix element of GFO in the coordinate representation such that two successive GFTs is still a GFT. The ABCD rule of the Gaussian beam propagation is directly demonstrated in quantum optics. With the aid of entangled state representation the entangled Fresnel transform is proposed; new eigenfunctions of the complex fractional Fourier transform and fractional Hankel transform are obtained; the two-variable Hermite eigenmodes of light propagation are used in studying the Talbot effect in quadratic-index media; the complex wavelet transform and the condition of mother wavelet are studied in the context of quantum optics too. Moreover, quantum optical version of classical z-transforms is obtained on the basis of the eigenvector of creation operator. Throughout our discussions, the coherent state, squeezing operators and the technique of integration within an ordered product (IWOP) of operators are fully used.
READING COMPLEXITY IN CHUA'S OSCILLATOR THROUGH MUSIC. PART I: A NEW WAY OF UNDERSTANDING CHAOS
Authors: BILOTTA ELEONORA , GERVASI STEFANIA , PANTANO PIETRO
Published: May 2005

Modern Science is finding new methods of looking at biological, physical or social phenomena. Traditional methods of quantification are no longer sufficient and new approaches are emerging. These approaches make it apparent that the phenomena the observer is looking at are not classifiable by conventional methods. These phenomena are complex. A complex system, as Chua's oscillator, is a nonlinear configuration whose dynamical behavior is chaotic. Chua's oscillator equations allow to define the basic behavior of a dynamical system and to detect the changes in the qualitative behavior of a system when bifurcation occurs, as parameters are varied. The typical set of behavior of a dynamical system can be detailed as equilibrium points, limit cycles, strange attractors. The concepts, methods and paradigms of Dynamical Systems Theory can be applied to understand human behavior. Human behavior is emergent and behavior patterns emerge thanks to the way the parts or the processes are coordinated among themselves. In fact, the listening process in humans is complex and it develops over time as well. Sound and music can be both inside and outside humans. This tutorial concerns the translation of Chua's oscillators into music, in order to find a new way of understanding complexity by using music. By building up many computational models which allow the translation of some quantitative features of Chua's oscillator into sound and music, we have created many acoustical and musical compositions, which in turn present the characteristics of dynamical systems from a perceptual point of view. We have found interesting relationships between dynamical systems behavior and their musical translation since, in the process of listening, human subjects perceive many of the structures as possible to perceive in the behavior of Chua's oscillator. In other words, human cognitive abilities can analyze the large and complicated patterns produced by Chua's systems translated into music, achieving the cognitive economy and the coordination and synthesis of countless data at our disposal that occur in the perception of dynamic events in the real world. Music can be considered the semantics of dynamical systems, which gives us a powerful method for interpreting complexity.
SET STABILIZATION OF A MODIFIED CHUA'S CIRCUIT
Authors: LI SHIHUA , TIAN YU-PING
Published: May 2005

In this paper, we develop a simple linear feedback controller, which employs only one of the states of the system, to stabilize the modified Chua's circuit to an invariant set which consists of its nontrivial equilibria. Moreover, we show for the first time that the closed loop modified Chua's circuit satisfies set stability which can be considered as a generalization of common Lyapunov stability of an equilibrium point. Simulation results are presented to verify our method.
LAG SYNCHRONIZATION OF CHAOTIC LUR'E SYSTEMS VIA REPLACING VARIABLES CONTROL
Authors: WU XIAOFENG , ZHAO YI , ZHOU SHENG
Published: May 2005

In this paper, we propose a method to research lag synchronization of the identical master-slave chaotic Lur'e systems via replacing variables control with time delay. By means of absolute stability theory, we prove two types of sufficient conditions for the lag synchronization: Lur'e criterion and frequency domain criterion. Based on the criteria, we suggest an optimization scheme to design the control variables. Applying the scheme to general Chua's circuits, we obtain the parameter ranges in which the master-slave Chua's circuits laggingly synchronize or not by varied single-variable control. Finally, we cite the examples by illustration of the results.
NOVEL NUMERICAL APPROACH TO SOLITARY–WAVE SOLUTIONS IDENTIFICATION OF BOUSSINESQ AND KORTEWEG–DE VRIES EQUATIONS
Authors: MARINOV TCHAVDAR T. , CHRISTOV CHRISTO I. , MARINOVA ROSSITZA S.
Published: May 2005

A special numerical technique has been developed for identification of solitary wave solutions of Boussinesq and Korteweg–de Vries equations. Stationary localized waves are considered in the frame moving to the right. The original ill-posed problem is transferred into a problem of the unknown coefficient from over-posed boundary data in which the trivial solution is excluded. The Method of Variational Imbedding is used for solving the inverse problem. The generalized sixth-order Boussinesq equation is considered for illustrations.
RAPID FLUCTUATIONS OF SNAPSHOTS OF ONE-DIMENSIONAL LINEAR WAVE EQUATION WITH A VAN DER POL NONLINEAR BOUNDARY CONDITION
Authors: HUANG YU , LUO JUN , ZHOU ZUOLING
Published: May 2005

In this paper, we consider a linear wave equation on an interval with a van der Pol nonlinear boundary condition at one end and an energy-pumping condition at the other end. We study the dynamical behavior of the Riemann invariants (u,v) of the wave equation in terms of the growth rates of the total variations of the snapshots on the spatial interval. Our main contributions here are the detection of rapid fluctuations of the snapshots of u and v in the long run. The results here sharpen those in the earlier works of [Chen et al., 2001] and [Huang, 2003].
SYNCHRONIZATION OF CHUA CHAOTIC CIRCUITS WITH APPLICATION TO THE BIDIRECTIONAL SECURE COMMUNICATION SYSTEMS
Authors: TSAY SHUH-CHUAN , HUANG CHUAN-KUEI , CHEN WAN-TAI , WU YU-REN
Published: May 2005

In this paper, a scheme of a bidirectional hyperchaotic communication system is proposed. The hyperchaotic communication system including the transmitter and the receiver is composed of a pair of Chua circuit with coupling characteristics respectively. From the viewpoint of communication security, directly adopting the bidirectional communication system would provide a so-called "theoretical security". This is caused by the coupling relationship between the transmitter and the receiver. With the technique of frequency spectrum, the theoretical security of bidirectional communication systems can be proven. In other words, even if an intruder knows the parameter values of the system, he could not steal information from the system. As a result, it is not necessary for us to use the additional encryption. On the other hand, to achieve the synchronization of bidirectional communications, the method which applies a suitable Lyapunov function and the property of positive definite of a matrix is proposed to design the feedback controllers. Therefore, the message masked by chaotic signal from the transmitter can be perfectly recovered in the receiver. Finally, the simulation results can verify that the proposed method and the scheme of the bidirectional communication are favorable.
STRONG CHAOS IN A FORCED NEGATIVE CONDUCTANCE SERIES LCR CIRCUIT
Authors: THAMILMARAN K. , SENTHILKUMAR D. V. , LAKSHMANAN M. , AHAMED A. ISHAQ
Published: May 2005

A negative conductance forced LCR circuit exhibiting strong chaos via the torus breakdown route as well as period-doubling route is described. The strong chaoticity is evidenced by the high value of the largest Lyapunov exponent and statistical studies. The dual nature of this circuit exhibiting the rich dynamics of both the Murali–Lakshmanan–Chua (MLC) circuit [Murali et al., 1994] and the circuit due to Inaba and Mori [1991] is also explored. The performance of the circuit is investigated by means of laboratory experiments, PSpice circuit simulation, numerical integration of appropriate mathematical model and explicit analytical studies, which all agree well with each other.
PLANE MAPS WITH DENOMINATOR. PART III: NONSIMPLE FOCAL POINTS AND RELATED BIFURCATIONS
Authors: BISCHI GIAN-ITALO , GARDINI LAURA , MIRA CHRISTIAN
Published: May 2005

This paper continues the study of the global dynamic properties specific to maps of the plane characterized by the presence of a denominator that vanishes in a one-dimensional submanifold. After two previous papers by the same authors, where the definitions of new kinds of singularities, called focal points and prefocal sets, are given, as well as the particular structures of the basins and the global bifurcations related to the presence of such singularities, this third paper is devoted to the analysis of nonsimple focal points, and the bifurcations associated with them. We prove the existence of a one-to-one relation between the points of a prefocal curve and arcs through the focal point having all the same tangent but different curvatures. In the case of nonsimple focal points, such a relation replaces the one-to-one correspondence between the slopes of arcs through a focal point and the points along the associated prefocal curve that have been proved and extensively discussed in the previous papers. Moreover, when dealing with noninvertible maps, other kinds of relations can be obtained in the presence of nonsimple focal points or prefocal curves, and some of them are associated with qualitative changes of the critical sets, i.e. with the structure of the Riemann foliation of the plane.
CHAOTIFICATION OF DISCRETE DYNAMICAL SYSTEMS GOVERNED BY CONTINUOUS MAPS
Authors: SHI YUMING , CHEN GUANRONG
Published: May 2005

This paper is concerned with chaotification of discrete dynamical systems in finite-dimensional real spaces, via feedback control techniques. A chaotification theorem for one-dimensional discrete dynamical systems and a chaotification theorem for general higher-dimensional discrete dynamical systems are established, respectively. The controlled systems are proved to be chaotic in the sense of Devaney. In particular, the maps corresponding to the original systems and designed controllers are only required to satisfy some mild assumptions on two very small disjoint closed subsets in the domains of interest. This condition is weaker than those in the existing relevant literature.
ACHIEVABLE RANKS OF INTERSECTIONS OF FINITELY GENERATED FREE GROUPS
Authors: KENT RICHARD P.
Published: May 2005

We answer a question due to A. Myasnikov by proving that all expected ranks occur as the ranks of intersections of finitely generated subgroups of free groups.
A BOUND ON THE NUMBER OF UNARY POLYNOMIAL FUNCTIONS AND A DECIDABILITY RESULT FOR NEAR-RINGS
Authors: AICHINGER ERHARD
Published: May 2005

Given a finite zero-symmetric near-ring with identity N, we ask whether there is a group G such that N is isomorphic to the inner automorphism near-ring , or whether N is a compatible near-ring. We will show that there are algorithms that decide these questions. To this end, we study polynomial functions on subdirectly irreducible expanded groups. We prove that the size of a finite subdirectly irreducible expanded group is bounded from above by a function of the number of its zero-preserving unary polynomial functions.
PRESENTATIONS FOR SEMIGROUPS AND SEMIGROUPOIDS
Authors: KAMBITES MARK
Published: May 2005

We consider the relationship between the combinatorial properties of semigroupoids in general and semigroups in particular. We show that a semigroupoid is finitely generated [finitely presentable] exactly if the corresponding categorical-at-zero semigroup is finitely generated [respectively, finitely presentable]. This allows us to extend some of the main results of [17], to show that finite generation and presentability are preserved under finite extension of semigroupoids and the taking of cofinite subsemigroupoids. We apply this result to extend the results of [6], giving characterizations of finite generation and finite presentability in Rees matrix semigroups over semigroupoids.
ABOUT NORMS AND CAUSES
Authors: KAYSER DANIEL , NOUIOUA FARID
Published: May 2005

Knowing the norms of a domain is crucial, but there exists no repository of norms. We propose a method to extract them from texts: narrative texts generally do not describe a norm, but rather the discrepancies between what actually happened, and the corresponding normal sequence of events. Answers about the causes of an event often reveal the implicit norms. We apply this idea to the domain of driving, and validate it by designing algorithms that identify, in a text, the "basic" norms to which it refers implicitly.
A LOCAL SEARCH/CONSTRAINT PROPAGATION HYBRID FOR A NETWORK ROUTING PROBLEM
Authors: LEVER JONATHAN
Published: May 2005

This paper presents a hybrid algorithm that combines local search and constraint programming techniques to solve a network routing problem. The problem considered is that of routing traffic demands from a set of requests over a network with limited capacity so as to minimise the cost of any unrouted demands. The hybridisation is twofold: pure local search is used to find a good cost bound for a subsequent branch-and-bound optimisation phase, with local search again applied at the nodes of the branch-and-bound search tree. Constraint propagation occurs in the search tree to reduce the domains of the decision variable, using a set of constraints that are independent of the action of local search at the nodes. In contrast to previous constraint programming/local search hybridisations, here local search is used to satisfy the hard problem constraints, while optimisation is handled in the framework of constraint programming. The resulting algorithm is incomplete, but is shown to compare favourably with a complete approach to this problem.
ITERATIVE STRUCTURE DISCOVERY IN GRAPH-BASED DATA
Authors: COBLE JEFFREY A. , RATHI RUNU , COOK DIANE J. , HOLDER LAWRENCE B.
Published: May 2005

Much of current data mining research is focused on discovering sets of attributes that discriminate data entities into classes, such as shopping trends for a particular demographic group. In contrast, we are working to develop data mining techniques to discover patterns consisting of complex relationships between entities. Our research is particularly applicable to domains in which the data is event-driven or relationally structured. In this paper we present approaches to address two related challenges; the need to assimilate incremental data updates and the need to mine monolithic datasets. Many realistic problems are continuous in nature and therefore require a data mining approach that can evolve discovered knowledge over time. Similarly, many problems present data sets that are too large to fit into dynamic memory on conventional computer systems. We address incremental data mining by introducing a mechanism for summarizing discoveries from previous data increments so that the globally-best patterns can be computed by mining only the new data increment. To address monolithic datasets we introduce a technique by which these datasets can be partitioned and mined serially with minimal impact on the result quality. We present applications of our work in both the counter-terrorism and bioinformatics domains.
DISAMBIGUATION VIA DEFAULT RULES UNDER ANSWERING COMPLEX QUESTIONS
Authors: GALITSKY BORIS
Published: May 2005

We develop the default logic for pragmatic analysis of natural language queries. Ambiguous sentences are considered so that each set of meanings is assigned an extension of default system. The approach is applied to natural language question answering, where even a correct semantic representation needs to be modified in accordance to the set of default rules to better match a knowledge domain.
CLUSTERING SPATIAL DATA IN THE PRESENCE OF OBSTACLES
Authors: WANG XIN , HAMILTON HOWARD J.
Published: May 2005

Dealing with constraints due to obstacles is an important topic in constraint-based spatial clustering. In this paper, we proposed the DBRS_O method to identify clusters in the presence of intersected obstacles. Without doing any preprocessing, DBRS_O processes the constraints during clustering. DBRS_O can also avoid unnecessary computations when obstacles do not affect the clustering result. As well, DBRS_O can find clusters with arbitrary shapes, varying densities, deal with significant non-spatial attributes and handle large datasets.
FUNCTION GRANULARITY ESTIMATION FOR MULTIMODAL OPTIMIZATION
Authors: ZHANG JIAN , YUAN XIAOHUI , BUCKLES BILL P.
Published: May 2005

In this article, we study the subspace function granularity and present a method to estimate the sharing distance and the optimal population size. To achieve multimodal function optimization, niching techniques diversify the population of Evolutionary Algorithms (EA) and encourage heterogeneous convergence to multiple optima. The key to a successful diversification is effective resource sharing. Without knowing the fitness landscape, resource sharing is usually determined by uninformative assumptions on the number of peaks. Using the Probably Approximately Correct (PAC) learning theory and the ∊-cover concept, a PAC neighborhood for a set of samples is derived. Within this neighborhood, we sample the fitness landscape and compute the subspace Fitness Distance Correlation (FDC) coefficients. Using the estimated granularity feature of the fitness landscape, the sharing distance and the population size are determined. Experiments demonstrate that by using the estimated population size and sharing distance an Evolutionary Algorithm successfully identifies multiple optima.
ITERATIVE DESIGN OF NEURAL NETWORK CLASSIFIERS THROUGH REGRESSION
Authors: GORE R. G. , LI J. , MANRY M. T. , LIU L. M. , YU C. , WEI J.
Published: May 2005

A method which modifies the objective function used far designing neural network classifiers is presented. The classical mean-square error criteria is relaxed by introducing two types of local error bias which are treated like free parameters. Open and closed form solutions are given for finding these bias parameters. The new objective function is seamlessly integrated into existing training algorithms such as back propagation (BP), output weight optimization (OWO), and hidden weight optimization (HWO). The resulting algorithms are successfully applied in training neural net classifiers having a linear final layer. Classifiers are trained and tested on several data sets from pattern recognition applications. Improvement over classical iterative regression methods is clearly demonstrated.
CELLULAR AUTOMATA APPROACH TO AIRCRAFT CORROSION GROWTH
Authors: PIDAPARTI RAMANA M. , PALAKAL MATHEW J. , FANG LONG
Published: May 2005

Corrosion is one of the degrading mechanisms that greatly affect the structural integrity of aerospace components. Corrosion begins with small imperfections in the given material referred to as "pits". Over time, and with exposure to the environment and loading stresses, these pits grow into structural cracks. These cracks, under further exposure to elements and stress, will eventually lead to material failure. To better understand how corrosion growth process takes place in materials, research is being conducted to simulate corrosion pit growth process using computational intelligence methods. The objective of this study is to develop a discrete dynamic model using cellular automata to simulate the pitting corrosion growth process in aircraft materials, and see how it affects the structural integrity.