Gene function prediction from synthetic lethality networks via ranking on demand.

MOTIVATION: Synthetic lethal interactions represent pairs of genes whose individual mutations are not lethal, while the double mutation of both genes does incur lethality. Several studies have shown a correlation between functional similarity of genes and their distances in networks based on synthetic lethal interactions. However, there is a lack of algorithms for predicting gene function from synthetic lethality interaction networks. RESULTS: In this article, we present a novel technique called kernelROD for gene function prediction from synthetic lethal interaction networks based on kernel machines. We apply our novel algorithm to Gene Ontology functional annotation prediction in yeast. Our experiments show that our method leads to improved gene function prediction compared with state-of-the-art competitors and that combining genetic and congruence networks leads to a further improvement in prediction accuracy.

Accurate real-time feedback of surface EMG during fMRI.

Real-time acquisition of EMG during functional MRI (fMRI) provides a novel method of controlling motor experiments in the scanner using feedback of EMG. Because of the redundancy in the human muscle system, this is not possible from recordings of joint torque and kinematics alone, because these provide no information about individual muscle activation. This is particularly critical during brain imaging because brain activations are not only related to joint torques and kinematics but are also related to individual muscle activation. However, EMG collected during imaging is corrupted by large artifacts induced by the varying magnetic fields and radio frequency (RF) pulses in the scanner. Methods proposed in literature for artifact removal are complex, computationally expensive, and difficult to implement for real-time noise removal. We describe an acquisition system and algorithm that enables real-time acquisition for the first time. The algorithm removes particular frequencies from the EMG spectrum in which the noise is concentrated. Although this decreases the power content of the EMG, this method provides excellent estimates of EMG with good resolution. Comparisons show that the cleaned EMG obtained with the algorithm is, like actual EMG, very well correlated with joint torque and can thus be used for real-time visual feedback during functional studies.

Decay of vibrations along deepwater mooring lines

Model tests for global design verification of deepwater floating structures cannot be made at reasonable scales. An overview of recent research efforts to tackle this challenge is given first, introducing the concept of line truncation techniques. In such a method the upper sections of each line are modelled in detail, capturing the wave action zone and all coupling effects with the vessel. These terminate to an approximate analytical model, that aims to simulate the remainder of the line. The rationale for this is that in deep water the transverse elastic waves of a line are likely to decay before they are reflected at the seabed. The focus of this paper is the verification of this rationale and the ongoing work, which is considering ways to produce a truncation model. Transverse dynamics of a mooring line are modelled using the equations of motion of an inextensible taut string, submerged in still water, one end fixed at the bottom the other assumed to follow the vessel response, which can be harmonic or random. Nonlinear hydrodynamic damping is included; bending and VIV effects are neglected. A dimensional analysis, supported by exact benchmark numerical solutions, has shown that it is possible to produce a universal curve for the decay of transverse vibrations along the line, which is suitable for any kind of line with any top motion. This has a significant engineering benefit, allowing for a rapid assessment of line dynamics - it is very useful in deciding whether a truncated line model is appropriate, and if so, at which point truncation might be applied. Initial efforts in developing a truncated model show that a linearized numerical solution in the frequency domain matches very closely the exact benchmark. Copyright © 2011 by ASME.

Novel applications of BEM based Poisson level set approach

Accurate and efficient computation of the distance function d for a given domain is important for many areas of numerical modeling. Partial differential (e.g. HamiltonJacobi type) equation based distance function algorithms have desirable computational efficiency and accuracy. In this study, as an alternative, a Poisson equation based level set (distance function) is considered and solved using the meshless boundary element method (BEM). The application of this for shape topology analysis, including the medial axis for domain decomposition, geometric de-featuring and other aspects of numerical modeling is assessed. © 2011 Elsevier Ltd. All rights reserved.

A novel modeling approach for design studies of brushless doubly fed induction generator based on magnetic equivalent circuit

Brushless doubly fed induction generator (BDFIG) has substantial benefits, which make it an attractive alternative as a wind turbine generator. However, it suffers from lower efficiency and larger dimensions in comparison to DFIG. Hence, optimizing the BDFIG structure is necessary for enhancing its situation commercially. In previous studies, a simple model has been used in BDFIG design procedure that is insufficiently accurate. Furthermore, magnetic saturation and iron loss are not considered because of difficulties in determination of flux density distributions. The aim of this paper is to establish an accurate yet computationally fast model suitable for BDFIG design studies. The proposed approach combines three equivalent circuits including electric, magnetic and thermal models. Utilizing electric equivalent circuit makes it possible to apply static form of magnetic equivalent circuit, because the elapsed time to reach steady-state results in the dynamic form is too long for using in population-based design studies. The operating characteristics, which are necessary for evaluating the objective function and constraints values of the optimization problem, can be calculated using the presented approach considering iron loss, saturation, and geometrical details. The simulation results of a D-180 prototype BDFIG are compared with measured data in order to validate the developed model. © 1986-2012 IEEE.