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Weakly nonlinear analysis of impulsively-forced Faraday waves.

Parametrically-excited surface waves, forced by a repeating sequence of delta-function impulses, are considered within the framework of the Zhang-Viñals model [W. Zhang and J. Viñals, J. Fluid Mech. 336, 301 (1997)]. With impulsive forcing, the linear stability analysis can be carried out exactly and leads to an implicit equation for the neutral stability curves. As noted previously [J. Bechhoefer and B. Johnson, Am. J. Phys. 64, 1482 (1996)], in the simplest case of N=2 equally-spaced impulses per period (which alternate up and down) there are only subharmonic modes of instability. The familiar situation of alternating subharmonic and harmonic resonance tongues emerges only if an asymmetry in the spacing between the impulses is introduced. We extend the linear analysis for N=2 impulses per period to the weakly nonlinear regime, where we determine the leading order nonlinear saturation of one-dimensional standing waves as a function of forcing strength. Specifically, an analytic expression for the cubic Landau coefficient in the bifurcation equation is derived as a function of the dimensionless spacing between the two impulses and the fluid parameters that appear in the Zhang-Viñals model. As the capillary parameter is varied, one finds a parameter regime of wave amplitude suppression, which is due to a familiar 1:2 spatiotemporal resonance between the subharmonic mode of instability and a damped harmonic mode. This resonance occurs for impulsive forcing even when harmonic resonance tongues are absent from the neutral stability curves. The strength of this resonance feature can be tuned by varying the spacing between the impulses. This finding is interpreted in terms of a recent symmetry-based analysis of multifrequency forced Faraday waves [J. Porter, C. M. Topaz, and M. Silber, Phys. Lett. 93, 034502 (2004); C. M. Topaz, J. Porter, and M. Silber, Phys. Rev. E 70, 066206 (2004)].

Journal Article↗

Nonspecific binding of the OR repressors CI and Cro of bacteriophage lambda.

We estimate the Gibbs free energy for nonspecific binding (DeltaGNSB) to the Escherichia coli DNA for two regulatory proteins of the lambda phage, CI and Cro. By means of a statistical-mechanical approach, we calculate the cI and cro activities associated with the operator OR of an introduced lambda phage genome (prophage). In this statistical model we apply in vitro-measured binding free energies to fit in vivo experimental data for cI and cro activities, respectively, where DeltaGNSB is introduced as a free (fitting) parameter. Without nonspecific binding included in the model, the quality of the description is fairly poor, whereas data are nicely correlating with our model with nonspecific binding included over the entire data range. The obtained values of DeltaGNSB are -4.1+/-0.9 kcal/mol, for CI, and -4.2+/-0.8 kcal/mol, for Cro. In particular, in a lysogen (approximately 250 CI monomers per cell) we conclude that 86% of the total CI in the cell is nonspecifically bound, leaving on average around 10 CI dimers freely available in the E. coli cytoplasma. These findings corroborate the view that due to low free cellular particle numbers a dynamical analysis of genetic regulation at OR and comparable systems should include a stochastic component. In addition, we perform a stability analysis of the OR system in the presence of nonspecific binding.

Bacteriophage lambda↗

Characterization of the endogenous plasmid from Pseudomonas alcaligenes NCIB 9867: DNA sequence and mechanism of transfer.

The endogenous plasmid pRA2 from Pseudomonas alcaligenes NCIB 9867 was determined to have 32,743 bp with a G+C content of 59.8%. Sequence analysis predicted a total of 29 open reading frames, with approximately half of them contributing towards the functions of plasmid replication, mobilization, and stability. The Pac25I restriction-modification system and two mobile elements, Tn5563 and IS1633, were physically localized. An additional eight open reading frames with unknown functions were also detected. pRA2 was genetically tagged with the OmegaStr(r)/Spc(r) gene cassette by homologous recombination. Intrastrain transfer of pRA2-encoded genetic markers between isogenic mutants of P. alcaligenes NCIB 9867 were observed at high frequencies (2.4 x 10(-4) per donor). This transfer was determined to be mediated by a natural transformation process that required cell-cell contact and was completely sensitive to DNase I (1 mg/ml). Efficient transformation was also observed when pRA2 DNA was applied directly onto the cells, while transformation with foreign plasmid DNAs was not observed. pRA2 could be conjugally transferred into Pseudomonas putida RA713 and KT2440 recipients only when plasmid RK2/RP4 transfer functions were provided in trans. Plasmid stability analysis demonstrated that pRA2 could be stably maintained in its original host, P. alcaligenes NCIB 9867, as well as in P. putida RA713 after 100 generations of nonselective growth. Disruption of the pRA2 pac25I restriction endonuclease gene did not alter plasmid stability, while the pRA2 minireplicon exhibited only partial stability. This indicates that other pRA2-encoded determinants could have significant roles in influencing plasmid stability.

Bacterial Proteins↗

Instabilities in a free granular fluid described by the Enskog equation.

A linear stability analysis of the hydrodynamic equations with respect to the homogeneous cooling state is carried out to identify the conditions for stability as functions of the wave vector, the dissipation, and the density. In contrast to previous studies, this description is based on the results derived from the Enskog equation for inelastic hard spheres [V. Garzó and J. W. Dufty, Phys. Rev. E 59, 5895 (1999)], which takes into account the dependence of the transport coefficients on dissipation. As expected, linear stability shows two transversal (shear) modes and a longitudinal "heat") mode to be unstable with respect to long enough wavelength excitations. Comparison with previous results (which neglect the influence of dissipation on transport) shows quantitative discrepancies for strong dissipation.

Journal Article↗

Induction of the urokinase plasminogen activator system by oncostatin M promotes endothelial migration.

Oncostatin M (OSM) is an inflammatory cytokine produced by activated macrophages and T-lymphocytes. We have previously demonstrated that OSM-induced endothelial cell migration, unlike endothelial cell proliferation and spindle formation, is independent of basic fibroblast growth factor expression (Wijelath et al. [1997] J. Cell. Sci. 110:871-879). To better understand the mechanism of OSM-induced endothelial cell migration, this study examined the potential role of the plasminogen activator system in promoting OSM mediated endothelial cell migration. OSM stimulated increased mRNA levels of urokinase-plasminogen activator (uPA) and urokinase-plasminogen activator receptor (uPAR) in a time and dose-dependent manner. Transcriptional run-off and mRNA stability analysis demonstrated that the increase in uPA and uPAR mRNA levels was due to both increased gene transcription and mRNA stability. The increase in mRNA correlated with increased protein levels of both uPA and uPAR. This increase was reflected in elevated levels of membrane-bound plasmin activity. OSM-induced endothelial cell migration was only partially dependent on plasmin activity since incubating endothelial cells without plasminogen or, in the presence of aprotinin, resulted in suppression of endothelial cell migration, indicating that OSM promoted endothelial cell migration through both a plasmin-dependent and -independent mechanism. Our results imply a role for OSM in promoting endothelial cell migration via a plasmin-dependent pathway and a uPAR-mediated pathway. Together, these and other recent studies support a role for OSM in modulating the different phases of angiogenesis.

Cells, Cultured↗

Modelling epidemics with variable contact rates.

In this paper we look at models for epidemics where the contact rate is a monotone increasing function of the population density. The background death rate also depends on the population density. We first examine the case of a constant contact rate (motivated by AIDS) and here obtain some global stability results. We consider an SIR model where a typical individual starts off susceptible, at some stage catches the disease and after a short infectious period becomes permanently immune. We also look at the effects of vaccination. First we perform an equilibrium and local stability analysis. Next we reformulate the model in terms of the proportions of individuals susceptible, infected, and immune to obtain some global stability results. We find three possible equilibrium values: one where the population is extinct, one where the disease has died out but the population has not died out, and a unique equilibrium where disease is present. We determine conditions for global stability of these equilibria. For certain parameter values none of these equilibria are locally stable. In this case there is a formal proportional endemic equilibrium with a strictly positive proportion of infected individuals. We expect the population size to die out but the proportions of susceptible, infected, and immune individuals to tend to this endemic proportional equilibrium. We find two critical contact rates which help determine the behaviour of the system. Next we extend some of these results to the case where the contact rate depends on population density. Finally the paper examines these results further using numerical methods.

Acquired Immunodeficiency Syndrome↗

Pattern formation in crystal growth under parabolic shear flow.

Morphological instability of the solid-liquid interface occurring in a crystal growing from an undercooled thin liquid bounded on one side by a free surface and flowing down inclined plane, is investigated by a linear stability analysis under shear flow. It is found that restoring forces due to gravity and surface tension is an important factor for stabilization of the solid-liquid interface on long length scales. This is a stabilizing effect different from the Gibbs-Thomson effect. A particular long wavelength mode of about 1 cm of wavy pattern, observed on the surface of icicles covered with a thin layer of flowing water is obtained from the dispersion relation, including the effect of flow and restoring forces.

Journal Article↗

Instability of solitary wave solutions to long-wavelength transverse perturbationsin the generalized Kadomtsev-Petviashvili equation with negative dispersion.

The present paper is a more detailed article of the previously published Letter [Phys. Rev. Lett. 84, 3065 (2000)]], which discovered the transversely unstable solitary wave solutions of the generalized Kadomtsev-Petviashvili (GKP) equation with negative dispersion. In addition to detailed explanation of stability analysis to long-wavelength transverse perturbations, numerical calculation of the GKP equation is carried out here to study the transverse stability to perturbations of finite wavelength. The numerical results show that there is a short-wavelength cutoff to the transverse instability. Moreover, we reveal the existence of transversely unstable solitons.

Journal Article↗

Evaluation of a noninvasive method for cardiac output measurement in critical care patients.

OBJECTIVE: Thermodilution (TD) is the gold standard to monitor cardiac output (CO) in critical care. However, there is concern about the safety of right-ventricular catheterization. The CO(2) rebreathing technique allows noninvasive CO determination by means of the indirect Fick principle. Our objectives were: (a) to assess the accuracy of a new system of CO measurement using the CO(2) partial rebreathing method (PRCO); (b) to evaluate whether the PRCO itself may induce changes in CO. DESIGN AND SETTING: Prospective study in the intensive care department in a university-affiliated hospital. PATIENTS: Twenty-two mechanically ventilated critically ill patients. INTERVENTIONS: CO measured simultaneously by PRCO and TDCO. MEASUREMENTS AND RESULTS: PRCO and TDCO values were compared by concordance analysis. Stability of cardiac output during PRCO was evaluated by comparing the TDCO measurements before, during, and after the partial rebreathing period using analysis of variance. From a total of 79 valid sets of measurements, bias and precision was calculated at -0.18+/-1.39 l/min. The concordance analysis of lower and intermediate CO values (<7 l/min) yielded a bias and precision calculation of -0.07+/-0.91 l/min. No changes in hemodynamics were observed during the partial rebreathing period. CONCLUSIONS: The noninvasive partial CO(2) rebreathing technique may be an alternative method for CO determination in mechanically ventilated critically ill patients. The rebreathing maneuver alone does not induce changes in CO.

Breath Tests↗

To each genotype a separate strategy--a dynamic game theory model of a general diploid system.

A dynamic game theory model is presented for a diploid system in which each genotype corresponds to a different strategy. The population mates randomly and the strategy, which is determined by a single locus, is expressed only in the male. A general analytic solution for any number of alleles does not appear to be possible, but the cases of two and three alleles are treated in detail. A stability analysis applicable to any number of alleles is presented, so that any equilibria located by numerical methods can be checked for local stability. Computer programs for doing all of these calculations are available from the author.

Alleles↗

Effects of time-delayed feedback on chaotic oscillators.

We study the effects of time-delayed feedback on chaotic systems where the delay time is both fixed (static case) and varying (dynamic case) in time. For the static case, typical phase coherent and incoherent chaotic oscillators are investigated. Detailed phase diagrams are investigated in the parameter space of feedback gain ( K ) and delay time ( tau ). Linear stability analysis, by assuming the time-delayed perturbation, varies as e(lambdat) where lambda is the eigenvalue, gives the boundaries of the stability islands and critical feedback gains ( K(c) ) for both Rössler oscillators and Lorenz oscillators. We also found that the stability island are found when the delay time is about tau= (n+ 1 / 2 ) T , where n is an integer and T is the average period of the chaotic oscillator. It is shown that these analytical predictions agree well with the numerical results. For the dynamic case, we investigate Rössler oscillator with periodically modulated delay time. Stability regimes are found for parameter space of feedback gain and modulation frequency in which it was impossible to be stabilized for a fixed delay time. We also trace the detailed routes to the stability near the island boundaries for both cases by investigating bifurcation diagrams.

Journal Article↗

Surface stability and immunogenicity of the human immunodeficiency virus envelope glycoprotein: role of the cytoplasmic domain.

The effects of two functional domains, the membrane-proximal YXXPhi motif and the membrane-distal inhibitory sequence in the long cytoplasmic tail of the human immunodeficiency virus type 1 (HIV-1) envelope protein (Env), on immunogenicity of the envelope protein were investigated. Genes with codons optimized for mammalian expression were synthesized for the HIV 89.6 Env and a truncated Env with 50 amino acids in the cytoplasmic domain to delete the membrane distal inhibitory sequence for surface expression. Additional genes were generated in which the tyrosine residue in the YXXPhi motif was changed into a serine. Pulse-chase radioactive labeling and immunoprecipitation studies indicated that both domains can mediate endocytosis of the HIV Env, and removal of both domains is required to enhance HIV Env protein surface stability. Analysis of immune responses induced by DNA immunization of mice showed that the DNA construct for the mutant Env exhibiting enhanced surface stability induced significantly higher levels of antibody responses against the HIV Env protein. Our results suggest that the HIV Env cytoplasmic domain may play important roles in virus infection and pathogenesis by modulating its immunogenicity.

Amino Acid Motifs↗

Bifurcation analysis of the travelling waveform of FitzHugh-Nagumo nerve conduction model equation.

The FitzHugh-Nagumo model for travelling wave type neuron excitation is studied in detail. Carrying out a linear stability analysis near the equilibrium point, we bring out various interesting bifurcations which the system admits when a specific Z(2) symmetry is present and when it is not. Based on a center manifold reduction and normal form analysis, the Hopf normal form is deduced. The condition for the onset of limit cycle oscillations is found to agree well with the numerical results. We further demonstrate numerically that the system admits a period doubling route to chaos both in the presence as well as in the absence of constant external stimuli. (c) 1997 American Institute of Physics.

Journal Article↗

Phylogenetic analysis of partial sequences of elongation factor 1alpha identifies major groups of lice (Insecta: Phthiraptera).

As a first attempt to use molecular data to resolve the relationships between the four suborders of lice and within the suborder Ischnocera, we sequenced a 347-bp fragment of the elongation factor 1alpha gene of 127 lice (Insecta: Phthiraptera) as well as outgroup taxa from the order Psocoptera. A number of well-supported monophyletic groups were found but the relationships among many of these groups could not be resolved. While it is probable that multiple substitutions at high divergences and ancient radiation over a short period of time have contributed to the problem, we attribute most of this lack of resolution to the high ratio of taxa to characters. Nevertheless, the sequence data unequivocally support a number of important relationships that are at variance with the conclusions of morphological taxonomy. These include the sister group relationship of Chelopistes and Oxylipeurus, two lice occupying different ecological niches on the same host, which have previously been assigned to different families. These results provide evidence in support of the hypothesis that lice have speciated in situ on the host in response to niche specialization and that this has given rise to convergent morphologies in the lice of different host groups which share similar ecological niches. We discuss our attempts to overcome the limitations of this large data set, including the use of leaf stability analysis, a new method for analyzing the stability of taxa in a phylogenetic tree, and examine a number of hypotheses of relationships based on both traditional taxonomy and host associations.

Animals↗

Theoretical and numerical study of a bone remodeling model: the effect of osteocyte cells distribution.

It is well argued that osteocytes are mechanosensory cells and are involved in the regulation of bone remodeling. In previous works, the predictions from a simulation model have suggested that both the influencing distance of osteocytes and the magnitude of the mechanical loads determine the thickness of trabeculae whereas the number of osteocytes primarily affects the rate of bone remodeling. The question that remains not completely answered is: for the same number of osteocytes, what is the effect of different distributions on the remodeling process? Based on a particular regulatory bone remodeling model, the question is addressed, in part, by performing a stability analysis in connection with numerical simulations. The results allow us to demonstrate that, on one hand, we cannot reach a conclusion about the stability of the model for a nonuniform osteocyte distribution. This implies that there is no relationship between the different parameters conveying the stability of the model. On the other hand, we show that the osteocyte cell distribution has a significant influence on the bone morphology, which seems to be confirmed by simulations with real data obtained from rat tibia.

Animals↗

Generalized neural networks for spectral analysis: dynamics and Liapunov functions.

This paper analyzes local and global behavior of several dynamical systems which generalize some artificial neural network (ANN) semilinear models originally designed for principal component analysis (PCA) in the characterization of random vectors. These systems implicitly performed the spectral analysis of correlation (i.e. symmetric positive definite) matrices. Here, the proposed generalizations cover both nonsymmetric matrices as well as fully nonlinear models. Local stability analysis is performed via linearization and global behavior is analyzed by constructing several Liapunov functions.

Algorithms↗

Rayleigh-Benard convection in a vertically oscillated fluid layer

We report on the first quantitative observations of convection in a fluid layer driven by both heating from below and vertical sinusoidal oscillation. Just above onset, convection patterns are modulated either harmonically or subharmonically to the drive frequency. Single-frequency patterns exhibit nearly solid-body rotations with harmonic and subharmonic states always rotating in opposite directions. Flows with both harmonic and subharmonic responses are found near a codimension-two point, yielding novel coexisting patterns with symmetries not found in either single-frequency states. Predictions from linear stability analysis of the onset Rayleigh and wave numbers compare well with experiment, and phase boundaries for coexisting patterns track single-frequency marginal stability curves.

Journal Article↗

Estimation of the shelf-life of drugs with mixed effects models.

This paper proposes a normal mixed effects model for stability analysis. An EM algorithm is developed to compute the maximum likelihood estimates of regression coefficients of the fixed effects and random effects, and variance components. The likelihood ratio test is used for the preliminary testing of batch-to-batch variation. An example from a marketing stability study is given to illustrate the proposed procedure.

Algorithms↗