bluuebunny/crossref_metadata_2025 huggingface dataset:
A negative feedback loop involving small RNAs accelerates Vibrio cholerae’s transition out of quorum-sensing mode
Authors: Svenningsen Sine L. , Waters Christopher M. , Bassler Bonnie L.
Published: January 2008

Quorum sensing is a cell-to-cell communication process that allows bacteria to measure their population numbers and to synchronously alter gene expression in response to changes in cell population density. At the core of the Vibrio cholerae quorum-sensing signal transduction pathway lie four redundant small RNAs (sRNAs), named the Quorum Regulatory RNAs (Qrr1–4). Expression of qrr1–4 is cell population density-dependent due to a requirement for the quorum-sensing controlled phosphorylated response regulator LuxO-P, which is abundant only at low cell population density. When expressed, Qrr1–4 repress translation of HapR, the “master” quorum-sensing transcription factor. Here we show a negative feedback loop in which HapR activates transcription of the qrr genes, which indirectly leads to hapR repression. Efficient feedback activation of the qrr genes requires the simultaneous presence of LuxO-P (present only at low cell population density) and HapR (present only at high cell population density). For this reason, the feedback loop does not influence quorum sensing at steady-state low or high cell population density. However, LuxO-P and HapR are simultaneously present immediately following the switch from high to low cell density conditions. In this state, the HapR feedback loop dramatically accelerates V. cholerae’s transition from the high to the low cell density mode.
Global transcriptional regulation of the locus encoding the skeletal muscle determination genes Mrf4 and Myf5
Authors: Carvajal Jaime J. , Keith Annette , Rigby Peter W.J.
Published: January 2008

The linked Mrf4 and Myf5 genes encode two transcription factors essential for the determination and differentiation of skeletal muscle in the embryo. The locus is controlled by a multitude of interdigitated enhancers that activate gene expression at different times and in precisely defined progenitor cell populations. Manipulation of the enhancer–promoter composition of the locus reveals a novel mechanism for the regulation of such a gene cluster. Enhancers, promoters, and a new class of elements we call transcription balancing sequences, which can act as cryptic promoters, exist in a series of equilibria to ensure that enhancers and promoters together produce the highly dynamic and exquisitely specific expression patterns of the two genes. The proposed model depends upon nonproductive interactions between enhancers and both minimal and cryptic promoters, and is distinct from those developed for the β-globin and Hox clusters. Moreover, it provides an explanation for the unexpected phenotypes of the three Mrf4 knockout alleles.
A PHOTOCHEMICAL TECHNIQUE TO ENHANCE SENSITIVITY OF DETECTION OF FLUORESCENCE RESONANCE ENERGY TRANSFER
Authors: Mekler Vladimir M.
Published: January 2008

Abstract: A photochemical kinetic method of measuring small values of efficiency of fluorescence resonance energy transfer (FRET) between special probes is proposed. The FRET efficiency (ω) is determined from kinetics of the photochemical reaction of the energy acceptor sensitized by FRET from the energy donor. The choice of an appropriate donor‐acceptor pair permits the minimization of background reactions. Application of the method is demonstrated by the detection of FRET from 2,5‐bis(5‐tert‐butyl‐2‐benzoxasolyl)thiophen (BBOT) to acridine orange (AO) in phospholipid vesicles. Photobleaching of AO in the presence of CBr4 was applied as a photochemical reaction of the acceptor. The reaction was monitored by steady‐state fluorescence measurements. The FRET measurements were carried out by the proposed technique when the probe/lipid ratio and ω were as small as 1.1 × 10−5M/M and 0.0017, respectively. Under these conditions, the rate constant of AO photobleaching was increased by 26% as compared with that of the reference sample without BBOT. The results suggest that applications of the technique may be useful in the study of the membrane topography.
POSSIBLE ROLE OF METALLOTHIONEIN IN THE CELLULAR DEFENSE MECHANISM AGAINST UVB IRRADIATION IN NEONATAL HUMAN SKIN FIBROBLASTS
Authors: Kobayashi Shizuko , Hirota Yumiko , Sayato‐Suzuki Junko , Takehana Makoto , Nishimura Hisao , Nishimura Noriko , Tohyama Chiharu
Published: January 2008

Abstract: The role of metallothionein (MT) in protecting skin cells against UVB irradiation was investigated. Fibroblast strains from normal adult (HS‐K) and neonatal (NB1RGB) human skins as well as keratinocyte strains from human skin (SV40‐HSK) and newborn Balb/c mouse skin (Pam 212) were exposed to UVB irradiation.

The sensitivity of HS‐K and NB1RGB cells to UVB irradiation was similar; those of SV40‐HSK and Pam 212 cells were two‐ and six‐fold as sensitive to UVB irradiation as HS‐K cells, respectively. The HS‐K cells contained the greatest cellular reduced form of glutathione (GSH) levels compared to the three other skin cells: the levels were 13‐, 7‐ and 6‐fold of those in NB1RGB, SV40‐HSK and Pam 212 cells, respectively. These results indicated that the sensitivity of skin cells to UVB irradiation was not always associated with their endogenous GSH levels. In particular, despite the fact that NB1RGB cells contained a relatively small amount of GSH, they were less sensitive to UVB irradiation.

NB1RGB cells contained 4–30 times more MT than those in other skin cells examined. The sulfhydryl residues of MT molecules in the NB1RGB cells were estimated to be mostly unoccupied by metals, suggesting they act in a similar way to those of GSH. Moreover, NB1RGB cells in which the MT content was elevated by dexamethasone (1 μM) or Zn2+ (7 μg/mL) treatment were more resistant to UVB irradiation than nontreated ones.

These results suggest that, at least in neonatal human skin fibroblasts, MT may play a role in protection against UVB irradiation.
CHEMIEXCITATION IN THE PEROXIDATIVE METABOLISM OF N‐METHYLCARBAZOLE: MECHANISTIC IMPLICATIONS
Authors: de Melo Mariza Pires , Cilento Giuseppe
Published: January 2008

Abstract: The peroxidative metabolism of N‐methylcarbazole emits light independently of the presence of oxygen. It is likely that two chemiexcited transients are formed by electron transfer to the activated peroxidase, the cation radical by one electron transfer and a cation biradical by two electron transfer consistent with the failure to observe horseradish peroxidase‐II in the steady state of the reaction. In the spectral range investigated (390–700 nm) the observed emission (570–700 nm) is ascribed to the biradical, as the latter is equivalent to an excited state of the postulated iminium cation.

While lipoxygenase has no effect upon N‐methylcarbazole, it markedly enhances the emission if peroxidase is present. This effect requires oxygen and is ascribed to an excited product formed by lipoxygenase acting upon an intermediate hydroperoxide of the aerobic process promoted by peroxidase.

Our results are of importance on two counts. First they extend to N‐rnethylcarbazole the formation of excited species in the peroxidative metabolism of important xenobiotics. Second, the mechanistic information they provide supports the scheme of metabolism postulated by Kedderis et al. (1986, J. Biol. Chem. 261, 15910–15914).
Exclusive Free Radical Mechanisms of Cellular Photosensitization
Authors: Aveline Beatrice M. , Redmond Robert W.
Published: January 2008

In order to determine the specific effects of radical‐induced reactions in the absence of complicating excited‐state pathways, four different thiohydroxamic esters and their parent molecule,N‐hydroxypyridine‐2(1H)‐thione, have been studied in murine L1210 leukemia cells for their ability to produce photobiological damage. Irradiation (Xexc= 355 nm) of cells in the presence of thiopyridone esters, specific photolytic precursors of sulfur‐, carbon‐ and oxygen‐centered radicals, caused toxicity that was unambiguously demonstrated to result from radical photosensitization mechanisms. Cellular morphological changes were observed following irradiation but apoptosis was not found to take place. A good correlation was evident between lipid peroxidation, measured by the thiobarbituric acid method, and phototoxicity, assessed by the trypan blue exclusion assay, indicating that the ester derivatives exert their effects mainly in plasma and/ or subcellular membranes. Irradiation performed under deaerated conditions also induced significant phototoxicity but the effects of deaeration were dependent on the ester used and are discussed in terms of the nature of the primary radical species generated in each case. Irradiation of L1210 cells in the presence ofN‐hydroxypyridine‐2(1H)‐thione, a nonspecific, photochemical source of hydroxyl radical, was also found to trigger phototoxicity and lipid peroxidation. However in this case, photodamage cannot yet be definitely attributed to a radical or type II mechanism although the apparent oxygen independence of phototoxicity would indicate that type II contribution is not significant.
Light Dosimetry for Intraperitoneal Photodynamic Therapy in a Murine Xenograft Model of Human Epithelial Ovarian Carcinoma
Authors: Lilge Lothar , Molpus Kelly , Hasan Tayyaba , Wilson Brian C.
Published: January 2008

Few studies have been published to date measuring spatially resolved fluence rates in complex tissue geometries. Here the light distributions of three different intraperitoneal light delivery geometries in a murine ovarian cancer model were investigated to assess their influence on the tumorcidal efficacy of photodynamic therapy (PDT). In vivo fluence rate measurements in the peritoneal cavities of mice, with the light intensity being mapped in three transverse planes, were performed using fiber‐optic detectors. Three different source fiber designs and placements were tested for their ability to provide uniform irradiation of the peritoneal cavity. The biological response to a PDT protocol comprising three separate treatments administered at 72 h intervals, each consisting of a 0.25 mg kg intraperitoneal injection of benzopor‐phyrin derivative‐mono acid ring A followed 90 min later by delivery of 15 J of 690 nm light, was measured. The tissue response was evaluated by measuring the number of remaining visible lesions and the total residual tumor mass. Fluence rate measurements showed large variations in the fluence rate distribution for similar intended treatments. The most uniform and reproducible illumination was achieved using two 18 mm long cylindrical emitting optical fibers. The biological response was comparable to that produced when a flat‐cleaved end optical fiber is used to illuminate the four quadrants of the abdomen sequentially. While a good reproducibility in tumor induction in this animal model exists, no correlation was found between the fluence rate distribution measured in one group of animals and the biological response in a separate group of similarly treated animals. Due to the large intra‐animal variability in fluence rate distribution, representative fluence rate mapping in complex tissue geometries is of limited value when applied to an individual PDT treatment. Thus, surveillance of the fluence rate during individual treatments will be required for acceptable PDT dosimetry. To improve the versatility of this particular animal model for PDT research, a large number of extended sources are required to increase uniformity of the illumination in order to reduce unwanted cytotoxic side effects resulting from foci of high fluence rates. In this way, subsequent increase of the total energy delivered to the tumor may be possible.
Probing the Binding Region of the Single‐Stranded DNA‐Binding Domain of Rat DNA Polymerase β Using Nanosecond‐Pulse Laser‐Induced Cross‐Linking and Mass Spectrometry
Authors: Connor Dallas A. , Falick Arnold M. , Young Mark C. , Shetlar Martin D.
Published: January 2008

In recent years, there has been a significant number of studies in which UV light has been used as a reagent to induce cross‐links in nucleic acid‐protein complexes. An area of considerable interest among those interested in structural biology is the garnering of information about the sites of cross‐linking within the protein and nucleic acid members of photolinked conjugates, under the assumption that such knowledge should lead to identification of contact regions or sites within the native complexes. In this paper, we present our results from a photocross‐linking study of the complex of the single‐stranded DNA‐binding domain of rat DNA polymerase β (pol β‐ss) with the oligonucleotide d(ATATATA). In this study, we have used single nanosecond laser pulses as the cross‐linking reagent and matrix‐assisted laser desorp‐tion/ionization‐time of flight mass spectrometry as an analytical tool to identify cross‐linked peptides purified from proteolytic digests of the cross‐linked complex. Six cross‐linked peptides have been identified in tryptic digests of the protein‐oligonucleotide conjugates that result from irradiation of the pol β‐ss‐d(ATATATA) complex with a single laser pulse. Comparisons with NMR data in the literature for the same complex show that each of the cross‐linked peptides contains amino acids that are in contact with the nucleic acid component of the complex.
Porphyrins and Related Compounds as Photoactivatable Insecticides. 2. Phototoxic Activity of Meso‐Substituted Porphyrins
Authors: Amor T. Ben , Bortolotto L. , Jori G.
Published: January 2008

We have recently proposed the use of porphyrin sensitizers as photoinsecticidal agents. Our present findings show that the phototoxic efficiency of porphyrins toward the Mediterranean fruit fly Ceratitis capitata is strongly dependent on their chemical structure. Thus, two highly hydrophilic porphyrins, such as a tetraanionic and a te‐tracationic meso‐substituted derivative, show a very low photoactivity even upon prolonged irradiation with full‐spectrum visible light. The phototoxicity increases upon increasing the hydrophobicity of the porphyrin molecule; out of the compounds examined by us, the highest pho‐tocidal activity is exhibited by a dicationic amphophilic porphyrin, namely cis‐(JV‐methyl‐piridyl), c/s‐diphenyl‐porphine, which causes 100% mortality upon 1 h irradiation with a fluence rate of 1220 μ.E s‐lm‐2even at a concentration as low as 0.85 mM. The differences in photoactivity are not related to differences in the photo‐physical and photobiological properties or to differences in the rate of porphyrin uptake and clearance by the flies.
Release of Inflammatory Mediators (PGE2, IL‐6) by Fenofibric Acid‐Photosensitized Human Keratinocytes and Fibroblasts
Authors: Terencio Mari Carmen , Guillen Isabel , Gomez‐Lechon Marfa Jose , Miranda Miguel A. , Castell Jose V.
Published: January 2008

Ultraviolet‐A radiation has weak effects on the release of inflammatory mediators by skin cells due to the poor overlap between UVA wavelengths and the absorption spectra of the relevant chromophores of key biomole‐cules. However, this situation could be very different in the presence of a photosensitizing drug. To investigate this issue, we have irradiated human skin cells (keratinocytes and fibroblasts) in the presence of fenofibric acid (the active phototoxic metabolite of fenofibrate). The results of this research show a dual effect on the production/release of inflammatory mediators: the synthesis of the proinflammatory cytokine interleukin‐6 becomes strongly inhibited at photosensitizer concentrations that clearly stimulate the production of prostaglandins (PGE2) by skin cells. We have found evidences showing that the de novo synthesis of cytokines is inhibited in photosensitized cells due to the fact that cellular mRNA is degraded. Interestingly, when the medium taken from irradiated cultures is added to nonexposed cells, a significant stimulation of cytokine synthesis is observed that can be inhibited by anti‐PGE2 antibodies. These observations may be relevant in vivo, where prostaglandins released by photosensitized skin cells could stimulate cytokine synthesis by underlying, nonirradiated cells.
Photoelectrochemical Verification of Proton‐Releasing Groups in Bacteriorhodopsin
Authors: Koyama Koichi , Miyasaka Tsutomu , Needleman Richard , Lanyi Janos K.
Published: January 2008

Light‐induced transient currents of bacteriorhodopsin (bR) and its mutants (D96N, D85N, E204Q and E194Q) were measured at the interface of an electrode and the aqueous solution in an electrochemical cell. The transient positive (cathodic) and negative (anodic) photocurrents generated upon the onsets of continuous illumination and of turning off light, respectively, were investigated at different electrolyte pH. The wild type exhibits both positive and negative responses, with the sign of the response inverted at pH lt 5. In D85N the response is entirely suppressed, while D96N lacks the negative response. Laser pulse excitation (532 nm) of bR and the mutants showed the response rise time of the positive transient to be uniformly about 100 μs, indicating that the response is linked to the L to M transition in the photocycle. According to these results the positive and negative signals originate from the proton release and uptake reactions, respectively. Photoexcitation of the mutants E204Q and E194Q that lack protonatable residues at position 204 and 194, respectively, produced a negative response at neutral pH, which indicates that in these proteins proton uptake precedes proton release. This result is consistent with our observations made earlier with pH indicator dyes and demonstrates that Glu‐204 and Glu‐194 constitute the terminal proton release complex in the extracellular region of bR.
Light Irradiation of Mouse Spermatozoa: Stimulation of In Vitro Fertilization and Calcium Signals
Authors: Cohen Natalie , Lubart Rachel , Rubinstein Sara , Breitbart Haim
Published: January 2008

Irradiation of mouse spermatozoa by 630 nm He‐Ne laser was found to enhance the intracellular calcium levels and fertilizing potential of these cells. The effect of light on calcium transport and on fertilization rate was abrogated in the absence of Ca2+during the irradiation time, indicating that the effect of light is Ca2+dependent. The stimulatory effect of light on Ca2+uptake was abolished in the presence of a voltage‐dependent Ca2+‐channel inhibitor nifedipine, indicating the involvement of a plasma membrane voltage‐dependent Ca2+channel. Furthermore, the stimulatory effect of light was completely inhibited by the mitochondrial uncoupler FCCP, indicating that laser irradiation might affect the mitochondrial Ca2+transport mechanisms. A causal association between laser irradiation, reactive oxygen species (ROS) generation and sperm function was indicated by studies with ROS scavengers, superoxide dismutase (SOD) and catalase, and exogenous hydrogen peroxide. The SOD treatment, which enhanced H2O2 production, resulted in increased Ca2+uptake and enhanced fertilization rate. On the other hand, catalase, which decomposes H2O2, impaired the light‐induced stimulation in Ca2+uptake and the fertilization rate. Taken together, the data suggest that H2O2 might be involved in the irradiation effects, and indeed laser irradiation enhances the production of H2O2, by spermatozoa. These results indicate that the effect of 630 nm He‐Ne laser irradiation is mediated through the generation of H2O2 by the spermatozoa and that this effect plays a significant role in the augmentation of the sperm cells' capability to fertilize metaphase H‐arrested eggs in vitro.
Blue Light Requirement for HC03 Uptake and Its Action Spectrum in Monoraphidium braunii
Authors: Giráldez N. , Aparicio P. J. , Quiñones M. A.
Published: January 2008

The uptake and assimilation of HCO3 by the green unicellular alga Monoraphidium braunii can be monitored by the alkalinization of the external medium or by the O2 evolution associated with the uptake and reduction of this anion. The activation of HCO3 uptake in this microalga required the irradiation of the cell suspensions with low photon fluence rates of short wavelength radiation. Thus, when the cells were irradiated with strong red light in the presence of HCO3, very little alkalinization of the external medium or O2 evolution could be observed. The O2 evolution rates measured under red light could be due to the assimilation of the CO2 derived from the HCO3 present in the medium. The blue light‐dependent O2 evolution rates were not diminished by a periplasmic carbonic anhydrase inhibitor, suggesting that HCO3 ‐dependent O2 evolution was due to the photoactivation of a selective HCO3 uptake system at the plasma membrane. The action spectrum for HCO3‐ uptake in M. braunii was very similar to those reported for NO3‐ and CI‐ suggested that a flavoprotein may be the photoreceptor for this response.
Selection for High-Level Telithromycin Resistance in
Staphylococcus aureus
Yields Mutants Resulting from an
rplB
-to-
rplV
Gene Conversion-Like Event
Authors: Gentry Daniel R. , Holmes David J.
Published: January 2008

While most
Staphylococcus aureus
telithromycin-resistant mutants isolated in this study possessed duplications within
rplV
(encoding ribosomal protein L22), four isolates possessed insertions within
rplV
that were identical to a portion of the gene
rplB
(encoding ribosomal protein L2). This novel type of mutation is the result of an apparent gene conversion-like event.
Reliability of the WIDERYST Susceptibility Testing System for Detection of In Vitro Antifungal Resistance in Yeasts
Authors: Cuenca-Estrella Manuel , Gomez-Lopez Alicia , Gutierrez M. Olga , Buitrago M. Jose , Rodriguez-Tudela Juan L.
Published: January 2008

This study evaluated the WIDERYST system, a commercially available computer-assisted image-processing device for the antifungal susceptibility testing of yeasts. A collection of 90 clinical isolates selected to represent ranges of susceptibilities in vitro as broad as possible was tested. An evaluation compared the results obtained by the new system with those achieved by both the Clinical and Laboratory Standards Institute (CLSI) microdilution reference procedure and the antifungal susceptibility standard of the European Committee for Antimicrobial Susceptibility Testing (EUCAST). Overall, the agreement and the correlation index between results obtained by the EUCAST method and the WIDERYST system were 89% and 0.84 (
P
< 0.01), respectively, and agreement and correlation index between data obtained by the CLSI procedure and the WIDERYST system were 90% and 0.86 (
P
< 0.01), respectively. The system was able to detect amphotericin B-resistant isolates. All
Candida
sp. isolates with resistance in vitro to azole agents were detected as well. The system misclassified some isolates belonging to the slowly growing genera
Dipodascus
and
Pichia
. A total of 2.7% very major errors were detected for fluconazole. The WIDERYST system is an alternative to reference procedures for antifungal susceptibility testing of clinical isolates of yeasts, particularly for
Candida
and
Cryptococcus
species.
Acinetobacter radioresistensas a Silent Source of Carbapenem Resistance forAcinetobacterspp
Authors: Poirel Laurent , Figueiredo Samy , Cattoir Vincent , Carattoli Alessandra , Nordmann Patrice
Published: January 2008

Carbapenem resistance results mostly from the expression of acquired carbapenem-hydrolyzing oxacillinases inAcinetobacter baumannii. TheblaOXA-23oxacillinase gene is increasingly reported worldwide and may represent an emerging threat. Our goal was to identify the progenitor of that carbapenemase gene. A collection of 50Acinetobactersp. strains corresponding to severalAcinetobacterspecies was screened forblaOXA-23-like genes by PCR and hybridization techniques. FiveAcinetobacter radioresistensisolates that were susceptible to carbapenems harbored chromosomally encodedblaOXA-23-like genes. A similar plasmid backbone was identified in severalblaOXA-23-positiveA. baumanniiandA. radioresistensisolates, further strengthening the vectors of exchanges for theseblaOXA-23-like genes. Therefore,A. radioresistens, a commensal bacterial species which is identified on the skin of hospitalized and healthy patients (a property shared withA. baumannii), was identified as the source of theblaOXA-23gene.
Bordetella pertussis
Expresses a Functional Type III Secretion System That Subverts Protective Innate and Adaptive Immune Responses
Authors: Fennelly Neil K. , Sisti Federico , Higgins Sarah C. , Ross Pádraig J. , van der Heide Han , Mooi Frits R. , Boyd Aoife , Mills Kingston H. G.
Published: January 2008

Certain bacteria use a type III secretion system (TTSS) to deliver effector proteins that interfere with cell function into host cells. While transcription of genes encoding TTSS components has been demonstrated, studies to date have failed to identify TTSS effector proteins in
Bordetella pertussis
. Here we present the first evidence of a functionally active TTSS in
B. pertussis
. Three known TTSS effectors, Bsp22, BopN, and BopD, were identified as TTSS substrates in
B. pertussis
12743. We found expression of Bsp22 in a significant proportion of clinical isolates but not in common laboratory-adapted strains of
B. pertussis
. We generated a TTSS mutant of
B. pertussis
12743 and showed that it induced significantly lower respiratory tract colonization in mice than the wild-type bacteria. Respiratory infection of mice with the mutant bacteria induced significantly greater innate proinflammatory cytokine production in the lungs soon after challenge, and this correlated with significantly higher antigen-specific interleukin-17, gamma interferon, and immunoglobulin G responses later in infection. Our findings suggest that the TTSS subverts innate and adaptive immune responses during infection of the lungs and may be a functionally important virulence factor for
B. pertussis
infection of humans.
FIRST PRINCIPLE CALCULATION WITH INTERPOLATING SCALING FUNCTION ON ADAPTIVE GRIDDING
Authors: KUO WANG-CHUANG , WANG JEN-CHUNG
Published: January 2008

A new multi-resolution scheme based on interpolating scaling function (ISF) on adaptive gridding (AG) shows promise in the first principle calculation. It is simpler than the wavelet scheme and fully implements the fast wavelet transformation. Although the scheme is similar to the AG scheme on real space, ISF can represent fields more effectively and needs less grids than the scheme of real space does. This simple and effective method provides an alternative to both real space and wavelet methods in the first principle calculation.
UNCERTAINTY IN THE FLUCTUATIONS OF THE PRICE OF STOCKS
Authors: JAFARI G. R. , SADEGH MOVAHED M. , NOROUZZADEH P. , BAHRAMINASAB A. , SAHIMI MUHAMMAD , GHASEMI F. , RAHIMI TABAR M. REZA
Published: January 2008

We report on a study of the Tehran Price Index (TEPIX) from 2001 to 2006 as an emerging market that has been affected by several political crises during the recent years, and analyze the non-Gaussian probability density function (PDF) of the log returns of the stock prices. We show that while the average of the index did not fall very much over the time period of the study, its day-to-day fluctuations strongly increased due to the crises. Using an approach based on multiplicative processes with a detrending procedure, we study the scale-dependence of the non-Gaussian PDFs, and show that the temporal dependence of their tails indicates a gradual and systematic increase in the probability of the appearance of large increments in the returns on approaching distinct critical time scales over which the TEPIX has exhibited maximum uncertainty.
A DISTRIBUTED COMPUTING APPROACH TO THE SIMULATION OF LIQUID CRYSTAL LATTICE MODELS
Authors: CHICCOLI CESARE , PASINI PAOLO , SEMERIA FRANCO , ZANNONI CLAUDIO
Published: January 2008

We have studied a lattice spin model of nematic liquid crystal-polymer composite films by means of extensive Monte Carlo simulations over a distributed computing network. The Condor processing system installed on the Italian Nuclear Physics Institute computer network was used. The use of several geometries and boundary conditions allowed us to investigate a wide number of different realistic or speculative models. Many of the simulations differ only by a small number of parameters and they can be effectively performed in parallel. The results of the simulations can be analyzed globally when all the computations are completed and then for example, employed to extrapolate phase diagrams or other complex physical quantities. They provide an effective example of wide area distributed computing applications which could be also implemented in future GRID approaches.
NONLINEAR TIME SERIES ANALYSIS IN EPILEPSY
Authors: OSTERHAGE HANNES , LEHNERTZ KLAUS
Published: January 2008

The framework of the theory of nonlinear dynamics provides powerful concepts and algorithms to study complicated dynamics such as brain electrical activity (electroencephalogram, EEG). Although different influencing factors render the use of nonlinear measures in a strict sense problematic, converging evidence from various investigations now indicates that nonlinear EEG analysis provides a means to reliably characterize different states of physiological and pathophysiological brain function. We here focus on applications of nonlinear EEG analysis in epileptology. Epilepsy affects more than 50 million individuals worldwide – approximately 1% of the world's population. The disease is characterized by a recurrent and sudden malfunction of the brain that is termed seizure. Nonlinear EEG analysis techniques allow to reliably identify the seizure generating structure (epileptic focus) in different areas of the brain even during seizure-free intervals, to disentangle complex spatio-temporal interactions between the epileptic focus and other areas of the brain, and to define a specific state predictive of an impending seizure. Nonlinear EEG analysis provides supplementary information about the epileptogenic process in humans, contributes to an improvement of the presurgical evaluation of epilepsy patients, and offers a basis for the development of new therapy concepts for seizure prevention.
COHERENCE RESONANCE IN A FITZHUGH–NAGUMO ELECTRONIC SYSTEM
Authors: BRUGIONI STEFANO , HWANG DONG UK , MEUCCI RICCARDO , BOCCALETTI STEFANO
Published: January 2008

We investigate Coherence Resonance phenomenon in an electronic circuit obeying the FitzHugh–Nagumo dynamics. The phenomenon is induced with a noise source exhibiting different nature. The resonance behavior results are significantly reinforced when experimental parameters are tuned in order to place the stable fixed point closer to the excitability threshold of spiking behavior, as well as when the time scales of the circuit are properly modified.
SYNCHRONIZATION OF HIGHER HARMONICS IN COUPLED ORGAN PIPES
Authors: ABEL M. , BERGWEILER S.
Published: January 2008

We report results on the synchronization of two organ pipes positioned side by side. Special attention is put on the synchronization of the higher harmonics. As possible explanation, classical theory provides the amplitude death as explanation for the reduction to almost silence of two coupled organ pipes. With our measurements we exclude this scenario. The higher harmonics show a behavior in perfect coincidence with synchronization theory. In addition we investigate the dependence on the coupling of two pipes by varying their distance. In the context of synchronization in networks, a new synchronization effect is observed for extended systems with two distributed, slightly different delays.
DRIVING PHASE SYNCHRONOUS PLASMA DISCHARGES WITH SUPERIMPOSED SIGNALS
Authors: DAVIS MATTHEW S. , NUTTER NATHAN G. , ROSA EPAMINONDAS
Published: January 2008

Numerical simulations and experimental measurements performed on a plasma discharge, simultaneously paced with two independent sinusoidal functions, show the plasma moving from one synchronous state to another, back and forth, between the two independent pacers. Different approaches for studying this competition for phase synchronization indicate the relevance of the relative frequency values of the two sinusoidal functions with respect to the predominant frequency characteristic of the unpaced plasma discharge.
NETWORK AS A CHAOTIC DYNAMICAL SYSTEM
Authors: MIYAZAKI SYUJI , NAGASHIMA YASUSHI
Published: January 2008

A directed network such as the WWW can be represented by a transition matrix. Comparing this matrix to a Frobenius–Perron matrix of a chaotic piecewise-linear one-dimensional map whose domain can be divided into Markov subintervals, we are able to relate the network structure itself to chaotic dynamics. Just like various large deviation properties of local expansion rates (finite-time Lyapunov exponents) related to chaotic dynamics, we can also discuss those properties of network structure.
PHASE SYNCHRONIZATION AND COHERENCE ANALYSIS: SENSITIVITY AND SPECIFICITY
Authors: SCHELTER BJÖRN , WINTERHALDER MATTHIAS , TIMMER JENS , KURTHS JÜRGEN
Published: January 2008

In Nonlinear Dynamics synchronization of oscillators is examined. Alternatively for linear stochastic systems, coherence analysis is utilized to detect interdependencies in transfer function systems. In contrast to the latter, oscillators continue oscillating in the absence of interaction between the processes. For transfer function systems the output ceases to exist without an input. Analysis techniques able to differentiate these considerably different classes of dynamics are desired in various applications. We show that conclusions from analysis techniques to the underlying dynamics have to be taken with care due to missing specificity. Moreover, we present an approach towards higher specificity.
ENSEMBLE APPROACH FOR RECOVERING PHASE SYNCHRONIZATION FROM TIME SERIES
Authors: TOKUDA ISAO , KURTHS JÜRGEN , PARLITZ ULRICH
Published: January 2008

An ensemble approach is presented for the reconstruction of a phase synchronization diagram from time series. As an example system, we analyze a forced Colpitts oscillator to show that synchronization diagram reconstructed by a single nonlinear model depends sensitively upon the model parameters, which should be estimated with a considerable amount of care. This dependence can be crucial for a precise recovery of the synchronization phenomena. To overcome this weakness, an ensemble approach is introduced. Two types of techniques, namely, (I) ensemble regression and (II) ensemble classification, are developed to show that they provide much more robust and reliable reconstruction of the synchronization diagram compared to the conventional single modeling approach.
ZERO-CROSS INSTANTANEOUS STATE SETTING FOR CONTROL OF A BIFURCATING H-BRIDGE INVERTER
Authors: AKATSU SATOSHI , TORIKAI HIROYUKI , SAITO TOSHIMICHI
Published: January 2008

This paper studies stabilization of low-period unstable periodic orbits (UPOs) in a simplified model of a current mode H-bridge inverter. The switching of the inverter is controlled by pulse-width modulation signal depending on the sampled inductor current. The inverter can exhibit rich nonlinear phenomena including period doubling bifurcation and chaos. Our control method is realized by instantaneous opening of inductor at a zero-crossing moment of an objective UPO and can stabilize the UPO instantaneously as far as the UPO crosses zero in principle. Typical system operations can be confirmed by numerical experiments.
NUMERICAL STEADY-STATE ANALYSIS OF NONLINEAR ANALOG CIRCUITS DRIVEN BY MULTITONE SIGNALS
Authors: DUMITRIU LUCIA , IORDACHE MIHAI
Published: January 2008

Widely-separated time scales appear in many electronic circuits, making traditional analysis difficult, even impossible, if the circuits are highly nonlinear. This paper presents a new version of the modified nodal method in two time variables for the analysis of the circuit with widely separated time scales. By applying this approach the differential algebraic equations (DAE) describing the nonlinear analog circuits driven by multitone signals are transformed into multitime partial differential equations (MPDEs). In order to solve MPDEs, associated resistive discrete equivalent circuits (companion circuits) for the dynamic circuit elements are used. The boundary conditions are detailed and simulation results are presented.
METHOD TO SOLVE THE NONLINEAR INFINITE HORIZON OPTIMAL CONTROL PROBLEM WITH APPLICATION TO THE TRACK CONTROL OF A MOBILE ROBOT
Authors: HOLZHÜTER THOMAS , KLINKER THOMAS
Published: January 2008

We present a numerical method to solve the infinite time horizon optimal control problem for low dimensional nonlinear systems. Starting from the linear-quadratic approximation close to the origin, the extremal field is efficiently calculated by solving the Euler–Lagrange equations backward in time. The resulting controller is given numerically on an interpolation grid. We use the method to obtain the optimal track controller for a mobile robot. The result is a globally asymptotically stable nonlinear controller, obtained without any specific insight into the system dynamics.
DISCRETE DYNAMICAL SYSTEMS CONSISTING OF SINGLE-ELECTRON CIRCUITS
Authors: KIKOMBO ANDREW KILINGA , OYA TAKAHIDE , ASAI TETSUYA , AMEMIYA YOSHIHITO
Published: January 2008

The single-electron circuit in the nature of discrete dynamical systems because it changes its state discontinuously because of electron tunneling. To confirm this, we designed a sample circuit consisting of two single-electron oscillators coupled with each other through a coupling capacitor. The oscillators produce relaxation oscillation and interact with each other to generate synchronization and entrainment. The operation of the circuit is expressed with a set of discrete difference equations combined with continuous differential equations. Computer simulation shows that the circuit exhibits a variety of periodic oscillations and produces a series of bifurcations as the coupling capacitance increases.
IMPLEMENTATION OF A LABORATORY TOOL FOR STUDYING MIXED-MODE CHAOTIC CIRCUIT
Authors: KILIÇ RECAI , KARAUZ BARIŞ
Published: January 2008

Although many authors have prepared useful papers to illustrate the existence of chaos and to enhance the reader's understanding of chaos by using theoretical, simulation or experimental setups, any chaos-based laboratory work-board has not been designed or implemented for studying chaotic circuits and systems. We designed and implemented a laboratory tool for studying mixed-mode chaotic circuits. In this paper, we will introduce this versatile laboratory tool.
ADAPTIVE PROCEDURE FOR THE PARAMETER ESTIMATION OF A MODEL OF A CO2 CHAOTIC LASER
Authors: MARIÑO I. P. , ZAMBRANO S. , SANJUÁN M. A. F. , SALVADORI F. , MEUCCI R. , ARECCHI F. T.
Published: January 2008

We have proposed an adaptive procedure in order to estimate unknown parameters of a numerical model of a chaotic CO 2 laser, which is observed through a time series that represents the output intensity of the laser. To do that, we consider a coupled system with the same functional form and adjustable parameters. The salient feature of the proposed technique is that accurate parameter estimation and identical synchronization can be jointly achieved by adaptively adjusting the desired parameters of the coupled system.
SOLVABLE THREE-DIMENSIONAL RATIONAL CHAOTIC MAP DEFINED BY JACOBIAN ELLIPTIC FUNCTIONS
Authors: ONO ASUKA , KOHDA TOHRU
Published: January 2008

Cryptanalysis needs a lot of pseudo-random numbers. In particular, a sequence of independent and identically distributed (i.i.d.) binary random variables plays an important role in modern digital communication systems. Sufficient conditions have been recently provided for a class of ergodic maps of an interval onto itself: R1 → R1 and its associated binary function to generate a sequence of i.i.d. random variables. In order to get more i.i.d. binary random vectors, Jacobian elliptic Chebyshev rational map, its derivative and second derivative which define a Jacobian elliptic space curve have been introduced. Using duplication formula gives three-dimensional real-valued sequences on the space curve onto itself: R3 → R3. This also defines three projective onto mappings, represented in the form of rational functions of xn, yn, zn. These maps generate a three-dimensional sequence of i.i.d. random vectors.
SOME ANALYTIC CALCULATIONS OF THE CHARACTERISTIC EXPONENTS
Authors: VAN DER KLOET P. , NEERHOFF F. L. , WANING N. H.
Published: January 2008

As is well known, the variational equations of nonlinear dynamic systems are linear time-varying (LTV) by nature. In the modal solutions for these LTV equations, the earlier introduced dynamic eigenvalues play a key role. They are closely related to the Lyapunov- and Floquet-exponents of the corresponding nonlinear systems.

In this contribution, we present some simple examples for which analytic solutions exist. It is also demonstrated by example how the classical linear time-invariant (LTI) solutions are related to the equilibrium points of the general LTV solutions.
ANALYTICAL DETERMINATION OF INITIAL CONDITIONS LEADING TO FIRING IN NERVE FIBERS
Authors: JACQUIR SABIR , BINCZAK STEPHANE , BILBAULT JEAN-MARIE
Published: January 2008

An analytical solution characterizing initial conditions leading to action potential firing in smooth nerve fibers is determined, using the bistable equation. In the first place, we present a nontrivial stationary solution wave, then, using the perturbative method, we analyze the stability of this stationary wave. We show that it corresponds to a frontier between the initiation of the travelling waves and a decay to the resting state. Eventually, this analytical approach is extended to FitzHugh–Nagumo model.
ROBUST FACE DETECTION FOR MOVING PICTURES UNDER POSE, ROTATION, ILLUMINATION AND OCCLUSION CHANGES
Authors: PHAM-NGOC PHUONG-TRINH , KIM TAE-HO , JO KANG-HYUN
Published: January 2008

Face detection has been a key step in face analysis systems for decades. However, it is still a challenging task due to the variation in image background, view, pose, occlusion, etc. This paper proposes a simple and effective tool to detect human faces in moving pictures under such conditions. An improved approach aiming to reduce impacts of illumination, scale and connection of faces to receive rapidly skin homogeneous regions considered as the most potential face candidates is presented. A hybrid classifier, applied in retrieved face candidates, is based on template matching and appearance-based method providing a robust face detection. This verification achieves advantages of the powerful discrimination of Local Binary Patterns (LBPs) and the high speed detection capability of embedded Hidden Markov Models (eHMMs). Experiments were performed with different image databases and video sequences such as NRC-IIT facial video database, Caltech database, etc. Our system is effective in detecting not only frontal faces but also profile, rotated, occluded and connected ones for real-time application.
VISION-BASED VELOCITY ESTIMATION FOR UNMANNED GROUND VEHICLES
Authors: SONG XIAOJING , SENEVIRATNE LAKMAL D. , ALTHOEFER KASPAR , SONG ZIBIN
Published: January 2008

A novel vision-based velocity estimation technique is presented in this paper. A monocular camera rigidly attached to an unmanned ground vehicle (UGV) is used to capture image sequences of the terrain surface and compute the image velocities using an optical flow method. Combining with the proposed camera model, the velocity of the UGV can be directly estimated. This velocity estimation method is validated over coarse sand, fine sand and mixture of coarse sand and gravel separately. Estimated velocities are compared to measured velocities from highly accurate optical encoders, showing the maximum error is less than 1.5%. The effect of feature window size and the distance between the camera projection center and the terrain surface on the velocity estimation is investigated. Random white noise is added to test the robustness of the algorithm and the results are encouraging. The proposed velocity estimation method has many promising potential applications.
STATISTICAL VECTORS OF ACOUSTIC FEATURES FOR THE AUTOMATIC CLASSIFICATION OF INFANT CRY
Authors: AMARO-CAMARGO ERIKA , REYES-GARCÍA CARLOS A. , ARCH-TIRADO EMILIO , MANDUJANO-VALDÉS MARIO
Published: January 2008

With the objective of helping diagnose some pathologies in recently born babies, we present the experiments and results obtained in the classification of infant cry using a variety of single classifiers, and ensembles from the combination of them. Three kinds of cry were classified: normal, hypoacoustic (deaf), and asphyxia. The feature vectors were formed by the extraction of Mel Frequency Cepstral Coefficients (MFCC). The vectors were then processed and reduced through the application of five statistics operations, namely: minimum, maximum, average, standard deviation and variance. LDA, a data reduction technique is implemented with the purpose of comparing the results of our proposed method. Four supervised machine learning methods including Support Vector Machines, Neural Networks, J48, Random Forest and Naive Bayes are used. The ensembles tested were combinations of these under different approaches like Majority Vote, Staking, Bagging and Boosting.
PRIORITY-BASED CONGESTION CONTROL IN MULTI-PATH WIRELESS SENSOR NETWORKS
Authors: LI ZHIBIN , LIU PETER X.
Published: January 2008

In wireless sensor networks (WSNs), congestion will cause packet loss which in turn wastes energy and reduces the lifetime of WSNs, and therefore congestion in WSNs must be controlled or avoided in either a fairness or a weighted-fairness way. It is very important to achieve weighted fairness for many WSN applications, and this problem becomes more complicated when the data flow is forwarded to multiple routing paths. In this paper we propose a joint priority-based algorithm (JPA) that eliminates congestion and achieves weighted fairness in multi-path and multi-hop wireless sensor networks. Weighted fairness is achieved when the source node with high source priority (SP) sends more packets than the one with low SP in response to congestion. JPA defines a new variable, joint priority (JP) for each node and link, as the expected value of SP. The JP of a node or link indicates the arithmetic means of SP of source nodes whose data flow passes through that particular node or link, and the sending rate of each node is adjusted based on the value of JP when congestion occurs. The JPA algorithm is simulated and evaluated in different scenarios.