bluuebunny/crossref_metadata_2025 huggingface dataset:
Klebsiella pneumoniae
Capsule Polysaccharide Impedes the Expression of β-Defensins by Airway Epithelial Cells
Authors: Moranta David , Regueiro Verónica , March Catalina , Llobet Enrique , Margareto Javier , Larrate Eider , Garmendia Junkal , Bengoechea José A.
Published: December 2009

Human β-defensins (hBDs) contribute to the protection of the respiratory tract against pathogens. It is reasonable to postulate that pathogens have developed countermeasures to resist them.
Klebsiella pneumoniae
capsule polysaccharide (CPS), but not the lipopolysaccharide O antigen, mediated resistance against hBD1 and hBD2. hBD3 was the most potent hBD against
Klebsiella
. We investigated the possibility that as a strategy for survival in the lung,
K. pneumoniae
may not activate the expression of hBDs. Infection of A549 and normal human bronchial cells with 52145-Δ
wca
K2
, a CPS mutant, increased the expression of hBD2 and hBD3. Neither the wild type nor the lipopolysaccharide O antigen mutant increased the expression of hBDs.
In vivo
, 52145-Δ
wca
K2
induced higher levels of mBD4 and mBD14, possible mouse orthologues of hBD2 and hBD3, respectively, than the wild type. 52145-Δ
wca
K2
-dependent upregulation of hBD2 occurred via NF-κB and mitogen-activated protein kinases (MAPKs) p44/42, Jun N-terminal protein kinase (JNK)-dependent pathways. The increase in hBD3 expression was dependent on the MAPK JNK. 52145-Δ
wca
K2
engaged Toll-like receptors 2 and 4 (TLR2 and TLR4) to activate hBD2, whereas hBD3 expression was dependent on NOD1.
K. pneumoniae
induced the expression of CYLD and MKP-1, which act as negative regulators for 52145-Δ
wca
K2
-induced expression of hBDs. Bacterial engagement of pattern recognition receptors induced CYLD and MKP-1, which may initiate the attenuation of proinflammatory pathways. The results of this study indicate that
K. pneumoniae
CPS not only protects the pathogen from the bactericidal action of defensins but also impedes their expression. These features of
K. pneumoniae
CPS may facilitate pathogen survival in the hostile environment of the lung.
Cigarette Smoke Exposure Impairs Pulmonary Bacterial Clearance and Alveolar Macrophage Complement-Mediated Phagocytosis of
Streptococcus pneumoniae
Authors: Phipps John C. , Aronoff David M. , Curtis Jeffrey L. , Goel Deepti , O'Brien Edmund , Mancuso Peter
Published: December 2009

Cigarette smoke exposure increases the risk of pulmonary and invasive infections caused by
Streptococcus pneumoniae
, the most commonly isolated organism from patients with community-acquired pneumonia. Despite this association, the mechanisms by which cigarette smoke exposure diminishes host defense against
S. pneumoniae
infections are poorly understood. In this study, we compared the responses of BALB/c mice following an intratracheal challenge with
S. pneumoniae
after 5 weeks of exposure to room air or cigarette smoke in a whole-body exposure chamber
in vivo
and the effects of cigarette smoke on alveolar macrophage phagocytosis of
S. pneumoniae in vitro
. Bacterial burdens in cigarette smoke-exposed mice were increased at 24 and 48 h postinfection, and this was accompanied by a more pronounced clinical appearance of illness, hypothermia, and increased lung homogenate cytokines interleukin-1β (IL-1β), IL-6, IL-10, and tumor necrosis factor alpha (TNF-α). We also found greater numbers of neutrophils in bronchoalveolar lavage fluid recovered from cigarette smoke-exposed mice following a challenge with heat-killed
S. pneumoniae
. Interestingly, overnight culture of alveolar macrophages with 1% cigarette smoke extract, a level that did not affect alveolar macrophage viability, reduced complement-mediated phagocytosis of
S. pneumoniae
, while the ingestion of unopsonized bacteria or IgG-coated microspheres was not affected. This murine model provides robust additional support to the hypothesis that cigarette smoke exposure increases the risk of pneumococcal pneumonia and defines a novel cellular mechanism to help explain this immunosuppressive effect.
Toll-Like Receptor 4 Signaling Leads to Severe Fungal Infection Associated with Enhanced Proinflammatory Immunity and Impaired Expansion of Regulatory T Cells
Authors: Loures Flávio V. , Pina Adriana , Felonato Maíra , Araújo Eliseu F. , Leite Katia R. M. , Calich Vera L. G.
Published: December 2009

Toll-like receptors (TLRs) present in innate immune cells recognize pathogen molecular patterns and influence immunity to control the host-parasite interaction. The objective of this study was to characterize the involvement of TLR4 in the innate and adaptive immunity toParacoccidioides brasiliensis, the most important primary fungal pathogen of Latin America. We compared the responses of C3H/HeJ mice, which are naturally defective in TLR4 signaling, with those of C3H/HePas mice, which express functional receptors, afterin vitroandin vivoinfection withP. brasiliensis. Unexpectedly, we verified that TLR4-defective macrophages infectedin vitrowithP. brasiliensispresented decreased fungal loads associated with impaired synthesis of nitric oxide, interleukin-12 (IL-12), and macrophage chemotactic protein 1 (MCP-1). After intratracheal infection with 1 million yeasts, TLR4-defective mice developed reduced fungal burdens and decreased levels of pulmonary nitric oxide, proinflammatory cytokines, and antibodies. TLR4-competent mice produced elevated levels of IL-12 and tumor necrosis factor alpha (TNF-α), besides cytokines of the Th17 pattern, indicating a proinflammatory role for TLR4 signaling. The more severe infection of TLR4-normal mice resulted in increased influx of activated macrophages and T cells to the lungs and progressive control of fungal burdens but impaired expansion of regulatory T cells (Treg cells). In contrast, TLR4-defective mice were not able to clear their diminished fungal burdens totally, a defect associated with deficient activation of T-cell immunity and enhanced development of Treg cells. These divergent patterns of immunity, however, resulted in equivalent mortality rates, indicating that control of elevated fungal growth mediated by vigorous inflammatory reactions is as deleterious to the hosts as low fungal loads inefficiently controlled by limited inflammatory reactions.
Getting around the legume nodule: I. The structure of the peripheral zone in four nodule types
Authors: Guinel Frédérique C.
Published: December 2009

Nodules in the family Leguminosae come in many different shapes and forms, depending partly on the host that bears them. This review focuses on the peripheral tissues that surround the infected tissues of four anatomically distinct classes of nodules: nodules with indeterminate meristems (from the Trifolieae and Fabeae tribes); desmodioid nodules with determinate meristems (from the Phaseoleae and Loteae tribes); aeschynomenoid nodules ( Arachis hypogaea L., peanut); and lupinoid nodules ( Lupinus sp. L., lupine). I have especially stressed the importance of the three-dimensionality of the organ, because not all nodules display a radial symmetry as it is often assumed. The goal of this review is to provide a strong base of nodule structure so that forthcoming molecular studies can integrate this information into their approach.
Getting around the legume nodule: II. Molecular biology of its peripheral zone and approaches to study its vasculature
Authors: Guinel Frédérique C.
Published: December 2009

All legume nodules exhibit a complex cortex composed of many types of cells and tissues. This zone, which surrounds the central infected zone, plays a critical role in regulating the exchange of oxygen between the rhizosphere and the bacteroids. Not often mentioned, but of importance, are the vascular traces that develop in the nodule inner cortex. Information on their ontogeny is scarce, although their existence is critical to the symbiosis because both the nitrogenous compounds formed as a result of nitrogenase activity and the energy-rich molecules obtained from plant photosynthesis use these conduits. Here, I focus on these tissues, reviewing what we know of their appearance in pseudonodules, boron-treated legumes, and in the vasculature mutants described to date. I also examine the genes known to be expressed in the peripheral tissues and attempt to place them in functional clusters. Finally, I propose that specific vasculature markers known from the Arabidopsis literature be applied to the study of the development of nodule vascular tissues. It is of interest that most of these markers are linked to specific growth regulators, especially auxins and cytokinins but to a lesser extent gibberellins and brassinosteroids.
Photoprotective mechanisms during leaf ontogeny: cuticular development and anthocyanin deposition in two morphs of Agave striata that differ in leaf coloration
Authors: Fondom Nicolas Y. , Castro-Nava Sergio , Huerta Alfredo J.
Published: December 2009

Our objectives were to test whether in Agave striata Zucc., a plant with crassulacean acid metabolism (CAM plant), leaf wax development is a delayed response to sunlight exposure following cutin development, and whether energy dissipation shifts from non-photochemical quenching to photochemical quenching during leaf ontogeny. Under field conditions, photosynthesis, cuticular development, and anthocyanin deposition were studied in two morphs of A. striata that differ in leaf coloration (green vs. red). We quantified leaf anthocyanin, wax, and cutin content, and also measured chlorophyll a fluorescence and leaf surface temperature. In addition, using three leaf reflectance indices, we measured relative chlorophyll and anthocyanin content, and also xanthophyll-cycle de-epoxidation state (xanthophyll conversion). Our results revealed that the main components of cuticle (wax and cutin) in leaves of A. striata are deposited during different developmental windows, which are similar to leaves of monocots such as grasses. Exposure to sunlight was found to be the most likely candidate to affect wax and anthocyanin deposition. Chlorophyll a fluorescence data revealed that the sunlight conditions experienced by both morphs predisposed the young leaves of the green morph and old leaves of both morphs to photoinhibition. Our results also revealed that old leaves of the red morph, which contain a reduced level of chlorophyll and anthocyanin, had additional photoprotection via xanthophyll conversion. The results presented here support the photoprotective function of leaf anthocyanins and wax accumulation during leaf ontogeny, indicating that their presence may compensate for the reduced dependence of non-photochemical quenching and the xanthophyll-cycle pigment conversion.
Shoot population recruitment from a bud bank over two seasons of undisturbed growth of Leymus chinensis
Authors: Zhang Ji-tao , Mu Chun-sheng , Wang De-li , Wang Jun-feng , Chen Gui-xiang
Published: December 2009

Shoots of many clonal species are iterated seasonally by programmed growth from bud banks. Buds are not all the same but differ in their positions; these positions determine their densities, trigger times, and seasonal dynamics. To determine how different bud types contribute to a shoot population in an undisturbed environment, the densities of each bud type and daughter-shoot type were investigated in Leymus chinensis (Trin.) Tzvelev. New horizontal rhizomes (A1-1) start to grow in late May, but new vertical buds (including the vertical apical rhizome buds (A1-2), axillary rhizome buds (B1), and axillary shoot buds (C1)) emerge in late June; after late June or late July, the density of A1-1 gradually decreased, whereas the vertical buds increased. In mid-season, the presence of a high proportion of A1-1, suggests that plants pursue a spreading strategy. Late in the season, a high proportion of vertical buds suggests that they adopt a propagation strategy. At the end of the growing season, the stable contributions of type-specific buds (A1-2, 16%; B1, 5%; C1, 79%) to the overall shoot population may explain the dominance of this species throughout the eastern Eurasian Steppe. Developing a clearer understanding of bud dynamics and their type-specific contributions under undisturbed conditions, is a necessary prerequisite for predicting their responses under disturbed conditions.
The mycoheterotroph Arachnitis uniflora has a unique association with arbuscular mycorrhizal fungi
Authors: Domínguez Laura S. , Melville Lewis , Sérsic Alicia , Faccio Antonella , Peterson R. Larry
Published: December 2009

Achlorophyllous plants that are dependent on an association with fungi linked to photosynthetic plants for their carbon source are known as mycoheterotrophs. Arachnitis uniflora Phil., a monotypic member of the monocotyledonous family Corsiaceae, fits this category, as it relies on a glomalean fungus belonging to Glomus Group A for carbon acquisition. Although basic structural features of root colonization have been reported for A. uniflora, the nutrient exchange interface has not been studied. This is the first study to use confocal microscopy, transmission electron microscopy, and cytochemical procedures to study the interface between a glomalean fungus and the roots of a mycoheterotrophic species. Results showed that arbuscules are never formed, and that the “vesicles in bundles” reported earlier are unlike typical glomalean vesicles, in that they form in clusters by the enlargement of hyphal branches and have a complex multilayered wall. The thick inner wall layer consists primarily of β-1,3-glucans (callose) and is surrounded by a thin outer layer of chitin. Each structure is surrounded by host cell wall material and a perifungal membrane, suggesting an involvement in nutrient exchange. The cytoplasm contains a complex of small β-1,3-glucan-containing vacuoles, lipid bodies, endobacteria, and many nuclei. These structures enlarge to occupy most of the cortical cell volume and then degrade, releasing lipids and other materials into the host cell. We suggest that these structures should not be equated with typical glomalean vesicles but are unique structures that may be involved, along with the hyphal coils, in nutrient acquisition by the host.
Effect of cold temperatures on properties of unfrozen Troll clay
Authors: Perkins Steven W. , Sjursen Morten
Published: December 2009

Oedometer and triaxial experiments have been performed on North Sea Troll clay previously warmed to room temperature and tested at both room temperature and 0 °C to assess the effect of cold temperature on undrained strength and consolidation properties. In general, both the undrained strength and preconsolidation pressure increase as the temperature decreases. Many subsea areas of development in extreme northern or southern latitudes experience seafloor temperatures continuously around 0 °C. These results suggest that conventional laboratory testing at room temperature of samples from these areas leads to an underestimation of strength and preconsolidation pressure. Therefore, additional testing is recommended to assess the effect of a warming and cooling cycle on strength and consolidation properties, as previous work suggests that some consolidation is induced by this temperature cycle and may be responsible for the ensuing strength gain.
Expanding collapse in partially submerged granular soil slopes
Authors: Michalowski Radoslaw L.
Published: December 2009

The traditional approach to stability analysis of granular slopes leads to the safety factor that is associated with a planar failure surface approaching the slope face, whether the slope is “dry” or submerged. However, for partially submerged slopes, a more critical, nonplanar failure surface can be formed. A family of geometrically similar surfaces can be found that is characterized by the same safety factor. If the safety factor drops down to unity and the slope becomes unstable, then a mechanism of any size can form. Alternatively, the failure may start at some small region and then the volume of the mechanism of failure can expand, giving rise to a progressive failure of a different kind that is typically associated with slopes. This progression has the character of a “disturbance” or a shock-like kinematic discontinuity propagating into the soil at rest. A quantitative analysis is presented and it is demonstrated that the soil dilates while the mechanism expands, leaving the slope weakened and susceptible to a deep failure. This is a plausible mode of failure of partially submerged slopes, the type that is most likely responsible for large subaqueous landslides, and is similar to the well-documented instability propagation in “quick clay.”
Wave-induced shallow slides and their features on the subaqueous Yellow River delta
Authors: Xu Guohui , Sun Yongfu , Wang Xin , Hu Guanghai , Song Yupeng
Published: December 2009

Slope instability processes occur widely on the underwater slopes of the Yellow River delta during storms. Roughly circular depressions on the upper delta front in water depths of 4 to 8 m have been detected by acoustic surveying and their processes were observed in the laboratory. This paper analyzes the properties of geomorphic and acoustic profiles of the upper delta front and compares the engineering geologic properties of samples from the disturbed and undisturbed areas. The results indicate that the weak superficial mass could oscillate with waves and the oscillation weakened the surrounding soil under the cyclic loading. The stratum was disturbed or even destroyed with depth, the area of the slide mass enlarged gradually, and finally a collapse depression formed.
Use of terrestrial laser scanning for the characterization of retrogressive landslides in sensitive clay and rotational landslides in river banks
Authors: Jaboyedoff Michel , Demers Denis , Locat Jacques , Locat Ariane , Locat Pascal , Oppikofer Thierry , Robitaille Denis , Turmel Dominique
Published: December 2009

For more than 10 years, digital elevation models (DEM) produced by light detection and ranging (LIDAR) technology have provided new tools for geomorphologic studies and especially for landslide studies. In particular, terrestrial laser scanning (TLS) provides a great versatility of use. TLS can be used either for monitoring purposes or in an emergency situation that necessitates a rapid DEM acquisition for assessing a hazard. Using three examples we demonstrate the usefulness of TLS for landslide volume quantification, profile creation, and time series analysis. These case studies are landslides located in sensitive clays of eastern Canada (Quebec, Canada) or small rotational slides in river banks (Switzerland).
HIGH-DIMENSIONAL CHAOS IN DISSIPATIVE AND DRIVEN DYNAMICAL SYSTEMS
Authors: MUSIELAK Z. E. , MUSIELAK D. E.
Published: December 2009

Studies of nonlinear dynamical systems with many degrees of freedom show that the behavior of these systems is significantly different as compared with the behavior of systems with less than two degrees of freedom. These findings motivated us to carry out a survey of research focusing on the behavior of high-dimensional chaos, which include onset of chaos, routes to chaos and the persistence of chaos. This paper reports on various methods of generating and investigating nonlinear, dissipative and driven dynamical systems that exhibit high-dimensional chaos, and reviews recent results in this new field of research. We study high-dimensional Lorenz, Duffing, Rössler and Van der Pol oscillators, modified canonical Chua's circuits, and other dynamical systems and maps, and we formulate general rules of high-dimensional chaos. Basic techniques of chaos control and synchronization developed for high-dimensional dynamical systems are also reviewed.
BIFURCATION ANALYSIS OF THE SWIFT–HOHENBERG EQUATION WITH QUINTIC NONLINEARITY
Authors: XIAO QINGKUN , GAO HONGJUN
Published: December 2009

This paper is concerned with the asymptotic behavior of the solutions u(x,t) of the Swift–Hohenberg equation with quintic nonlinearity on a one-dimensional domain (0, L). With α and the length L of the domain regarded as bifurcation parameters, branches of nontrivial solutions bifurcating from the trivial solution at certain points are shown. Local behavior of these branches are also studied. Global bounds for the solutions u(x,t) are established and then the global attractor is investigated. Finally, with the help of a center manifold analysis, two types of structures in the bifurcation diagrams are presented when the bifurcation points are closer, and their stabilities are analyzed.
MIXING PROPERTY AND ENTROPY CONJUGACY OF ℤ2 SUBSHIFT OF FINITE TYPE: A CASE STUDY
Authors: BAN JUNG-CHAO , LIN SZU-YU , LIN YIN-HENG
Published: December 2009

In the paper, the mixing property of ℤ2 subshift of finite type (SFT) is studied, some checkable conditions are provided to examine the property of mixing. Once the mixing property is checked, a class of examples can be found to show it possesses an entropy conjugacy property proposed in [Quas & Trow, 2000]. Finally, we construct an example of two shift spaces X and Y that are entropy conjugate but not conjugate.
COMPUTATION OF CONNECTION MATRICES USING THE SOFTWARE PACKAGE conley
Authors: BARAKAT MOHAMED , MAIER-PAAPE STANISLAUS
Published: December 2009

In this paper we demonstrate the power of the computer algebra package conley, which enables one to compute connection and transition matrices, two of the main algebraic tools of the CONLEY index theory. In particular, we study the CAHN–HILLIARD equation on the unit square and extend the results obtained in [Maier-Paape et al., 2007] to a bigger range of the bifurcation parameter. Besides providing several explicit computations using conley, the definition of connection matrices is reconsidered, simplified, and presented in a self-contained manner in the language of CONLEY index theory. Furthermore, we introduce so-called energy induced bifurcation intervals, which can be utilized by conley to differential equations with a parameter. These bifurcation intervals are used to automatically path-follow the set of connection matrices at bifurcation points of the underlying set of equilibria.
STABILITY SWITCHES IN DISCRETE FOOD-CHAIN PROBLEMS
Authors: LINDSTRÖM TORSTEN
Published: December 2009

In an already classical paper, May [1976] pointed out that simple nonlinear models in ecology can possess complicated dynamics. A long debate concerning the possible existence of chaotic ecologies has followed the appearance of this paper. Morris [1990] stressed that several problems exist when making conclusions regarding chaotic or nonchaotic dynamics as models are fitted to ecological data. Takens' theorem [1981] should, in principle, provide tools for solving some of these problems, but in reality essential assertions are most often violated. First, limits regarding the length of the used time-series must be assumed. Second, the theorem can be applied for evaluating positive Lyapunov exponents only, and is hence not applicable for distinguishing nonchaotic dynamics from chaotic.

We use a deterministic food-chain model that possesses a wide range of different dynamical patterns to demonstrate the existence of cases that are misclassified with respect to chaotic or nonchaotic motion as models are fitted to data in the various dynamical regimes. Our results are valid regardless of what finite data size is assumed. The results are best understood for high-periodic cases in the noise-free limit. If the relevant phase-space is not sufficiently well-populated with data in the vicinity of the periodic orbit, then sufficient complexity of the models are not supported by standard model selection criteria like AIC or GCV. Thus, the fitted models only in the best cases contain information concerning both the location of the periodic orbit and the eigenvalues of the Jacobians evaluated along the periodic orbit. If the space is moderately well populated with data, then the data is often described by an unstable periodic orbit of the fitted model. The attractor that was to be described by the fitted model was destabilized and is now a repeller. We call this phenomenon stability switches. It reminds about the noise-induced phenomenon reported by Rand and Wilson [1992], but we point out that the problem reported here is caused by the fitting procedure itself, not by the added noise.

The repeller that has been created by the model-fitting procedure can be located in the basins of attraction of some fixed point, the infinity, or some periodic or chaotic attractors of the fitted models. The situation seems similar when periodic attractors are not well enough populated with data for describing their location and when chaotic attractors are to be described by data. Similar stability switches occur and the dynamics of models fitted to data may differ or coincide with the dynamics of the attractor that generated the data in an unpredictable manner.
CHUA'S CIRCUITS SYNCHRONIZATION WITH DIFFUSIVE COUPLING: NEW RESULTS
Authors: BUSCARINO ARTURO , FORTUNA LUIGI , FRASCA MATTIA , SCIUTO GREGORIO
Published: December 2009

In this communication, synchronization of two diffusively coupled Chua's circuit is studied from the analytical and experimental points of view. The conditions under which complete synchronization is ensured are derived by applying a strategy based on the Master Stability Function. The experimental realization, that makes use of the State-Controlled Cellular Nonlinear Network based implementation of Chua's circuit, shows the synchronized behavior of two circuits coupled with a passive resistor as diffusion coefficient. The results obtained indicates diffusive coupling as a mutually reduced order state observer, in the sense that one circuit observes the other and vice versa. Moreover, the concept of synchronization by using passive elements can be extended to spatially extended reaction–diffusion systems.
ON SIMULTANEOUS CONSTRUCTION OF VORONOI DIAGRAM AND DELAUNAY TRIANGULATION BY PHYSARUM POLYCEPHALUM
Authors: SHIRAKAWA TOMOHIRO , ADAMATZKY ANDREW , GUNJI YUKIO-PEGIO , MIYAKE YOSHIHIRO
Published: December 2009

We experimentally demonstrate that both Voronoi diagram and its dual graph Delaunay triangulation are simultaneously constructed — for specific conditions — in cultures of plasmodium, a vegetative state of Physarum polycephalum. Every point of a given planar data set is represented by a tiny mass of plasmodium. The plasmodia spread from their initial locations but, in certain conditions, stop spreading when they encounter plasmodia originated from different locations. Thus space loci not occupied by the plasmodia represent edges of Voronoi diagram of the given planar set. At the same time, the plasmodia originating at neighboring locations form merging protoplasmic tubes, where the strongest tubes approximate Delaunay triangulation of the given planar set. The problems are solved by plasmodium only for limited data sets, however the results presented lay a sound ground for further investigations.
DYNAMICAL BEHAVIOR AND CONTROL OF COUPLED THRESHOLD ELEMENTS WITH SELF-INHIBITION
Authors: SCHUSTER H. G. , LE VAN QUYEN M. , CHAVEZ M. , KÖHLER J. , MAYER J. , CLAUSSEN J. C.
Published: December 2009

Coupled threshold elements with self-inhibition display a phase transition to an oscillating state where the elements fire in synchrony with a period T that is of the order of the dead-time caused by self-inhibition. This transition is noise-activated and therefore displays strong collectively enhanced stochastic resonance. For an exponentially decaying distribution of dead-times the transition to the oscillating state occurs, coming from high noise temperatures, via a Hopf bifurcation and coming from low temperatures, via a saddle node bifurcation. The transitions can be triggered externally by noise and oscillating signals. This opens up new possibilities for controlling slow wave sleep.
DELAY INDEPENDENT AND DEPENDENT STABILITY ANALYSIS FOR COHEN–GROSSBERG NEURAL NETWORKS WITH TIME-VARYING DELAYS
Authors: LIU YIGUANG , YOU ZHISHENG , LIU BINGBING
Published: December 2009

For Cohen–Grossberg neural networks with time-varying delays, by fixed point and contract mapping theorems, a sufficient condition ensuring the existence and uniqueness of an equilibrium is proposed. To guarantee the delay independent global stability of the equilibrium, two sufficient conditions are proposed by means of a time delay differential inequality and contradiction tricks, respectively. By virtue of a special Lyapunov functional as well as properties of M-matrices, a sufficient condition undertaking the delay dependent global stability of the equilibrium is introduced. Compared with known literatures, the presented results place slack restrictions on the activation functions, and are suitable for the networks with time-varying delays. Furthermore, most of the obtained results are independent of the amplification functions, making their applicability more far-reaching. Finally, two examples are numerically simulated to illustrate the validity as well as novelty of the criteria.
FROM THE BOX-WITHIN-A-BOX BIFURCATION STRUCTURE TO THE JULIA SET PART II: BIFURCATION ROUTES TO DIFFERENT JULIA SETS FROM AN INDIRECT EMBEDDING OF A QUADRATIC COMPLEX MAP
Authors: MIRA CHRISTIAN , AGLIARI ANNA , GARDINI LAURA
Published: December 2009

Part I of this paper has been devoted to properties of the different Julia set configurations, generated by the complex map TZ: z′ = z2 - c, c being a real parameter, -1/4 < c < 2. These properties were revisited from a detailed knowledge of the fractal organization (called "box-within-a-box"), generated by the map x′ = x2 - c with x a real variable. Here, the second part deals with an embedding of TZ into the two-dimensional noninvertible map [Formula: see text]; y′ = γ y + 4x2y, γ ≥ 0. For [Formula: see text] is semiconjugate to TZ in the invariant half plane (y ≤ 0). With a given value of c, and with γ decreasing, the identification of the global bifurcations sequence when γ → 0, permits to explain a route toward the Julia sets, from a study of the basin boundary of the attractor located on y = 0.
CHAOTIC DYNAMICS FOR MAPS IN ONE AND TWO DIMENSIONS: A GEOMETRICAL METHOD AND APPLICATIONS TO ECONOMICS
Authors: MEDIO ALFREDO , PIREDDU MARINA , ZANOLIN FABIO
Published: December 2009

This article describes a method — called here "the method of Stretching Along the Paths" (SAP) — to prove the existence of chaotic sets in discrete-time dynamical systems. The method of SAP, although mathematically rigorous, is based on some elementary geometrical considerations and is relatively easy to apply to models arising in applications. The paper provides a description of the basic mathematical ideas behind the method, as well as three applications to economic models. Incidentally, the paper also discusses some questions concerning the definition of chaos and some problems arising from economic models in which the dynamics are defined only implicitly.
THE ORDINAL STRUCTURE OF THE SIGNED SHIFT TRANSFORMATIONS
Authors: AMIGÓ JOSÉ MARÍA
Published: December 2009

Ordinal patterns bring in the dynamic novel aspects, difficult questions, and useful tools for entropy estimation, time series analysis and other applications. In [Amigó et al., 2008a], the structure of the ordinal patterns of the one- and two-sided shifts on N symbols was elucidated with great detail. The results are applied via order isomorphy to the ordinal structure of the sawtooth maps x ↦ Nx mod 1 and the baker map. In this paper, we generalize the technique employed there, to cope with the so-called signed shifts on N symbols and signed sawtooth maps.
FRACTIONAL-ORDER CHAOS: A NOVEL FOUR-WING ATTRACTOR IN COUPLED LORENZ SYSTEMS
Authors: CAFAGNA DONATO , GRASSI GIUSEPPE
Published: December 2009

By using a time-domain approach, this paper analyzes the chaotic dynamics of the fractional-order system obtained by coupling two fractional Lorenz systems. The work exploits the Adomian decomposition method (ADM), shows that the proposed fractional system with order as low as 2.88 exhibits a novel four-wing chaotic attractor. The existence of chaos is also confirmed by the application of the "0-1 test" for chaos. Finally, an analysis of the system equilibria is conducted, which shows that the fractional-order four-wing attractor is truly the counterpart of the recently introduced integer-order four-wing attractor.
ON THE WAVELET TRANSFORM APPLICATION TO A STUDY OF CHAOTIC VIBRATIONS OF THE INFINITE LENGTH FLEXIBLE PANELS DRIVEN LONGITUDINALLY
Authors: AWREJCEWICZ J. , KRYSKO A. V. , SOLDATOV V.
Published: December 2009

Both classical Fourier analysis and continuous wavelets transformation are applied to study non-linear vibrations of infinitely long flexible panels subject to longitudinal sign-changeable external load actions. First the governing PDEs are derived and then the Bubnov–Galerkin method is applied to yield 2N first order ODEs. The further used Lyapunov exponent computation is described. Transition scenarios from regular to chaotic dynamics of the being investigated plate strip are analyzed using different wavelets, and their suitability and advantages/disadvantages to nonlinear dynamics monitoring and quantifying are illustrated and discussed. A few novel results devoted to the beam nonlinear dynamics behavior are reported. In addition, links between the largest Lyapunov exponent computation and the wavelet spectrum numerical estimation are also illustrated and discussed.
EXPONENTIAL p-STABILITY OF STOCHASTIC REACTION–DIFFUSION CELLULAR NEURAL NETWORKS WITH MULTIPLE DELAYS
Authors: WU RANCHAO
Published: December 2009

In the current paper, a class of stochastic cellular neural networks with reaction–diffusion effects, both discrete and distributed time delays, is studied. Several sufficient conditions guaranteeing the almost sure and pth moment exponential stability of its equilibrium solution are respectively obtained through analytic methods such as employing Lyapunov functional, applying Itô's formula, inequality techniques, embedding in Banach space, Matrix analysis and semimartingale convergence theorem. The yielded conclusions, which are independent of diffusion terms and delays, assume much less restrictions on activation functions and interconnection weights, and can be applied within a broader range of neural networks. Moreover, through the obtained results, it could be noted that noise will affect the exponential stability of the system. For illustration, two examples are given to show the feasibility of results.
GLOBAL EXPONENTIAL STABILITY OF CHUA'S REACTION–DIFFUSION CNN
Authors: KE YUNQUAN , MIAO CHUNFANG
Published: December 2009

In this paper, the global exponential stability of Chua's reaction–diffusion CNN system is investigated. For this system, some sufficient conditions ensuring the existence and global exponential stability of the equilibrium point is derived by using homeomorphism mapping, the property of coefficient matrix and analytical techniques. Finally, three illustrative examples are given to show the effectiveness of our results.
SOME NONROBUST BERNOULLI-SHIFT RULES
Authors: CHEN LIN , CHEN FANGYUE , JIN WEIFENG , CHEN FANGFANG , CHEN GUANRONG
Published: December 2009

In this paper, it is shown that elementary cellular automata rule 172, as a member of the Chua's robust period-1 rules and the Wolfram class I, is also a nonrobust Bernoulli-shift rule. This rule actually exhibits complex Bernoulli-shift dynamics in the bi-infinite binary sequence space. More precisely, in this paper, it is rigorously proved that rule 172 is topologically mixing and has positive topological entropy on a subsystem. Hence, rule 172 is chaotic in the sense of both Li–Yorke and Devaney. The method developed in this paper is also applicable to checking the subshifts contained in other robust period-1 rules, for example, rules 168 and 40, which also represent nonrobust Bernoulli-shift dynamics.
GENERATION AND CHARACTERIZATION OF ABSOLUTE EQUILIBRIUM OF COMPRESSIBLE FLOWS
Authors: KRSTULOVIC GIORGIO , CARTES CARLOS , BRACHET MARC , TIRAPEGUI ENRIQUE
Published: December 2009

A short review is given of recent papers on the relaxation to (incompressible) absolute equilibrium. A new algorithm to construct absolute equilibrium of spectrally truncated compressible flows is described. The algorithm uses stochastic processes based on the Clebsch representation of the velocity field to generate density and velocity fields that follow by construction the absolute equilibrium stationary probability. The new method is shown to reproduce the well-known Gaussian results in the incompressible limit. The irrotational compressible absolute equilibrium case is characterized and the distribution is shown to be non-Gaussian. The high-temperature compressible spectra are found not to obey k2 scaling. Finally, oscillating behavior in constant-pressure variable-temperature relaxation is obtained, suggesting the presence of second sound.
PARAMETRICALLY DRIVEN INSTABILITY IN QUASI-REVERSAL SYSTEMS
Authors: CLERC MARCEL G. , COULIBALY SALIYA , LAROZE DAVID
Published: December 2009

Parametric instability of quasi-reversal system — i.e. time reversible systems perturbed with injection and dissipation of energy — is studied in a unified manner. We infer and characterize an adequate amplitude equation, which is the parametrically driven damped nonlinear Schrödinger equation, corrected with higher order terms. This model exhibits rich dynamical behavior which are lost in the parametrically driven damped nonlinear Schrödinger equation such as: uniform states, fronts and coherent states. The dynamical behavior of a simple parametrically driven system, the vertically driven chain of pendula, exhibits quite good agreement with the amended amplitude equation.
1D CAHN–HILLIARD EQUATION: OSTWALD RIPENING AND MODULATED PHASE SYSTEMS
Authors: VILLAIN-GUILLOT SIMON
Published: December 2009

We use a family of stationary solutions of the Cahn–Hilliard dynamics with the aim of describing the process of coarsening during a first order phase transition. With this analytical ansatz, we can compute the characteristic time for one step of period doubling in Langer's self-similar scenario for Ostwald ripening. As an application, the same ansatz is also used to compute the thermodynamically stable period of a 1D modulated phase pattern, described by a modified Cahn–Hilliard dynamics with a long range interaction term.
LOCAL DYNAMICS OF DEFECTS IN PARAMETRICALLY EXCITED WAVES
Authors: FALCÓN CLAUDIO , FAUVE STÉPHAN
Published: December 2009

We present an experimental study on the local dynamics of parametrically excited waves at an air–water interface when defects are present in the wave pattern. The probability density function (PDF) of the local wave amplitude displays an exponential part for values close to the average amplitude and decreases sharply to zero for large amplitudes. The power spectral density (PSD) of the local amplitude fluctuations shows a power-law behavior over one decade which we relate to a regime of defect-mediated turbulence.
MULTISPECTRAL UNMIXING OF FLUORESCENCE MOLECULAR TOMOGRAPHY DATA
Authors: SIMANTIRAKI MARIA , FAVICCHIO ROSY , PSYCHARAKIS STELIOS , ZACHARAKIS GIANNIS , RIPOLL JORGE
Published: December 2009

Even though multispectral imaging is considered very significant in biological imaging, it is only commonly used in microscopy in a 2D approach. Here, we present a Fluorescence Molecular Tomography system capable of recording simultaneously tomographic data at several spectral windows, enabling multispectral tomography. 3D reconstructed data from several spectral windows is used to construct a linear unmixing algorithm for multispectral deconvolution of overlapping fluorescence signals. The method is applied on tomographic 3D fluorescence concentration maps in tissue-mimicking phantoms, yielding absolute quantification of the concentration of each individual fluorophore. Results are compared to the case when unmixing is performed in the raw 2D data instead of the reconstructed 3D concentration map, showing greater accuracy when unmixing algorithms are applied in the reconstructed data. Both the reflection and transmission geometries are considered.
QUANTITATIVE REDOX SCANNING OF TISSUE SAMPLES USING A CALIBRATION PROCEDURE
Authors: XU HE N. , WU BAOHUA , NIOKA SHOKO , CHANCE BRITTON , LI LIN Z.
Published: December 2009

The fluorescence properties of reduced nicotinamide adenine dinucleotide (NADH) and oxidized flavoproteins (Fp) including flavin adenine dinucleotide (FAD) in the respiratory chain are sensitive indicators of intracellular metabolic states and have been applied to the studies of mitochondrial function with energy-linked processes. The redox scanner, a three-dimensional (3D) low temperature imager previously developed by Chance et al., measures the in vivo metabolic properties of tissue samples by acquiring fluorescence images of NADH and Fp. The redox ratios, i.e. Fp/(Fp+NADH) and NADH/(Fp+NADH), provided a sensitive index of the mitochondrial redox state and were determined based on relative signal intensity ratios. Here we report the further development of the redox scanning technique by using a calibration method to quantify the nominal concentration of the fluorophores in tissues. The redox scanner exhibited very good linear response in the range of NADH concentration between 165–1318 μM and Fp between 90–720 μM using snap-frozen solution standards. Tissue samples such as human tumor mouse xenografts and various mouse organs were redox-scanned together with adjacent NADH and Fp standards of known concentration at liquid nitrogen temperature. The nominal NADH and Fp concentrations as well as the redox ratios in the tissue samples were quantified by normalizing the tissue NADH and Fp fluorescence signal to that of the snap-frozen solution standards. This calibration procedure allows comparing redox images obtained at different time, independent of instrument settings. The quantitative multi-slice redox images revealed heterogeneity in mitochondrial redox state in the tissues.
Fc-DIRECTED ANTIBODY CONJUGATION OF MAGNETIC NANOPARTICLES FOR ENHANCED MOLECULAR TARGETING
Authors: REZAEIPOOR ROBABEH , JOHN RENU , ADIE STEVEN G. , CHANEY ERIC J. , MARJANOVIC MARINA , OLDENBURG AMY L. , RINNE STEPHANIE A. , BOPPART STEPHEN A.
Published: December 2009

In this study, we report the fabrication of engineered iron oxide magnetic nanoparticles (MNPs) functionalized with anti-human epidermal growth factor receptor type 2 (HER2) antibody to target the tumor antigen HER2. The Fc-directed conjugation of antibodies to the MNPs aids their efficient immunospecific targeting through free Fab portions. The directional specificity of conjugation was verified on a macrophage cell line. Immunofluorescence studies on macrophages treated with functionalized MNPs and free anti-HER2 antibody revealed that the antibody molecules bind to the MNPs predominantly through their Fc portion. Different cell lines with different HER2 expression levels were used to test the specificity of our functionalized nanoprobe for molecular targeting applications. The results of cell line targeting demonstrate that these engineered MNPs are able to differentiate between cell lines with different levels of HER2 expression.
IMAGING RNA IN LIVING CELLS WITH MOLECULAR BEACONS: CURRENT PERSPECTIVES AND CHALLENGES
Authors: CHEN ANTONY K. , TSOURKAS ANDREW
Published: December 2009

There is a growing realization that cell-to-cell variations in gene expression have important biological consequences underlying phenotype diversity and cell fate. Although analytical tools for measuring gene expression, such as DNA microarrays, reverse-transcriptase PCR and in situ hybridization have been widely utilized to discover the role of genetic variations in governing cellular behavior, these methods are performed in cell lysates and/or on fixed cells, and therefore lack the ability to provide comprehensive spatial-dynamic information on gene expression. This has invoked the recent development of molecular imaging strategies capable of illuminating the distribution and dynamics of RNA molecules in living cells. In this review, we describe a class of molecular imaging probes known as molecular beacons (MBs), which have increasingly become the probe of choice for imaging RNA in living cells. In addition, we present the major challenges that can limit the ability of MBs to provide accurate measurements of RNA, and discuss efforts that have been made to overcome these challenges. It is envisioned that with continued refinement of the MB design, MBs will eventually become an indispensable tool for analyzing gene expression in biology and medicine.
FLUORESCENT IMAGES OF MITOCHONDRIAL REDOX STATES ININ SITUMOUSE HYPOXIC ISCHEMIC INTESTINES
Authors: RANJI MAHSA , NIOKA SHOKO , XU HE N. , WU BAOHUA , LI LIN Z. , JAGGARD DWIGHT L. , CHANCE BRITTON
Published: December 2009

We have imaged mitochondrial oxidation–reduction states by taking a ratio of mitochondrial fluorophores: NADH (reduced nicotinamide adenine dinucleotide) to Fp (oxidized flavoprotein). Although NADH has been investigated for tissue metabolic state in cancer and in oxygen deprived tissues, it alone is not an adequate measure of mitochondrial metabolic state since the NADH signal is altered by dependence on the number of mitochondria and by blood absorption. The redox ratio, NADH/(Fp + NADH), gives a more accurate measure of steady-state tissue metabolism since it is less dependent on mitochondrial number and it compensates effectively for hemodynamic changes. This ratio provides important diagnostic information in living tissues. In this study, the emitted fluorescence of mouse colon in situ is passed through an emission filter wheel and imaged on a CCD camera. Redox ratio images of the healthy and hypoxic mouse intestines clearly showed significant differences. Furthermore, the corrected redox ratio indicated an increase from an average value of 0.51 ± 0.10 in the healthy state to 0.92 ± 0.03 in dead tissue due to severe ischemia (N = 5). We show that the CCD imaging system is capable of displaying the metabolic differences in normal and ischemic tissues as well as quantifying the redox ratio in vivo as a marker of these changes.
MITOCHONDRIAL REDOX IMAGING FOR CANCER DIAGNOSTIC AND THERAPEUTIC STUDIES
Authors: LI LIN Z. , XU HE N. , RANJI MAHSA , NIOKA SHOKO , CHANCE BRITTON
Published: December 2009

Mitochondrial redox states provide important information about energy-linked biological processes and signaling events in tissues for various disease phenotypes including cancer. The redox scanning method developed at the Chance laboratory about 30 years ago has allowed 3D high-resolution (~50 × 50 × 10 μm3) imaging of mitochondrial redox state in tissue on the basis of the fluorescence of NADH (reduced nicotinamide adenine dinucleotide) and Fp (oxidized flavoproteins including flavin adenine dinucleotide, i.e., FAD). In this review, we illustrate its basic principles, recent technical developments, and biomedical applications to cancer diagnostic and therapeutic studies in small animal models. Recently developed calibration procedures for the redox imaging using reference standards allow quantification of nominal NADH and Fp concentrations, and the concentration-based redox ratios, e.g., Fp/(Fp+NADH) and NADH/(Fp+NADH) in tissues. This calibration facilitates the comparison of redox imaging results acquired for different metabolic states at different times and/or with different instrumental settings. A redox imager using a CCD detector has been developed to acquire 3D images faster and with a higher in-plane resolution down to 10 μm. Ex vivo imaging and in vivo imaging of tissue mitochondrial redox status have been demonstrated with the CCD imager. Applications of tissue redox imaging in small animal cancer models include metabolic imaging of glioma and myc-induced mouse mammary tumors, predicting the metastatic potentials of human melanoma and breast cancer mouse xenografts, differentiating precancerous and normal tissues, and monitoring the tumor treatment response to photodynamic therapy. Possible future directions for the development of redox imaging are also discussed.