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

Viscous coupling of shear-free turbulence across nearly flat fluid interfaces

The interactions between shear-free turbulence in two regions (denoted as + and − on either side of a nearly flat horizontal interface are shown here to be controlled by several mechanisms, which depend on the magnitudes of the ratios of the densities, ρ+/ρ−, and kinematic viscosities of the fluids, μ+/μ−, and the root mean square (r.m.s.) velocities of the turbulence, u0+/u0−, above and below the interface. This study focuses on gas–liquid interfaces so that ρ+/ρ− ≪ 1 and also on where turbulence is generated either above or below the interface so that u0+/u0− is either very large or very small. It is assumed that vertical buoyancy forces across the interface are much larger than internal forces so that the interface is nearly flat, and coupling between turbulence on either side of the interface is determined by viscous stresses. A formal linearized rapid-distortion analysis with viscous effects is developed by extending the previous study by Hunt & Graham (J. Fluid Mech., vol. 84, 1978, pp. 209–235) of shear-free turbulence near rigid plane boundaries. The physical processes accounted for in our model include both the blocking effect of the interface on normal components of the turbulence and the viscous coupling of the horizontal field across thin interfacial viscous boundary layers. The horizontal divergence in the perturbation velocity field in the viscous layer drives weak inviscid irrotational velocity fluctuations outside the viscous boundary layers in a mechanism analogous to Ekman pumping. The analysis shows the following. (i) The blocking effects are similar to those near rigid boundaries on each side of the interface, but through the action of the thin viscous layers above and below the interface, the horizontal and vertical velocity components differ from those near a rigid surface and are correlated or anti-correlated respectively. (ii) Because of the growth of the viscous layers on either side of the interface, the ratio uI/u0, where uI is the r.m.s. of the interfacial velocity fluctuations and u0 the r.m.s. of the homogeneous turbulence far from the interface, does not vary with time. If the turbulence is driven in the lower layer with ρ+/ρ− ≪ 1 and u0+/u0− ≪ 1, then uI/u0− ~ 1 when Re (=u0−L−/ν−) ≫ 1 and R = (ρ−/ρ+)(v−/v+)1/2 ≫ 1. If the turbulence is driven in the upper layer with ρ+/ρ− ≪ 1 and u0+/u0− ≫ 1, then uI/u0+ ~ 1/(1 + R). (iii) Nonlinear effects become significant over periods greater than Lagrangian time scales. When turbulence is generated in the lower layer, and the Reynolds number is high enough, motions in the upper viscous layer are turbulent. The horizontal vorticity tends to decrease, and the vertical vorticity of the eddies dominates their asymptotic structure. When turbulence is generated in the upper layer, and the Reynolds number is less than about 106–107, the fluctuations in the viscous layer do not become turbulent. Nonlinear processes at the interface increase the ratio uI/u0+ for sheared or shear-free turbulence in the gas above its linear value of uI/u0+ ~ 1/(1 + R) to (ρ+/ρ−)1/2 ~ 1/30 for air–water interfaces. This estimate agrees with the direct numerical simulation results from Lombardi, De Angelis & Bannerjee (Phys. Fluids, vol. 8, no. 6, 1996, pp. 1643–1665). Because the linear viscous–inertial coupling mechanism is still significant, the eddy motions on either side of the interface have a similar horizontal structure, although their vertical structure differs

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

Online identification and nonlinear control of the electrically stimulated quadriceps muscle

A new approach for estimating nonlinear models of the electrically stimulated quadriceps muscle group under nonisometric conditions is investigated. The model can be used for designing controlled neuro-prostheses. In order to identify the muscle dynamics (stimulation pulsewidth-active knee moment relation) from discrete-time angle measurements only, a hybrid model structure is postulated for the shank-quadriceps dynamics. The model consists of a relatively well known time-invariant passive component and an uncertain time-variant active component. Rigid body dynamics, described by the Equation of Motion (EoM), and passive joint properties form the time-invariant part. The actuator, i.e. the electrically stimulated muscle group, represents the uncertain time-varying section. A recursive algorithm is outlined for identifying online the stimulated quadriceps muscle group. The algorithm requires EoM and passive joint characteristics to be known a priori. The muscle dynamics represent the product of a continuous-time nonlinear activation dynamics and a nonlinear static contraction function described by a Normalised Radial Basis Function (NRBF) network which has knee-joint angle and angular velocity as input arguments. An Extended Kalman Filter (EKF) approach is chosen to estimate muscle dynamics parameters and to obtain full state estimates of the shank-quadriceps dynamics simultaneously. The latter is important for implementing state feedback controllers. A nonlinear state feedback controller using the backstepping method is explicitly designed whereas the model was identified a priori using the developed identification procedure

Heart rate control during treadmill exercise using input-sensitivity shaping for disturbance rejection of very-low-frequency heart rate variability

AbstractBackgroundAutomatic and accurate control of heart rate (HR) during treadmill exercise is important for prescription and implementation of training protocols. The principal design issue for feedback control of HR is to achieve disturbance rejection of very-low-frequency heart rate variability (VLF-HRV) with a level of control signal activity (treadmill speed) which is sufficiently smooth and acceptable to the runner. This work aimed to develop a new method for feedback control of heart rate during treadmill exercise based on shaping of the input sensitivity function, and to empirically evaluate quantitative performance outcomes in an experimental study.MethodsThirty healthy male subjects participated. 20 subjects were included in a preceding study to determine an approximate, average nominal model of heart rate dynamics, and 10 were not. The design method guarantees that the input sensitivity function gain monotonically decreases with frequency, is therefore devoid of peaking, and has a pre-specified value at a chosen critical frequency, thus avoiding unwanted amplification of HRV disturbances in the very-low-frequency band. Controllers were designed using the existing approximate nominal plant model which was not specific to any of the subjects tested.ResultsAccurate, stable and robust overall performance was observed for all 30 subjects, with a mean RMS tracking error of 2.96beats/min and a smooth, low-power control signal. There were no significant differences in tracking accuracy or control signal power between the 10 subjects who were not in the preceding identification study and a matched subgroup of subjects who were (respectively: mean RMSE 2.69 vs. 3.28beats/min, p=0.24; mean control signal power 15.62 vs. 16.31×10−4m2/s2, p=0.37). Substantial and significant reductions over time in RMS tracking error and average control signal power were observed.ConclusionsThe input-sensitivity-shaping method provides a direct way to address the principal design challenge for HR control, namely disturbance rejection in relation to VLF-HRV, and delivered robust and accurate tracking with a smooth, low-power control signal. Issues of parametric and structural plant uncertainty are secondary because a simple approximate plant model, not specific to any of the subjects tested, was sufficient to achieve accurate, stable and robust heart rate control performance

Isolation of a DNA fragment that encodes part of an ATP dependent RNA helicase in Neurospora crassa.

A DNA fragment encoding part of an ATP dependent RNA Helicase was isolated as part of a search for an unrelated gene. The sequence is reported here and homology to other related genes is described

The HI content of extremely metal-deficient blue compact dwarf galaxies

We have obtained new HI observations with the 100m Green Bank Telescope (GBT) for a sample of 29 extremely metal-deficient star-forming Blue Compact Dwarf (BCD) galaxies, selected from the Sloan Digital Sky Survey spectral data base to be extremely metal-deficient (12+logO/H<7.6). Neutral hydrogen was detected in 28 galaxies, a 97% detection rate. Combining the HI data with SDSS optical spectra for the BCD sample and adding complementary galaxy samples from the literature to extend the metallicity and mass ranges, we have studied how the HI content of a galaxy varies with various global galaxian properties. There is a clear trend of increasing gas mass fraction with decreasing metallicity, mass and luminosity. We obtain the relation M(HI)/L(g)~L(g)^{-0.3}, in agreement with previous studies based on samples with a smaller luminosity range. The median gas mass fraction f(gas) for the GBT sample is equal to 0.94 while the mean gas mass fraction is 0.90+/-0.15, with a lower limit of ~0.65. The HI depletion time is independent of metallicity, with a large scatter around the median value of 3.4 Gyr. The ratio of the baryonic mass to the dynamical mass of the metal-deficient BCDs varies from 0.05 to 0.80, with a median value of ~0.2. About 65% of the BCDs in our sample have an effective yield larger than the true yield, implying that the neutral gas envelope in BCDs is more metal-deficient by a factor of 1.5-20, as compared to the ionized gas.Comment: 21 pages, 13 figures, accepted for publication in MNRA

NF04-594 Resistanct Management for YieldGard Rootworm™ \u3cem\u3eBt\u3c/em\u3e Corn

In 2003, the U.S. Environmental Protection Agency and Monsanto announced the registration of YieldGard Rootworm™ corn containing event MON863. These hybrids express a protein in the roots from the soil bacterium, Bacillus thuringiensis (Bt) that is toxic to larval corn rootworms. This NebFact discusses management requirements, refuge considerations, within-field configurations when using YieldGard Rootworm™

Index-driven XML data integration to support functional genomics

We identify a new type of data integration problem that arises in functional genomics research in the context of large-scale experiments involving arrays, 2-dimensional protein gels and mass-spectrometry. We explore the current practice of data analysis that involves repeated web queries iterating over long lists of gene or protein names. We postulate a new approach to solve this problem, applicable to data sets stored in XML format. We propose to discover data redundancies using an XML index we construct and to remove them from the results returned by the query. We combine XML indexing with queries carried out on top of relational tables. We believe our approach could support semi-automated data integration such as that required in the interpretation of large-scale biological experiments

SAMBA: Superconducting antenna-coupled, multi-frequency, bolometric array

We present a design for a multipixel, multiband (100 GHz, 200 GHz and 400 GHz) submillimeter instrument: SAMBA (Superconducting Antenna-coupled, Multi-frequency, Bolometric Array). SAMBA uses slot antenna coupled bolometers and microstrip filters. The concept allows for a much more compact, multiband imager compared to a comparable feedhorn-coupled bolometric system. SAMBA incorporates an array of slot antennas, superconducting transmission lines, a wide band multiplexer and superconducting transition edge bolometers. The transition-edge film measures the millimeter-wave power deposited in the resistor that terminates the transmission line