Copasetic analysis: Automated analysis of biological gene expression images

Copyright [2004] IEEE. This material is posted here with permission of the IEEE. Such permission of the IEEE does not in any way imply IEEE endorsement of any of Brunel University's products or services. Internal or personal use of this material is permitted. However, permission to reprint/republish this material for advertising or promotional purposes or for creating new collective works for resale or redistribution must be obtained from the IEEE by writing to [email protected]. By choosing to view this document, you agree to all provisions of the copyright laws protecting it.In the past decade computational biology has come to the forefront of the public's perception with advancements in domain knowledge and a variety of analysis techniques. With the recent completion of projects like the human genome sequence, and the development of microarray chips it has become possible to simultaneously analyse expression levels for thousands of genes. Typically, a slide surface of less than 24 cm2, receptors for 30,000 genes can be printed, but currently the analysis process is a time consuming semi-autonomous step requiring human guidance. The paper proposes a framework, which facilitates automated processing of these images. This is supported by real world examples, which demonstrate the technique's capabilities along with results, which show a marked improvement over existing implementations

Can graph-cutting improve microarray gene expression reconstructions?

Microarrays produce high-resolution image data that are, unfortunately, permeated with a great deal of “noise” that must be removed for precision purposes. This paper presents a technique for such a removal process. On completion of this non-trivial task, a new surface (devoid of gene spots) is subtracted from the original to render more precise gene expressions. The graph-cutting technique as implemented has the benefits that only the most appropriate pixels are replaced and these replacements are replicates rather than estimates. This means the influence of outliers and other artifacts are handled more appropriately (than in previous methods) as well as the variability of the final gene expressions being considerably reduced. Experiments are carried out to test the technique against commercial and previously researched reconstruction methods. Final results show that the graph-cutting inspired identification mechanism has a positive significant impact on reconstruction accuracy

Supporting siblings of children with a special educational need or disability : an evaluation of Sibs Talk, a one‐to‐one intervention delivered by staff in mainstream schools

A group often overlooked for specific supports in schools are siblings of children with a disability, special educational needs or a serious long‐term condition (SEND). In this article we review the current sibling research and identify a lack of literature on interventions, particularly within a school context. We then present a description of Sibs Talk, an example of a new school‐based intervention to support siblings. Sibs Talk is a ten‐session, one‐to‐one intervention approach for schools to complete with Key Stage 2 children who have a brother or sister with SEND. Finally, we present an initial evaluation of the effectiveness of Sibs Talk, using a pre and post evaluation format with a sample of 55 children from 11 schools. The data presented in this evaluation indicate that Sibs Talk may have contributed to positive outcomes for participating children

Robust filtering for stochastic genetic regulatory networks with time-varying delay

This is the post print version of the article. The official published version can be obtained from the link - Copyright 2009 Elsevier LtdThis paper addresses the robust filtering problem for a class of linear genetic regulatory networks (GRNs) with stochastic disturbances, parameter uncertainties and time delays. The parameter uncertainties are assumed to reside in a polytopic region, the stochastic disturbance is state-dependent described by a scalar Brownian motion, and the time-varying delays enter into both the translation process and the feedback regulation process. We aim to estimate the true concentrations of mRNA and protein by designing a linear filter such that, for all admissible time delays, stochastic disturbances as well as polytopic uncertainties, the augmented state estimation dynamics is exponentially mean square stable with an expected decay rate. A delay-dependent linear matrix inequality (LMI) approach is first developed to derive sufficient conditions that guarantee the exponential stability of the augmented dynamics, and then the filter gains are parameterized in terms of the solution to a set of LMIs. Note that LMIs can be easily solved by using standard software packages. A simulation example is exploited in order to illustrate the effectiveness of the proposed design procedures.This work was supported in part by the Biotechnology and Biological Sciences Research Council (BBSRC) of the U.K. under Grants BB/C506264/1 and 100/EGM17735, an International Joint Project sponsored by the Royal Society of the U.K., the Research Grants Council of Hong Kong under Grant HKU 7031/06P, the National Natural Science Foundation of China under Grant 60804028, and the Alexander von Humboldt Foundation of Germany

Weakly-bound rare isotopes with a coupled-channel approach that includes resonant levels

The question of how the scattering cross section changes when the spectra of the colliding nuclei have low-excitation particle-emitting resonances is explored using a multi-channel algebraic scattering (MCAS) method. As a test case, the light-mass nuclear target 8Be, being particle-unstable, has been considered. Nucleon-nucleus scattering cross sections, as well as the spectra of the compound nuclei formed, have been determined from calculations that do, and do not, consider particle emission widths of the target nuclear states. The resonant character of the unstable excited states introduces a problem because the low-energy tails of these resonances can intrude into the sub-threshold, bound-state region. This unphysical behaviour needs to be corrected by modifying, in an energy-dependent way, the shape of the target resonances from the usual Lorentzian one. The resonance function must smoothly reach zero at the elastic threshold. Ways of achieving this condition are explored in this paper.Comment: Contribution presented at INPC 2010, Vancouve