bluuebunny/crossref_metadata_2025 huggingface dataset:
Signaling and apoptosis differences between severe hypoxia and desferoxamine treatment of human epithelial cells
Authors: Box Adrian Harold , Yuen Carol , Ponjevic Dragana , Fick Gordon H. , Demetrick Douglas James
Published: October 2008

The mechanisms by which cells undergo proliferation arrest or cell death in response to hypoxia are still not completely understood. Originally, we showed that HeLa and Hep3B carcinoma cells undergo different proliferation responses in hypoxia. We now show that these 2 cell lines also have different cell death responses to severe hypoxia, with HeLa showing both cell cycle arrest and apoptosis (as early as 12 h after hypoxia treatment), and Hep3B showing resistance to both. Hypoxia-induced apoptosis in Hela was associated with decreases of both phospho-S473- and -T308-AKT and loss of AKT function, whereas Hep3B cells were resistant to hypoxia-induced apoptosis and did not lose phospho-AKT or AKT function. We then decided to test if our observations were confirmed using a hypoxia mimic, desferoxamine. Desferoxamine treatment yielded cell cycle arrest in HeLa and moderate arrest in Hep3B but, surprisingly, did not induce notable apoptosis of either cell line with up to 24 h of treatment. Hypoxia-treated normal human mammary epithelial cells also showed hypoxia-induced apoptosis. Interestingly, in these cell lines, there was a complete correlation between loss of phospho-AKT and (or) total AKT, and susceptibility to hypoxia-induced apoptosis. Our data suggests a model in which regulated loss of active AKT at a precise time point in hypoxia may be associated with apoptosis in susceptible cells.
Identification of a DNA processing complex fromDeinococcus radiodurans
Authors: Kota Swathi , Misra Hari S.
Published: October 2008

An efficient DNA strand break repair contributes to the radioresistance of Deinococcus radiodurans , which harbors the DNA repair pathways nearly identical to Escherichia coli . The molecular mechanisms of these proteins functioning in 2 diverse classes of bacteria seem to be different. The macromolecular interactions and formation of multiprotein complexes in vivo have gained significant importance in explaining the mechanism of the complex cellular processes. Here, we report the identification of a novel DNA metabolic protein complex from D. radiodurans. A similar complex has, however, not been found in E. coli. Mass spectrometric analysis showed the presence of a few known DNA repair proteins, molecular chaperones, and a large number of uncharacterized proteins from D. radiodurans R1. Biochemical and immunoblotting results indicated the presence of the protein promoting DNA repair A, DNA polymerase, Mg2+, and (or) Mn2+-dependent 5′→3′ exonuclease activity along with protein kinase activity and phosphoproteins. DNA ligase activity was completely dependent upon the ATP requirement, as no ligase activity was seen in the presence of NAD as a cofactor. These results suggest the molecular interactions of the known DNA repair proteins with uncharacterized proteins in the macromolecular complex and the regulation of DNA degradation with the involvement of ATP and protein kinase functions.
Kinetics of human peptidylarginine deiminase 2 (hPAD2) — Reduction of Ca2+ dependence by phospholipids and assessment of proposed inhibition by paclitaxel side chains
Authors: Musse Abdiwahab A. , Polverini Eugenia , Raijmakers Reinout , Harauz George
Published: October 2008

Multiple sclerosis is a complex human neurodegenerative disease, characterized by the active destruction of the insulating myelin sheath around the axons in the central nervous system. The physical deterioration of myelin is mediated by hyperdeimination of myelin basic and other proteins, catalysed by the Ca2+-dependent enzyme peptidylarginine deiminase 2 (PAD2). Thus, inhibition of PAD2 may be of value in treatment of this disease. Here, we have first characterized the in vitro kinetic properties of the human peptidylarginine deiminase isoform 2 (hPAD2). Phosphatidylserine and phosphatidylcholine reduced its Ca2+ dependence by almost twofold. Second, we have explored the putative inhibitory action of the methyl ester side chain of paclitaxel (TSME), which shares structural features with a synthetic PAD substrate, viz., the benzoyl-l-arginine ethyl ester (BAEE). Using the known crystallographic structure of the homologous enzyme hPAD4 and in silico molecular docking, we have shown that TSME interacted strongly with the catalytic site, albeit with a 100-fold lower affinity than BAEE. Despite paclitaxel having previously been shown to inhibit hPAD2 in vitro, the side chain of paclitaxel alone did not inhibit this enzyme’s activity.
Strain-specific alteration of zebrafish feeding behavior in response to aversive stimuli
Authors: Oswald M. , Robison B. D.
Published: October 2008

Behavioral management of risk, in which organisms must balance the requirements of obtaining food resources with the risk of predation, has been of considerable interest to ethologists for many years. Although numerous experiments have shown that animals alter their foraging behavior depending on the levels of perceived risk and demand for nutrients, few have considered the role of genetic variation in the trade-off between these variables. We performed a study of four zebrafish ( Danio rerio (Hamilton, 1822)) strains to test for genetic variation in foraging behavior and whether this variation affected their response to both aversive stimuli and nutrient restriction. Zebrafish strains differed significantly in their latency to begin foraging from the surface of the water under standard laboratory conditions. Fish fed sooner when nutrients were restricted, although this was only significant in the absence of aversive stimuli. Aversive stimuli caused fish to delay feeding in a strain-specific manner. Strains varied in food intake and specific growth rate, and feeding latency was significantly correlated with food intake. Our results indicate significant genetic variation in foraging behavior and the perception of risk in zebrafish, with a pattern of strain variation consistent with behavioral adaptation to captivity.
Temporal patterns of tissue glycogen, glucose, and glycogen phosphorylase activity prior to hibernation in freeze-tolerant chorus frogs, Pseudacris triseriata
Authors: Dinsmore Steve C. , Swanson David L.
Published: October 2008

Freezing survival may differ among winters in chorus frogs ( Pseudacris triseriata (Wied-Neuwied, 1838)), and low freezing survival is associated with low hepatic glycogen stores. The pattern of prehibernation liver glycogen accumulation in chorus frogs is unknown. Frogs might accumulate hepatic glycogen stores until a threshold level sufficient for winter survival is attained, after which frogs enter hibernation (critical threshold hypothesis). According to this model, frogs active late in the season should only be those with low hepatic glycogen stores. Alternatively, hepatic glycogen levels might continue to increase throughout the fall as long as frogs remain active (continuous increase hypothesis). We tested these hypotheses by measuring liver and leg muscle glycogen, glucose, and glycogen phosphorylase activities in chorus frogs throughout the fall prehibernation period in southeastern South Dakota. Hepatic glycogen levels were significantly related to date and increased throughout the fall period, consistent with the continuous increase hypothesis. This suggests that hepatic glycogen levels do not serve as a cue for entrance into hibernation. Liver phosphorylase activity did not vary significantly with progression of the fall season and activity was lower than in winter, suggesting that the winter increment of phosphorylase activity requires some stimulus during hibernation (e.g., low temperatures).
Antibodies against Salmonella is associated with reduced reproductive success in female alpine chamois (Rupicapra rupicapra)
Authors: Pioz Maryline , Loison Anne , Gibert Philippe , Jullien Jean-Michel , Artois Marc , Gilot-Fromont Emmanuelle
Published: October 2008

Microbial infections that affect reproduction are poorly studied in wildlife because reproductive disorders usually go unnoticed. However, such infections are a major concern in domestic ungulates, which raises the question of their influence on reproductive success and population dynamics of wild ungulates. Three bacterial abortive infections are frequent in domestic ruminants: salmonellosis caused by Salmonella enterica serovar Abortusovis, enzootic abortion caused by Chlamydophila abortus , and Q fever caused by Coxiella burnetii . They induce abortions and neonatal mortality in sheep ( Ovis aries L., 1758), goat ( Capra hircus L., 1758), and cattle ( Bos taurus L., 1758). However, little information is known about these bacteria in wild ungulates, particularly in mountain ungulates that may share alpine pastures with infected domestic ruminants. We investigated the relationship between female serological status against Salmonella, Chlamydophila, and Coxiella and her reproductive success. From 1986 to 2003, the reproductive and serological statuses of 125 female chamois ( Rupicapra rupicapra (L., 1758)) aged 2–10 years were available. Reproductive success was the lowest for 2-year-old females and for females born at the highest density. Moreover, we showed for the first time in a wild ungulate population that females with high titer in antibodies against Salmonella experienced a decrease in their reproductive success. Titers in antibodies against Chlamydophila and Coxiella were not related to the reproductive success of female chamois.
Amphibian predation on larval mosquitoes
Authors: DuRant Sarah E. , Hopkins William A.
Published: October 2008

Mosquitoes ( Culex pipiens L., 1758) are important vectors for diseases of both wildlife and humans. Understanding how natural factors influence mosquito abundance may provide insights into the ecology of various diseases, as well as solutions to controlling disease vectors. One of the natural factors regulating mosquito distributions and population sizes is predation. A poorly understood source of natural mosquito predation is amphibians. We determined the mosquito consumption capability of two amphibians, adult Red-spotted Newts ( Notophthalmus viridescens viridescens (Rafinesque, 1820)) and larval Mole Salamanders ( Ambystoma talpoideum (Holbrook, 1838)). We also compared mosquito consumption of eastern mosquitofish ( Gambusia holbrooki Girard, 1859), a known predator of mosquitoes, and A. talpoideum. Both salamander species were capable of consuming large numbers of mosquito larvae per day (least-square means ± 1 SE = 439 ± 20 and 316 ± 35 mosquitoes/day consumed by A. talpoideum and N. v. viridescens, respectively). In A. talpoideum, mosquito consumption scaled with body size, with the largest individual (4.4 g) ingesting 902 mosquitoes in 1 day. Gambusia holbrooki consumed 3.5× more mosquitoes during a 24 h feeding trial than similar-sized A. talpoideum. Our findings suggest that amphibians could have a substantial impact on mosquito larvae abundance, especially considering that amphibians can reach densities of up to 500 000 individuals/ha. Furthermore, we hypothesize that introduction of G. holbrooki could reduce abundances of native mosquito predators (e.g., salamanders) indirectly, through competition for invertebrate prey.
Photoperiod alters pain responsiveness via changes in pelage characteristics
Authors: Weil Zachary M. , Gatien Hotchkiss Michelle , Nelson Randy J.
Published: October 2008

Small mammals use day length to adjust morphology and physiology to anticipate seasonal changes in environmental conditions. The canonical photoperiod-mediated annual adaptation is seasonal breeding. However, increasing evidence suggests that day-length information can induce plasticity in the nervous system, and thus provoke behavioral plasticity that can aid in winter survival. We hypothesized that low temperatures and reduced food availability in the winter would necessitate the evolution of increased pain tolerance mediated by short day lengths. Siberian hamsters ( Phodopus sungorus (Pallas, 1773)) housed in short days regressed their reproductive tracts and molted to winter pelage. Short-day hamsters also displayed elevated latencies of nociceptive responses in the hot-plate test, suggesting reduced pain responsivity. Prior to assessing potential neuronal or neuroendocrine mediators of altered pain responses, however, we investigated the possibility that changes in fur characteristics mediated photoperiod differences in pain responsivity. Removal of fur with a depilatory cream eliminated photoperiod differences in pain responsivity. Taken together, these data indicate that day length regulates thermal pain responses via changes in fur properties; also, changes in pelage properties have both thermoregulatory and thermal insulatory properties.
Ecological factors influencing the spatial pattern of Canada lynx relative to its southern range edge in Alberta, Canada
Authors: Bayne Erin M. , Boutin Stan , Moses Richard A.
Published: October 2008

We examined the spatial pattern of Canada lynx ( Lynx canadensis Kerr, 1792) relative to its southern range edge at the boreal plains – prairie ecotone in Alberta, Canada. Relative to the original distribution of boreal forest in our study area, lynx range seems to have contracted up to 22%. In 100 km2 sampling areas, lynx occupancy rate increased 1.93 times every 100 km farther (north) from the range edge that we sampled. An information–theoretic approach was used to evaluate 31 models to see which environmental factors were the best predictors of this spatial pattern. Lynx were strongly correlated with track counts of their primary prey, the snowshoe hare ( Lepus americanus Erxleben, 1777), but this did not explain the observed increase in occupancy farther north. Rather, lynx occupancy was lower in areas with higher road densities and this effect was magnified in areas where coyote ( Canis latrans Say, 1823) activity was highest. The inclusion of these effects rendered the south–north pattern no longer significant. The rapid pace of road building and associated development in Alberta’s boreal forest seems to be reducing habitat quality for Canada lynx, particularly at the southern edge of its range. This may be leading to range contractions for lynx in Alberta, much like has happened elsewhere in North America.
Plasticity in sexual size dimorphism and Rensch’s rule in Mediterranean blennies (Blenniidae)
Authors: Lengkeek W. , Didderen K. , Côté I. M. , van der Zee E. M. , Snoek R. C. , Reynolds J. D.
Published: October 2008

Comparative analyses of sexual size dimorphism (SSD) across species have led to the discovery of Rensch’s rule. This rule states that SSD increases with body size when males are the largest sex, but decreases with increasing size when females are larger. Within-species comparisons of SSD in fish are rare, yet these may be a valuable tool to investigate evolutionary patterns on a fine scale. This study compares SSD among closely related populations of three species of Mediterranean blennies (Blenniidae): Microlipophrys canevae (Vinciguerra, 1880), Parablennius incognitus (Bath 1968), and Aidablennius sphynx (Valenciennes, 1836). SSD varied more among populations than among species and Rensch’s rule was confirmed within two species. It is not likely that the variation among populations in SSD mirrors genetic variation, as many of the populations were in close proximity of one another, with a high potential for genetic exchange. This study complements larger scale analyses of other taxa and demonstrates the fine scale on which evolutionary processes responsible for Rensch’s rule may be operating.
BIFURCATION AND FRACTAL OF THE COUPLED LOGISTIC MAP
Authors: WANG XINGYUAN , LUO CHAO
Published: October 2008

The nature of the fixed points of the coupled Logistic map is researched, and the boundary equation of the first bifurcation of the coupled Logistic map in the parameter space is given out. Using the quantitative criterion and rule of system chaos, i.e., phase graph, bifurcation graph, power spectra, the computation of the fractal dimension, and the Lyapunov exponent, the paper reveals the general characteristics of the coupled Logistic map transforming from regularity to chaos, the following conclusions are shown: (1) chaotic patterns of the coupled Logistic map may emerge out of double-periodic bifurcation and Hopf bifurcation, respectively; (2) during the process of double-period bifurcation, the system exhibits self-similarity and scale transform invariability in both the parameter space and the phase space. From the research of the attraction basin and Mandelbrot–Julia set of the coupled Logistic map, the following conclusions are indicated: (1) the boundary between periodic and quasiperiodic regions is fractal, and that indicates the impossibility to predict the moving result of the points in the phase plane; (2) the structures of the Mandelbrot–Julia sets are determined by the control parameters, and their boundaries have the fractal characteristic.
REALIZABLE QUANTUM BROADCASTING MULTI-SIGNATURE SCHEME
Authors: WEN XIAOJUN , LIU YUN , ZHOU NANRUN
Published: October 2008

Two quantum broadcasting multi-signature schemes are presented: one is used to sign classical digital messages and the other to sign quantum messages. The quantum one-way function is used to realize signature and verification in the digital multi-signature scheme, while quantum teleportation is used in the quantum multi-signature scheme. The proposed schemes support infinite amounts of signatories and provide a novel and experimentally feasible method to construct multi-signature quantum signature systems within current technology.
NUMERICAL SIMULATION OF FLOW WITH LARGE-AMPLITUDE OSCILLATION OF SOLID BOUNDARIES BY PENALTY FINITE ELEMENT FORMULATIONS
Authors: WANG W. Q. , ZHANG L. X. , YAN Y.
Published: October 2008

A penalty finite element method for the incompressible viscous Navier–Stokes equations is incorporated in an arbitrary Lagrangian–Eulerian formulation to model a flow in the fluid–structure interaction (FSI) with moving meshes. The formulation is derived based on the classical Ritz–Galerkin framework for forming a coupled formulation on the finite element method. In such a way, the pressure-constrained equation is incorporated in the momentum equations of the system with FSI. An improving spring smooth and remeshing technique is used to successively accommodate fluid meshes as the oscillation of a solid boundary in simulation. To demonstrate the performance of the proposed approach, the simulations of the flow with an elastic beam in water, that is oscillating in a large amplitude are presented. The simulations show that the methodology suggested in this paper has a good numerical stability and reliability, and the results are highly agreeable with the published reference.
THEORIES OF MULTI-PULSE GLOBAL BIFURCATIONS FOR HIGH-DIMENSIONAL SYSTEMS AND APPLICATION TO CANTILEVER BEAM
Authors: ZHANG W. , YAO M. H.
Published: October 2008

The aim of this survey paper is to illustrate the perspectives on the theories of the single- and multi-pulse global bifurcations and chaotic dynamics of high-dimensional nonlinear systems and applications to several engineering problems in the past two decades. Two main methods for studying the Shilnikov type multi-pulse homoclinic and heteroclinic orbits in high-dimensional nonlinear systems, which are the energy-phase method and generalized Melnikov method, are briefly demonstrated in the theoretical frame. In addition, the theory of normal form and an improved adjoint operator method for high-dimensional nonlinear systems is also applied to describe a reducing procedure to high-dimensional nonlinear systems. The aforementioned methods are utilized to investigate the Shilnikov type multi-pulse homoclinic bifurcations and chaotic dynamics for the nonlinear nonplanar oscillations of the cantilever beam subjected to a harmonic axial excitation and two transverse excitations at the free end. How to employ these methods to analyze the Shilnikov type multi-pulse homoclinic and heteroclinic bifurcations and chaotic dynamics of high-dimensional nonlinear systems in engineering applications is demonstrated through this example.
METHODS OF THE QUALITATIVE THEORY FOR THE HINDMARSH–ROSE MODEL: A CASE STUDY – A TUTORIAL
Authors: SHILNIKOV ANDREY , KOLOMIETS MARINA
Published: October 2008

Homoclinic bifurcations of both equilibria and periodic orbits are argued to be critical for understanding the dynamics of the Hindmarsh–Rose model in particular, as well as of some square-wave bursting models of neurons of the Hodgkin–Huxley type. They explain very well various transitions between the tonic spiking and bursting oscillations in the model. We present the approach that allows for constructing Poincaré return mapping via the averaging technique. We show that a modified model can exhibit the blue sky bifurcation, as well as, a bistability of the coexisting tonic spiking and bursting activities. A new technique for localizing a slow motion manifold and periodic orbits on it is also presented.
SYNTHESIS OF PIECEWISE-LINEAR CHAOTIC MAPS: INVARIANT DENSITIES, AUTOCORRELATIONS, AND SWITCHING
Authors: ROGERS ALAN , SHORTEN ROBERT , HEFFERNAN DANIEL M. , NAUGHTON DAVID
Published: October 2008

In this paper, we give a review of the Inverse Frobenius–Perron problem (IFPP): how to create chaotic maps with desired invariant densities. After describing some existing methods for solving the IFPP, we present a new and simple matrix method of doing this. We show how the invariant density and the autocorrelation properties of the maps can be controlled independently. We also give some fundamental results on switching between a number of different chaotic maps and the effect this has on the overall invariant density of the system. The invariant density of the switched system can be controlled by varying the probabilities of choosing each individual map. Finally, we present an interesting application of the matrix method to image generation, by synthesizing a two-dimensional map, which when iterated, generates a well-known image.
COMPUTATION AND VISUALIZATION OF BIFURCATION SURFACES
Authors: STIEFS DIRK , GROSS THILO , STEUER RALF , FEUDEL ULRIKE
Published: October 2008

The localization of critical parameter sets called bifurcations is often a central task of the analysis of a nonlinear dynamical system. Bifurcations of codimension 1 that can be directly observed in nature and experiments form surfaces in three-dimensional parameter spaces. In this paper, we propose an algorithm that combines adaptive triangulation with the theory of complex systems to compute and visualize such bifurcation surfaces in a very efficient way. The visualization can enhance the qualitative understanding of a system. Moreover, it can help to quickly locate more complex bifurcation situations corresponding to bifurcations of higher codimension at the intersections of bifurcation surfaces. Together with the approach of generalized models the proposed algorithm enables us to gain extensive insights in the local and global dynamics not only in one special system but in whole classes of systems. To illustrate this ability we analyze three examples from different fields of science.
BIFURCATIONS OF THE GLOBAL STABLE SET OF A PLANAR ENDOMORPHISM NEAR A CUSP SINGULARITY
Authors: HOBBS C. A. , OSINGA H. M.
Published: October 2008

The dynamics of a system defined by an endomorphism is essentially different from that of a system defined by a diffeomorphism due to interaction of invariant objects with the so-called critical locus. A planar endomorphism typically folds the phase space along curves J0 where the Jacobian of the map is singular. The critical locus, denoted J1, is the image of J0. It is often only piecewise smooth due to the presence of isolated cusp points that are persistent under perturbation. We investigate what happens when the stable set Ws of a fixed point or periodic orbit interacts with J1 near such a cusp point C1. Our approach is in the spirit of bifurcation theory, and we classify the different unfoldings of the codimension-two singularity where the curve Ws is tangent to J1 exactly at C1. The analysis uses a local normal-form setup that identifies the possible local phase portraits. These local phase portraits give rise to different global manifestations of the behavior as organized by five different global bifurcation diagrams.
BIFURCATIONS, AND TEMPORAL AND SPATIAL PATTERNS OF A MODIFIED LOTKA–VOLTERRA MODEL
Authors: MCGEHEE EDWARD A. , SCHUTT NOEL , VASQUEZ DESIDERIO A. , PEACOCK-LÓPEZ ENRIQUE
Published: October 2008

Bazykin proposed a Lotka–Volterra-type ecological model that accounts for simplified territoriality, which neither depends on territory size nor on food availability. In this study, we describe the global dynamics of the Bazykin model using analytical and numerical methods. We specifically focus on the effects of mutual predator interference and the prey carrying capacity since the variability of each could have especially dramatic ecological repercussions. The model displays a broad array of complex dynamics in space and time; for instance, we find the coexistence of a limit cycle and a steady state, and bistability of steady states. We also characterize super- and subcritical Poincaré–Andronov–Hopf bifurcations and a Bogdanov–Takens bifurcation. To illustrate the system's ability to naturally shift from stable to unstable dynamics, we construct bursting solutions, which depend on the slow dynamics of the carrying capacity. We also consider the stabilizing effect of the intraspecies interaction parameter, without which the system only shows either a stable steady state or oscillatory solutions with large amplitudes. We argue that this large amplitude behavior is the source of chaotic behavior reported in systems that use the MacArthur–Rosenzweig model to describe food-chain dynamics. Finally, we find the sufficient conditions in parameter space for Turing patterns and obtain the so-called "back-eye" pattern and localized structures.
EVOLUTIONARY METHODS FOR THE APPROXIMATION OF THE STABILITY DOMAIN AND FREQUENCY OPTIMIZATION OF CONSERVATIVE MAPS
Authors: PETALAS Y. G. , ANTONOPOULOS C. G. , BOUNTIS T. C. , VRAHATIS M. N.
Published: October 2008

Two methodologies are presented for the numerical approximation of the "domain of stability" of nonlinear conservative maps: (a) the Evolutionary Estimation of the Domain of Stability (EEDS) and (b) the Evolutionary Frequency Optimization (EFO), optimizing certain frequency parameters of these maps so that the domain of stability encompasses the maximum possible "volume" of bounded motion, known in the accelerator literature as the dynamic aperture. The central components of the proposed approaches are: The Differential Evolution algorithm (DE) based on concepts of Computational Intelligence and the method of the Smaller ALignment Index (SALI) used for the determination of chaotic dynamics. Initially, we give a brief description of the two methodologies and then demonstrate their usefulness by applying them to some well-known examples of 2D and 4D Hénon maps. The proposed methodologies can be easily applied to "volume" preserving maps which are not necessarily symplectic as well as to continuous dynamical systems (flows) and can also be generalized to treat conservative dynamical systems of any dimension.
SYMBOLIC DYNAMICS GENERATED BY A COMBINATION OF GRAPHS
Authors: BASIOS VASILEIOS , FORTI GIAN-LUIGI , NICOLIS GREGOIRE
Published: October 2008

In this paper we investigate the growth rate of the number of all possible paths in graphs with respect to their length in an exact analytical way. Apart from the typical rates of growth, i.e. exponential or polynomial, we identify conditions for a stretched exponential type of growth. This is made possible by combining two or more graphs over the same alphabet, in order to obtain a discrete dynamical system generated by a triangular map, which can also be interpreted as a discrete nonautonomous system. Since the vertices and the edges of a graph are usually used to depict the states and transitions between states of a discrete dynamical system, the combination of two (or more) graphs can be interpreted as the driving, or perturbation, of one system by another.
PULSE DYNAMICS IN COUPLED EXCITABLE FIBERS: SOLITON-LIKE COLLISION, PHASE LOCKING, AND RECOMBINATION
Authors: SUETANI HIROMICHI , YANAGITA TATSUO , AIHARA KAZUYUKI
Published: October 2008

We study the dynamics of a reaction–diffusion system composed of two mutually coupled excitable fibers. We focus on the situation in which dynamical properties of the two fibers are not identical because of the parameter difference between the fibers. Using the spatially one-dimensional FitzHugh–Nagumo equations as a model of a single excitable fiber, we show that the system exhibits a rich variety of dynamical behavior, including soliton-like collision between two pulses and recombination of a solitary pulse and synchronized pulses.
A GENERALIZED VERSION OF THE MCMULLEN DOMAIN
Authors: BLANCHARD PAUL , DEVANEY ROBERT L. , GARIJO ANTONIO , RUSSELL ELIZABETH D.
Published: October 2008

We study the family of complex maps given by Fλ(z) = zn + λ/zn + c where n ≥ 3 is an integer, λ is an arbitrarily small complex parameter, and c is chosen to be the center of a hyperbolic component of the corresponding Multibrot set. We focus on the structure of the Julia set for a map of this form generalizing a result of McMullen. We prove that it consists of a countable collection of Cantor sets of closed curves and an uncountable number of point components.
UNIVERSAL COMPUTATION WITH LIMITED RESOURCES: BELOUSOV–ZHABOTINSKY AND PHYSARUM COMPUTERS
Authors: ADAMATZKY ANDREW , DE LACY COSTELLO BEN , SHIRAKAWA TOMOHIRO
Published: October 2008

Using the examples of an excitable chemical system (the Belousov–Zhabotinsky medium) and plasmodium of Physarum polycephalum we show that universal computation in a geometrically unconstrained medium is only possible when resources (excitability or concentration of nutrients) are limited. In situations of limited resources the systems studied develop traveling localizations. These localizations are the elementary units of dynamical logical circuits in collision-based computing architectures.
COMPUTER ASSISTED VERIFICATION OF CHAOS IN THE SMOOTH CHUA'S EQUATION
Authors: YUAN QUAN , YANG XIAO-SONG
Published: October 2008

In this paper, chaos in the smooth Chua's equation is revisited. To confirm the chaotic behavior in the smooth Chua's equation demonstrated in numerical studies, we resort to Poincaré section and Poincaré map technique and present a computer assisted verification of existence of horseshoe chaos by virtue of topological horseshoes theory.
STABILITY OF THE CONTROLLED SYNCHRONIZATION MANIFOLD IN A RING OF MUTUALLY COUPLED CHAOTIC SYSTEMS
Authors: YAMAPI R. , AZIZ-ALAOUI M. A.
Published: October 2008

The active control of the unstable synchronization manifold in a shift-invariant ring of N mutually coupled chaotic oscillators is investigated. After deriving the bifurcation structures and chaotic states in the single oscillator, we find the regime of coupling parameters leading to stable and unstable synchronization phenomena in the ring, using the Master stability function approach with the transverse Lyapunov exponents. The active control technique is applied on the mutually coupled chaotic systems to suppress unstable synchronization states. We derive the range of control gain parameters which leads to a successful control and the stability of the control design. The effects of the amplitude of the parametric perturbations on the stability boundaries of the controlled unstable synchronization process are also studied.
AN ADAPTIVE OBSERVER DESIGN FOR AUTO-SYNCHRONIZATION OF LORENZ SYSTEM
Authors: LIU YING , TANG WALLACE , KOCAREV LJUPCO
Published: October 2008

Synchronization of chaotic systems with unknown parameters, or namely auto-synchronization, has aroused a lot of interest in the past few years. In this paper, we are interested in solving one of the critical cases in Lorenz system. Based on the past researches, it was concluded that the auto-synchronization of Lorenz system was inachievable if the unknown parameters resided in all of its three dynamical equations while only the first state was measurable. However, as demonstrated in this paper, this problem can be resolved by an adaptive observer following simple design rules. The design is justified with the conditional Lyapunov exponents, and its effectiveness is clearly illustrated in simulations.
OPTIMAL ATTRACTORS AND SWITCHED KANBAN CONTROL IN DISCRETE STRANGE BILLIARDS
Authors: RUNKLER THOMAS A.
Published: October 2008

Switched buffer systems are discretized switched flow systems. They are discrete, but can be handled with the same mathematical framework as hybrid systems. In particular, we show that switched buffer systems form discrete strange billiards. For any initialization, discrete strange billiards lead to a finite periodic attractor. The periods and the buffer switching rates are the most important performance measures for the practical use of switched buffer systems. Both measures depend on the sum of objects in the buffers. For each object sum multiple suboptimal attractors may exist. Onto which attractor the system converges depends on the initial buffer levels. We propose a switched Kanban control algorithm that forces the system onto the attractor with minimum buffer switching rate independently of the initialization of the buffer levels. This algorithm needs to perform only one single additional buffer switching operation. Also Heijunka control of switched buffer systems is considered in the framework of strange billiards. We show that Heijunka forms equilateral triangles in the state space. Heijunka is able to yield low buffer switching rates, but only if the buffer levels are optimally initialized. For suboptimal buffer level initializations very high (bad) buffer switching rates can be achieved. In an illustrative example, our proposed switched Kanban control algorithm outperforms conventional Kanban control by about 29% and Heijunka control by about 5%.
BRANCHED MANIFOLDS, KNOTTED SURFACES AND DYNAMICAL SYSTEMS
Authors: CHEN W. , BANKS S. P.
Published: October 2008

The main result of this paper is a proof of existence of a nontrivial knot on any embedded template, that was left as an open question to prove in [Ghrist et al., 1997] without using the Bennequin's inequality [Ghrist et al., 1997]. This result in the branched two-manifold case, which we prove by a sequence of lemmas showing our simple template (or ones with twists) containing nontrivial knots is (are) contained in every template as a subtemplate, enables us to generalize it later in this paper to certain forms of three-templates in four-dimensional dynamical systems by simply using the technique of "spinning" the knots in the lower dimensional templates to obtain the spun knotted surfaces.
THE EFFECT OF MEMORY IN CELLULAR AUTOMATA ONSCALE-FREENETWORKS: THE $\overline{K}=4$ CASE
Authors: ALONSO-SANZ RAMÓN , CÁRDENAS JUAN PABLO
Published: October 2008

In standard cellular automata the new state of a cell depends on the neighborhood configuration solely at the preceding time step. This study analyzes the effect of implementing memory in cells of cellular automata on networks with scale-free topology. As a rule, embedding memory in cells induces a notable depletion in the cell change rate, but it is not so effective in controlling the spread of damage.
A COMPARATIVE STUDY OF FINITE VOLUME AND FINITE ELEMENT ON SOME TRANSCRITICAL FREE SURFACE FLOW PROBLEMS
Authors: BOUSHABA FARID , CHAABELASRI ELMILOUD , SALHI NAJIM , ELMAHI IMAD , BENKHALDOUN FAYSSAL , BORTHWICK ALISTAIR G. L.
Published: October 2008

This paper presents details of finite volume and finite element numerical models based on unstructured triangular meshes that are used to solve the two-dimensional nonlinear shallow water equations (SWEs). The finite volume scheme uses Roe's approximate Riemann solver to evaluate the convection terms. Second order accuracy is achieved by means of the MUSCL approach with MinMod and VanAlbada limiters. The finite element model utilizes the Lax–Wendroff two-step scheme, which is second-order in space and time. The models are validated and their relative performance compared for several benchmark problems, including a hydraulic jump, and flows in converging and converging–diverging channels.
A COMPARATIVE STUDY OF PARALLELIZATION STRATEGIES FOR FRACTAL IMAGE COMPRESSION ON A CLUSTER OF WORKSTATIONS
Authors: QURESHI KALIM , HUSSAIN SYED SAJID
Published: October 2008

In this paper we implement and compare the performance of the Message Passing Interface (MPI) static master-worker and three strategies of MPI task farm implementations for fractal image compression on a Beowulf cluster of workstations, namely Local Predecimation with Range Index Communication (LPRI), Global Predecimation with Range Communication (GPR) and No Predecimation with Range Index Communication (NPRI). Our results show that the MPI task farm implementations balance the load effectively among workers as compared to the MPI static master-worker implementation. The task farm strategies are compared by measuring their speedup and worker idle time cost.
THE ACCURACY OF LEAST-SQUARES APPROXIMATION ON HIGHLY STRETCHED MESHES
Authors: PETROVSKAYA N. B.
Published: October 2008

The least-squares (LS) method is often used in computational aerodynamics to reconstruct a given function at certain points of a computational grid. In this paper we discuss the accuracy of the LS approximation on highly stretched meshes that are inherent in computational aerodynamics. A new definition of a distant point in a LS reconstruction stencil will be given in order to explain the poor performance of the method in a boundary layer region. Namely, based on the concept of outliers widely used in the statistics, we demonstrate that the definition of a distant point in a LS reconstruction stencil should take into account the solution properties and it cannot rely upon the geometric shape of the stencil only. Our approach is illustrated with numerical examples.
AN ADAPTIVE MESHLESS COMPUTATIONAL SYSTEM FOR ELASTOPLASTIC CONTACT PROBLEMS
Authors: ZHANG ZHENG , LIU GENG , LIU TIANXIANG , ZENG QUANREN , WU LIYAN
Published: October 2008

An adaptive meshless computational system is introduced in this paper to solve two-dimensional elastoplastic contact mechanics. An adaptive element-free Galerkin-finite element coupling computational model based on the gradient of strain energy and a linear programming technique with the initial stiffness method for elastoplastic contact problems are combined. Principle explanation and program realization are carried out. The modularization concept in software engineering is used, and the adaptive change of the influence domain radius and the elastoplastic property of material are also taken into account by the system. A rigid cylinder making contact with an elastic plane is analyzed to validate the system. Some key parameters in adaptive calculation are studied. The adaptive meshless computational system is also applied to elastoplastic contact of rough surfaces. Comparisons of the adaptive refinement solution with the uniform refinement solution are made, and the results show the satisfactory accuracy and efficiency of the solutions from the adaptive refinement model.
FUNCTIONAL CATHODE MATERIALS FOR Li-ION BATTERIES — PART II: LiFePO4 AND ITS COMPOSITE
Authors: MOLENDA JANINA , MARZEC JACEK
Published: October 2008

The paper presents a review of the structural, electrical and electrochemical properties of LiFePO 4 pospho-olivine dopped with W , Ti , Al and manganese substituted LiFe 1-y Mn y PO 4, synthesized at high temperatures as well as preparation method of LiFePO 4– Fe 2 P composite phases. The nature of the metallic type conductivity of doped phospho-olivine is discussed and some fundamental arguments against the bulk nature of the observed high electronic conductivity are presented.
ACCEPTOR MODULATED DEFECT AND ELECTRONIC STRUCTURES IN FERROELECTRIC LEAD TITANATE: AN AB INITIO STUDY
Authors: ZHANG ZHEN , WU PING , LU LI , SHU CHANG
Published: October 2008

Defects and electronic structures of the aliovalent acceptors substituted lead titanates were studied using density functional theory calculations. Three types of defect structures are identified in 3d transition metal and the group IIB and VB elements substituted systems. Cr substitute and oxygen vacancies are found to be dissociated from each other, forming an isolated point defect structure. In contrast, all other substitutes favor the immobile acceptor–oxygen–vacancy–acceptor defect clusters which weaken the space charge effects by limiting the motions of oxygen vacancies. Furthermore, two distinct defect-cluster structures (along the z direction and in the xy plane, respectively) are observed. We conclude that the defect structure in the xy plane induces head-to-head polarization patterns, which make the domain pinning effects even weaker. The electronic structures due to elements substitutions are also investigated and compared.
SYNTHESIS OF MESOPOROUS IRON OXIDE NANOPARTICLES FROM MESOPOROUS SILICA TEMPLATE VIA NANO-REPLICATION
Authors: SHON JEONG KUK , KONG SOO SUNG , KIM SUNG SOO , KANG MIN SUK , KIM JI MAN , SO BYUNG GUK
Published: October 2008

Highly ordered mesoporous iron oxide (α- Fe 2 O 3) material has been successfully obtained from mesoporous silica template, KIT-6 (3-D Cubic Ia3d symmetry), through nano-replication method. The mesoporous α- Fe 2 O 3 material thus obtained exhibits well-defined mesopores (2.7 nm in diameter), high surface area (148 m2/g), high pore volume (0.47 cm3/g) and crystalline frameworks. The morphology of the mesoporous α- Fe 2 O 3 material is very uniform in spherical shape of which the average particle size is about 100 nm in diameter.
Pheromone Communication in Amphibians and Reptiles
Authors: Houck Lynne D.
Published: October 2008

This selective review considers herpetological papers that feature the use of chemical cues, particularly pheromones involved in reproductive interactions between potential mates. Primary examples include garter snake females that attract males, lacertid lizards and the effects of their femoral gland secretions, aquatic male newts that chemically attract females, and terrestrial salamander males that chemically persuade a female to mate. Each case study spans a number of research approaches (molecular, biochemical, behavioral) and is related to sensory processing and the physiological effects of pheromone delivery. These and related studies show that natural pheromones can be identified, validated with behavioral tests, and incorporated in research on vomeronasal functional response.
Regulation of basal core promoter activity of human organic cation transporter 1 (OCT1/SLC22A1)
Authors: Kajiwara Moto , Terada Tomohiro , Asaka Jun-ichi , Aoki Masayo , Katsura Toshiya , Ikai Iwao , Inui Ken-ichi
Published: October 2008

Human organic cation transporter 1 (OCT1/SLC22A1) plays important roles in the hepatic uptake of cationic drugs. The functional characteristics of this transporter have been well evaluated, but molecular information regarding transcriptional regulation is limited. In the present study, therefore, we examined the gene regulation of OCT1 gene focusing on basal core expression. An ∼2.5-kb fragment of the OCT1 promoter region was isolated, and promoter activity was measured by luciferase assay in the human liver cell lines Huh7 and HepG2. Deletion analysis suggested that the region spanning −141/−69 was essential for the basal core transcriptional activity and that this region contained the sequence of a cognate E-box (CACGTG). The E-box is known to be bound by the basal transcription factors, upstream stimulating factors (USFs), and the functional involvements of USF1 and USF2 were confirmed by a transactivation effect, a mutational analysis of the E-box, and an electrophoretic mobility shift assay. The transactivation effect of USFs on the OCT1 promoter was further stimulated by hepatocyte nuclear factor 4α, a liver-enriched transcription factor. There were no polymorphisms in the proximal promoter region (about 400 bp) of OCT1 gene ( n = 109). These findings indicated that both USF1 and USF2 bind to an E-box sequence located in the OCT1 core promoter region and are required for the basal gene expression of this transporter.
Role of TNF-α-induced reactive oxygen species in endothelial dysfunction during reperfusion injury
Authors: Gao Xue , Zhang Hanrui , Belmadani Souad , Wu Junxi , Xu Xiangbin , Elford Howard , Potter Barry J. , Zhang Cuihua
Published: October 2008

We hypothesized that neutralization of TNF-α at the time of reperfusion exerts a salubrious role on endothelial function and reduces the production of reactive oxygen species. We employed a mouse model of myocardial ischemia-reperfusion (I/R, 30 min/90 min) and administered TNF-α neutralizing antibodies at the time of reperfusion. I/R elevated TNF-α expression (mRNA and protein), whereas administration of anti-TNF-α before reperfusion attenuated TNF-α expression. We detected TNF-α expression in vascular smooth muscle cells, mast cells, and macrophages, but not in the endothelial cells. I/R induced endothelial dysfunction and superoxide production. Administration of anti-TNF-α at the onset of reperfusion partially restored nitric oxide-mediated coronary arteriolar dilation and reduced superoxide production. I/R increased the activity of NAD(P)H oxidase and of xanthine oxidase and enhanced the formation of nitrotyrosine residues in untreated mice compared with shams. Administration of anti-TNF-α before reperfusion blocked the increase in activity of these enzymes. Inhibition of xanthine oxidase (allopurinol) or NAD(P)H oxidase (apocynin) improved endothelium-dependent dilation and reduced superoxide production in isolated coronary arterioles following I/R. Interestingly, I/R enhanced superoxide generation and reduced endothelial function in neutropenic animals and in mice treated with a neutrophil NAD(P)H oxidase inhibitor, indicating that the effects of TNF-α are not through neutrophil activation. We conclude that myocardial ischemia initiates TNF-α expression, which induces vascular oxidative stress, independent of neutrophil activation, and leads to coronary endothelial dysfunction.
Superior cardiac function via anaplerotic pyruvate in the immature swine heart after cardiopulmonary bypass and reperfusion
Authors: Olson Aaron K. , Hyyti Outi M. , Cohen Gordon A. , Ning Xue-Han , Sadilek Martin , Isern Nancy , Portman Michael A.
Published: October 2008

Pyruvate produces inotropic responses in the adult reperfused heart. Pyruvate oxidation and anaplerotic entry into the tricarboxylic acid (TCA) cycle via carboxylation are linked to the stimulation of contractile function. The goals of this study were to determine if these metabolic pathways operate and are maintained in the developing myocardium after reperfusion. Immature male swine (age: 10–18 days) were subjected to cardiopulmonary bypass (CPB). Intracoronary infusion of [2-13C]pyruvate (to achieve an estimated final concentration of 8 mM) was given for 35 min, starting either during weaning ( group I) and after its discontinuation ( group II) or without (control) CPB. Hemodynamic data were collected.13C NMR spectroscopy was used to determine the fraction of pyruvate entering the TCA cycle via pyruvate carboxylation (PC) to total TCA cycle entry (PC plus decarboxlyation via pyruvate dehydrogenase). Liquid chromatography-mass spectrometry was used to determine total glutamate enrichment. Pyruvate infusion starting during the weaning of mechanical circulatory support improved maximum dP/d t ( P < 0.05) but waiting to start the infusion until after the discontinuation of CPB did not. Glutamate fractional enrichment was confirmed by liquid chromatography-mass spectroscopy as adequate (>5%) to provide signal to noise in the NMR experiment in all groups. The ratio of pyruvate carboxylase to total pyruvate entry into the TCA cycle did not differ between groups ( group I: 20 ± 4%, group II: 23 ± 7%, and control: 27 ± 7%). These data show that robust PC operates in the neonatal pig heart and is maintained during reperfusion under conditions that emulate CPB and reperfusion in human infants.