VisGenome: visualization of single and comparative genome representations

VisGenome visualizes single and comparative representations for the rat, the mouse and the human chromosomes at different levels of detail. The tool offers smooth zooming and panning which is more flexible than seen in other browsers. It presents information available in Ensembl for single chromosomes, as well as homologies (orthologue predictions including ortholog one2one, apparent ortholog one2one, ortholog many2many) for any two chromosomes from different species. The application can query supporting data from Ensembl by invoking a link in a browser

Granular Flow in a Vertically Vibrating Hopper

The behavior of the flow of glass spheres in a vertically vibrating hopper is examined. A two-dimensional hopper is mounted on a shaker that provides sinusoidal, vertical vibrations. Both the frequency and amplitude of the vibrations are adjustable. Hopper discharge rates and flow patterns are measured as the acceleration amplitude of the vibrations is increased from 0 to 4g's. Comparisons are made with unvibrated hopper flows and with a two-dimensional discrete element simulation model

Integrated maneuvering and life support system simulation Final report

Integrated maneuvering and life support system simulatio

Local measurements of velocity fluctuations and diffusion coefficients for a granular material flow

Measurements were made of two components of the average and fluctuating velocities, and of the local self-diffusion coefficients in a flow of granular material. The experiments were performed in a 1 m-high vertical channel with roughened sidewalls and with polished glass plates at the front and the back to create a two-dimensional flow. The particles used were glass spheres with a nominal diameter of 3 mm. The flows were high density and were characterized by the presence of long-duration frictional contacts between particles. The velocity measurements indicated that the flows consisted of a central uniform regime and a shear regime close to the walls. The fluctuating velocities in the transverse direction increased in magnitude from the centre towards the walls. A similar variation was not observed for the streamwise fluctuations. The self-diffusion coefficients showed a significant dependence on the fluctuating velocities and the shear rate. The velocity fluctuations were highly anistropic with the streamwise components being 2 to 2.5 times the transverse components. The self-diffusion coefficients for the streamwise direction were an order-of-magnitude higher than those for the transverse direction. The surface roughness of the particles led to a decrease in the self-diffusion coefficients

Revisiting the 1954 Suspension Experiments of R. A.Bagnold

In 1954 R. A. Bagnold published his seminal findings on the rheological properties of a liquid-solid suspension. Although this work has been cited extensively over the last fifty years, there has not been a critical review of the experiments. The purpose of this study is to examine the work and to suggest an alternative reason for the experimental findings. The concentric cylinder rheometer was designed to measure simultaneously the shear and normal forces for a wide range of solid concentrations, fluid viscosities and shear rates. As presented by Bagnold, the analysis and experiments demonstrated that the shear and normal forces depended linearly on the shear rate in the 'macroviscous' regime; as the grain-to-grain interactions increased in the 'grain-inertia' regime, the stresses depended on the square of the shear rate and were independent of the fluid viscosity. These results, however, appear to be dictated by the design of the experimental facility. In Bagnold's experiments, the height (h) of the rheometer was relatively short compared to the spacing (t) between the rotating outer and stationary inner cylinder (h/t=4.6). Since the top and bottom end plates rotated with the outer cylinder, the flow contained two axisymmetric counter-rotating cells in which flow moved outward along the end plates and inward through the central region of the annulus. At higher Reynolds numbers, these cells contributed significantly to the measured torque, as demonstrated by comparing Bagnold's pure-fluid measurements with studies on laminar-to-turbulent transitions that pre-date the 1954 study. By accounting for the torque along the end walls, Bagnold's shear stress measurements can be estimated by modelling the liquid-solid mixture as a Newtonian fluid with a corrected viscosity that depends on the solids concentration. An analysis of the normal stress measurements was problematic because the gross measurements were not reported and could not be obtained

Diversity in parasitic nematode genomes: the microRNAs of Brugia pahangi and Haemonchus contortus are largely novel

<b>BACKGROUND:</b> MicroRNAs (miRNAs) play key roles in regulating post-transcriptional gene expression and are essential for development in the free-living nematode Caenorhabditis elegans and in higher organisms. Whether microRNAs are involved in regulating developmental programs of parasitic nematodes is currently unknown. Here we describe the the miRNA repertoire of two important parasitic nematodes as an essential first step in addressing this question. <b>RESULTS:</b> The small RNAs from larval and adult stages of two parasitic species, Brugia pahangi and Haemonchus contortus, were identified using deep-sequencing and bioinformatic approaches. Comparative analysis to known miRNA sequences reveals that the majority of these miRNAs are novel. Some novel miRNAs are abundantly expressed and display developmental regulation, suggesting important functional roles. Despite the lack of conservation in the miRNA repertoire, genomic positioning of certain miRNAs within or close to specific coding genes is remarkably conserved across diverse species, indicating selection for these associations. Endogenous small-interfering RNAs and Piwi-interacting (pi)RNAs, which regulate gene and transposon expression, were also identified. piRNAs are expressed in adult stage H. contortus, supporting a conserved role in germline maintenance in some parasitic nematodes. <b>CONCLUSIONS:</b> This in-depth comparative analysis of nematode miRNAs reveals the high level of divergence across species and identifies novel sequences potentially involved in development. Expression of novel miRNAs may reflect adaptations to different environments and lifestyles. Our findings provide a detailed foundation for further study of the evolution and function of miRNAs within nematodes and for identifying potential targets for intervention

Noise sustained propagation: Local versus global noise

We expand on prior results on noise supported signal propagation in arrays of coupled bistable elements. We present and compare experimental and numerical results for kink propagation under the influence of local and global fluctuations. As demonstrated previously for local noise, an optimum range of global noise power exists for which the medium acts as a reliable transmission ``channel''. We discuss implications for propagation failure in a model of cardiac tissue and present a general theoretical framework based on discrete kink statistics. Valid for generic bistable chains, the theory captures the essential features ob served in our experiments and numerical simulations.Comment: 1 latex file 20 pages, 9 figures. Accepted for publication in Physical Review

Order for materials, 6 October 1870

https://egrove.olemiss.edu/aldrichdocs/1405/thumbnail.jp

Parametric Feedback Resonance in Chaotic Systems

If one changes the control parameter of a chaotic system proportionally to the distance between an arbitrary point on the strange attractor and the actual trajectory, the lifetime τ of the most stable unstable periodic orbit in the vicinity of this point starts to diverge with a power law. The volume in parameter space where τ becomes infinite is finite and from its nonfractal boundaries one can determine directly the local Liapunov exponents. The experimental applicability of the method is demonstrated for two coupled diode resonators

Effects of vertical vibration on hopper flows of granular material

The discharge of granular material from a hopper subject to vertical sinusoidal oscillations was investigated using experiments and discrete element computer simulations. With the hopper exit closed, side-wall convection cells are observed, oriented such that particles move up along the inclined walls of the hopper and down at the center line. The convection cells are a result of the granular bed dilation during free fall and the subsequent interaction with the hopper walls. The mass discharge rate for a vibrating hopper scaled by the discharge rate without vibration reaches a maximum value at a dimensionless velocity amplitude just greater than 1. Further increases in the velocity decrease the discharge rate. The decrease occurs due to a decrease in the bulk density of the discharging material when vibration is applied