Construction of gene regulatory networks using biclustering and bayesian networks

<p>Abstract</p> <p>Background</p> <p>Understanding gene interactions in complex living systems can be seen as the ultimate goal of the systems biology revolution. Hence, to elucidate disease ontology fully and to reduce the cost of drug development, gene regulatory networks (GRNs) have to be constructed. During the last decade, many GRN inference algorithms based on genome-wide data have been developed to unravel the complexity of gene regulation. Time series transcriptomic data measured by genome-wide DNA microarrays are traditionally used for GRN modelling. One of the major problems with microarrays is that a dataset consists of relatively few time points with respect to the large number of genes. Dimensionality is one of the interesting problems in GRN modelling.</p> <p>Results</p> <p>In this paper, we develop a biclustering function enrichment analysis toolbox (BicAT-plus) to study the effect of biclustering in reducing data dimensions. The network generated from our system was validated via available interaction databases and was compared with previous methods. The results revealed the performance of our proposed method.</p> <p>Conclusions</p> <p>Because of the sparse nature of GRNs, the results of biclustering techniques differ significantly from those of previous methods.</p

An Optically Augmented Visual Aid for Individuals with Age-Related Macular Degeneration

Normal vision is a precious gift to mankind. Any vision defect or degradation is actually an intimidating problem for individuals and societies. Therefore, researchers are continually working to find effective solutions for vision disorders. In some retinal diseases such as Age-related Macular Degeneration (AMD), visual aids are required to improve vision ability and/or stop the progress of the disease. Recently, augmented vision techniques have been used to provide aid to people suffering from retinal impairment. However, in such techniques, the images of real scenes are electronically deformed to compensate for vision impairment. Therefore, the natural scene is displayed as an electronic image on glasses. Intuitively, it is annoying to the patient to see electronic rather than natural scenes. Moreover, these visual aids are bulky and produce electric fields that might be harmful with continuous use. In this work, a novel optical solution to provide a visual aid to patients with central vision loss has been proposed. The proposed optical solution deforms the wavefront of the scene to entirely fall on the healthy parts of the retina. This, in turn, conveys all scene information to the brain to be perceived by the patient. As it provides optical processing, the proposed solution overcomes all drawbacks of the electronic solutions. To prove the validity of the proposed solution, three lenses were designed, fabricated, and tested to visualize simple shapes, reading, and obtaining aid during walking and driving. Obtaining the expected results from these tests, they were tried by three volunteers to clinically prove the validity and feasibility of the proposed optical aid. The feedback from the three patients was promising since all of them could recognize some of the details they used to miss with at least one of the lenses

A Method for Medical Diagnosis Based on Optical Fluence Rate Distribution at Tissue Surface

Optical differentiation is a promising tool in biomedical diagnosis mainly because of its safety. The optical parameters’ values of biological tissues differ according to the histopathology of the tissue and hence could be used for differentiation. The optical fluence rate distribution on tissue boundaries depends on the optical parameters. So, providing image displays of such distributions can provide a visual means of biomedical diagnosis. In this work, an experimental setup was implemented to measure the spatially-resolved steady state diffuse reflectance and transmittance of native and coagulated chicken liver and native and boiled breast chicken skin at 635 and 808 nm wavelengths laser irradiation. With the measured values, the optical parameters of the samples were calculated in vitro using a combination of modified Kubelka-Munk model and Bouguer-Beer-Lambert law. The estimated optical parameters values were substituted in the diffusion equation to simulate the fluence rate at the tissue surface using the finite element method. Results were verified with Monte-Carlo simulation. The results obtained showed that the diffuse reflectance curves and fluence rate distribution images can provide discrimination tools between different tissue types and hence can be used for biomedical diagnosis

An Efficient Design of Inductive Transmitter and Receiver Coils for Wireless Power Transmission

Wireless power transmission (WPT) is commonly used today in many important daily applications, such as electric vehicles, mobile phones, and implanted medical devices. The transmitter and receiver coils are essential elements in the WPT system, and the coupling coefficient between these coils plays an important role in increasing the power transfer efficiency. In this work, we introduce a new approach to optimizing the coupling coefficient between the transmitter and the receiver coils by changing the geometries and locations of the coil turns. In the optimization process, the geometry of the turns varies from a rhombus to a circular and then a rectangular shape according to a quasi-elliptical parameter value. The Neuman formula is used to calculate the self-inductance, mutual inductance, and coupling coefficient for each specific geometry and turn location. The configuration with the highest coupling coefficient is then selected at the end of the optimization process. The final WPT coils are tested and verified using Ansys software through electromagnetic and AC analysis simulations. The results show that the new approach could achieve smooth and easily manufacturable coils with higher coupling coefficients, thereby increasing the power transfer efficiency of WPT