Mixed mode pattern in Doublefoot mutant mouse limb - Turing reaction-diffusion model on a growing domain during limb development

It has been suggested that the Turing reaction–diffusion model on a growing domain is applicable during limb development, but experimental evidence for this hypothesis has been lacking. In the present study, we found that in Doublefoot mutant mice, which have supernumerary digits due to overexpansion of the limb bud, thin digits exist in the proximal part of the hand or foot, which sometimes become normal abruptly at the distal part. We found that exactly the same behaviour can be reproduced by numerical simulation of the simplest possible Turing reaction–diffusion model on a growing domain. We analytically showed that this pattern is related to the saturation of activator kinetics in the model. Furthermore, we showed that a number of experimentally observed phenomena in this system can be explained within the context of a Turing reaction–diffusion model. Finally, we make some experimentally testable predictions

The role of intolerance of uncertainty in classical threat conditioning::Recent developments and directions for future research

Intolerance of uncertainty (IU), the tendency to find uncertainty aversive, is an important transdiagnostic dimension in mental health disorders. Over the last decade, there has been a surge of research on the role of IU in classical threat conditioning procedures, which serve as analogues to the development, treatment, and relapse of anxiety, obsessive-compulsive, and trauma- and stressor-related disorders. This review provides an overview of the existing literature on IU in classical threat conditioning procedures. The review integrates findings based on the shared or discrete parameters of uncertainty embedded within classical threat conditioning procedures. Under periods of unexpected uncertainty, where threat and safety contingencies change, high IU, over other self-reported measures of anxiety, is specifically associated with poorer threat extinction learning and retention, as well as overgeneralisation. Under periods of estimation and expected uncertainty, where the parameters of uncertainty are being learned or have been learned, such as threat acquisition training and avoidance learning, the findings are mixed for IU. These findings provide evidence that individual differences in IU play a significant role in maintaining learned fear and anxiety, particularly under volatile environments. Recommendations for future research are outlined, with discussion focusing on how parameters of uncertainty can be better defined to capture how IU is involved in the maintenance of learned fear and anxiety. Such work will be crucial for understanding the role of IU in neurobiological models of uncertainty-based maintenance of fear and anxiety and inform translational work aiming to improve the diagnosis and treatment of relevant psychopathology.</p

Microscopic expressions for the thermodynamic temperature

We show that arbitrary phase space vector fields can be used to generate phase functions whose ensemble averages give the thermodynamic temperature. We describe conditions for the validity of these functions in periodic boundary systems and the Molecular Dynamics (MD) ensemble, and test them with a short-ranged potential MD simulation.Comment: 21 pages, 2 figures, Revtex. Submitted to Phys. Rev.

Lyapunov instability for a periodic Lorentz gas thermostated by deterministic scattering

In recent work a deterministic and time-reversible boundary thermostat called thermostating by deterministic scattering has been introduced for the periodic Lorentz gas [Phys. Rev. Lett. {\bf 84}, 4268 (2000)]. Here we assess the nonlinear properties of this new dynamical system by numerically calculating its Lyapunov exponents. Based on a revised method for computing Lyapunov exponents, which employs periodic orthonormalization with a constraint, we present results for the Lyapunov exponents and related quantities in equilibrium and nonequilibrium. Finally, we check whether we obtain the same relations between quantities characterizing the microscopic chaotic dynamics and quantities characterizing macroscopic transport as obtained for conventional deterministic and time-reversible bulk thermostats.Comment: 18 pages (revtex), 7 figures (postscript

Stability ordering of cycle expansions

We propose that cycle expansions be ordered with respect to stability rather than orbit length for many chaotic systems, particularly those exhibiting crises. This is illustrated with the strong field Lorentz gas, where we obtain significant improvements over traditional approaches.Comment: Revtex, 5 incorporated figures, total size 200

A systematically coarse-grained model for DNA, and its predictions for persistence length, stacking, twist, and chirality

We introduce a coarse-grained model of DNA with bases modeled as rigid-body ellipsoids to capture their anisotropic stereochemistry. Interaction potentials are all physicochemical and generated from all-atom simulation/parameterization with minimal phenomenology. Persistence length, degree of stacking, and twist are studied by molecular dynamics simulation as functions of temperature, salt concentration, sequence, interaction potential strength, and local position along the chain, for both single- and double-stranded DNA where appropriate. The model of DNA shows several phase transitions and crossover regimes in addition to dehybridization, including unstacking, untwisting, and collapse which affect mechanical properties such as rigidity and persistence length. The model also exhibits chirality with a stable right-handed and metastable left-handed helix.Comment: 30 pages, 20 figures, Supplementary Material available at http://www.physics.ubc.ca/~steve/publications.htm

Integration through transients for Brownian particles under steady shear

Starting from the microscopic Smoluchowski equation for interacting Brownian particles under stationary shearing, exact expressions for shear-dependent steady-state averages, correlation and structure functions, and susceptibilities are obtained, which take the form of generalized Green-Kubo relations. They require integration of transient dynamics. Equations of motion with memory effects for transient density fluctuation functions are derived from the same microscopic starting point. We argue that the derived formal expressions provide useful starting points for approximations in order to describe the stationary non-equilibrium state of steadily sheared dense colloidal dispersions.Comment: 17 pages, Submitted to J. Phys.: Condens. Matter; revised version with minor correction

The impact of intolerance of uncertainty and cognitive behavioural instructions on safety learning

Background Difficulty updating threat associations to safe associations has been observed in individuals who score high in self-reported Intolerance of Uncertainty (IU). Here we sought to determine whether an instruction based on fundamental principles of Cognitive Behavioural Therapy could promote safety learning in individuals with higher levels of IU, whilst controlling for self-reported trait anxiety (STICSA). Methods We measured skin conductance response, pupil dilation and expectancy ratings during an associative threat learning task in which participants either received a cognitive behavioural instruction or no instruction prior to threat extinction (n = 92). Results Analyses revealed that both self-reported IU and STICSA similarly predicted differences in skin conductance response. Only individuals with lower IU/STICSA in the cognitive behavioural instruction condition displayed successful safety learning via skin conductance response. Conclusions These initial results provide some insight into how simple cognitive behavioural instructions combined with exposure are applied differently in individuals with varying levels of self-reported anxiety. The results further our understanding of the role of basic cognitive behavioural principles and self-reported anxiety in safety learning

The detection of tethered and rising bubbles using multiple acoustic techniques

There exists a range of acoustic techniques for characterizing bubble populations within liquids. Each technique has limitations, and complete characterization of a population requires the sequential or simultaneous use of several, so that the limitations of each find compensation in the others. Here, nine techniques are deployed using one experimental rig, and compared to determine how accurately and rapidly they can characterize given bubble populations. These are, specifically (i) two stationary bubbles attached to a wire; and (ii) injected, rising bubble