A database of orthologous exons in primates for comparative analysis of RNA-seq data

RNA-seq technology facilitates the study of gene expression at the level of individual exons and transcripts. Moreover, RNA-seq enables unbiased comparative analysis of expression levels across species. Such analyses typically start by mapping sequenced reads to the appropriate reference genome before comparing expression levels across species. However, this comparison requires prior knowledge of orthology at the exon level. With this in mind, I constructed a database of orthologous exons across three primate species (human, chimpanzee, and rhesus macaque). The database facilitates cross-species comparative analysis of exon- and transcript-level regulation. A web application allowing for an easy database query: http://giladlab.uchicago.edu/orthoExon

On rotational solutions for elliptically excited pendulum

The author considers the planar rotational motion of the mathematical pendulum with its pivot oscillating both vertically and horizontally, so the trajectory of the pivot is an ellipse close to a circle. The analysis is based on the exact rotational solutions in the case of circular pivot trajectory and zero gravity. The conditions for existence and stability of such solutions are derived. Assuming that the amplitudes of excitations are not small while the pivot trajectory has small ellipticity the approximate solutions are found both for high and small linear damping. Comparison between approximate and numerical solutions is made for different values of the damping parameter.Comment: 16 pages, 5 figures, 1 tabl

Synchronization of Huygens' clocks and the Poincare method

We study two models of connected pendulum clocks synchronizing their oscillations, a phenomenon originally observed by Huygens. The oscillation angles are assumed to be small so that the pendulums are modeled by harmonic oscillators, clock escapements are modeled by the van der Pol terms. The mass ratio of the pendulum bobs to their casings is taken as a small parameter. Analytic conditions for existence and stability of synchronization regimes, and analytic expressions for their stable amplitudes and period corrections are derived using the Poincare theorem on existence of periodic solutions in autonomous quasi-linear systems. The anti-phase regime always exists and is stable under variation of the system parameters. The in-phase regime may exist and be stable, exist and be unstable, or not exist at all depending on parameter values. As the damping in the frame connecting the clocks is increased the in-phase stable amplitude and period are decreasing until the regime first destabilizes and then disappears. The results are most complete for the traditional three degrees of freedom model, where the clock casings and the frame are consolidated into a single mass.Comment: 23 pages, 8 figure

Self-synchronization and controlled synchronization

An attempt is made to give a general formalism for synchronization in dynamical systems encompassing most of the known definitions and applications. The proposed set-up describes synchronization of interconnected systems with respect to a set of functionals and captures peculiarities of both self-synchronization and controlled synchronization. Various illustrative examples are give

Motion of Gas Bubbles and Rigid Particles in Vibrating Fluid-Filled Volumes

AbstractMotion of gas bubbles and rigid particles in an oscillating fluid is of fundamental interest for the theory of various widely used technological processes, in particular, for the flotation process. Therefore, many studies have been concerned with this problem, some of those being undertaken by eminent scientists. The main remarkable effects are heavy particles rising and light particles (gas bubbles) sinking in vibrating fluid's volume, and asynchronous self-induced vibration of emerging air cushion.In the authors’ recent papers, the problem has been solved by means of the concept of vibrational mechanics and the method of direct separation of motions; experimental studies have been also conducted. The present paper generalizes and supplements these studies. A special attention is given to the analysis of motion of bubbles and light rigid particles, whose sizes are small in comparison with the amplitude of external excitation; motion of larger (compressible) bubbles is also considered in the paper. It is shown that at certain parameters of external excitation such particles and bubbles will sink in the fluid, corresponding conditions are formulated

Revisiting the models of vibration screening process

This talk presents two approaches for modeling of the vibration screening process. The first approach is analytical. It models the screening process as a diffusion of undersize fraction taking into account the special term for vibration separation (the Brazil nut effect). The talk provides a solution of the corresponding partial differential equation. The solution in turn allows estimation of the screening performance dependence on both deterministic and stochastic factors as well as evaluation of the factors dominance conditions. The talk presents simple evaluation formulae for the screening process performance. The second approach is based on a simulation model. The model deals with monolayer dynamics. Embodying traditional concepts of vibration transportation, the approach introduces some novel techniques of evaluation of the effect of the granular particles shape. Taking into account the particle shape factor may significantly improve the modeling precision for nonspherical particles

Comparative metabolomics in primates reveals the effects of diet and gene regulatory variation on metabolic divergence.

Human diets differ from those of non-human primates. Among few obvious differences, humans consume more meat than most non-human primates and regularly cook their food. It is hypothesized that a dietary shift during human evolution has been accompanied by molecular adaptations in metabolic pathways. Consistent with this notion, comparative studies of gene expression levels in primates have found that the regulation of genes with metabolic functions tend to evolve rapidly in the human lineage. The metabolic consequences of these regulatory differences, however, remained unknown. To address this gap, we performed a comparative study using a combination of gene expression and metabolomic profiling in livers from humans, chimpanzees, and rhesus macaques. We show that dietary differences between species have a strong effect on metabolic concentrations. In addition, we found that differences in metabolic concentration across species are correlated with inter-species differences in the expression of the corresponding enzymes, which control the same metabolic reaction. We identified a number of metabolic compounds with lineage-specific profiles, including examples of human-species metabolic differences that may be directly related to dietary differences

Rare events – rare attractors; formalization and examples

Analogy between attractors in nonlinear dynamics, called “rare attractors” by M.V. Zakrzhevsky and his colleagues [1] and emergencies, such as natural and technogenic catastrophes as well as downfalls caused by risky economic policies and strategies has been discussed. Examples of rare but technically significant attractors in nonlinear dynamics have been give

Extension of the Method of Direct Separation of Motions for Problems of Oscillating Action on Dynamical Systems

AbstractA general approach to study oscillating action on nonlinear dynamical systems is developed. It implies a transition from initial governing equations of motion to much more simple equations describing only the main slow component of motions (the vibro-transformed dynamics equations). The approach is named as the Oscillatory Strobodynamics, since motions are perceived as under a stroboscopic light. The vibro-transformed dynamics equations comprise terms that represent the averaged effect of the oscillating action. The method of direct separation of motions (MDSM) appears to be an efficient and simple tool to derive these equations. A modification of the method applicable to study problems that do not imply restrictions on the spectrum of excitation frequencies is proposed. It allows also to abandon other restrictions usually introduced when employing the classical asymptotic methods, e.g. the requirement for the involved nonlinearities to be weak.Several relevant examples from Mechanics, Physics, Chemistry, and Biophysics are considered by means of the conventional MDSM and, in more details, by the modified MDSM, illustrating the efficiency the methods

Thermodynamic limit of the first-order phase transition in the Kuramoto model

In the Kuramoto model, a uniform distribution of the natural frequencies leads to a first-order (i.e., discontinuous) phase transition from incoherence to synchronization, at the critical coupling parameter $K_c$. We obtain the asymptotic dependence of the order parameter above criticality: $r-r_c \propto (K-K_c)^{2/3}$. For a finite population, we demonstrate that the population size $N$ may be included into a self-consistency equation relating $r$ and $K$ in the synchronized state. We analyze the convergence to the thermodynamic limit of two alternative schemes to set the natural frequencies. Other frequency distributions different from the uniform one are also considered.Comment: 6 page