Grid technology for collaborative ontology development

In contrast with the centrally-organised curation of the Gene Ontology, many biological ontologies are developed by loosely-organised groups who develop their ontology remotely. These groups tend to be formed from scientists and bio-informaticians from research groups with a common interest, who want to create a resource that will be useful to the community, rather than being formally mandated. Until recently, technological support for bio-ontology development relied on stand-alone editors running on users’ desk- tops for creating new ontology versions (e.g. OBO-Edit, COBrA and Protégé) and on private email, email lists and perhaps Wikis for the distribution of ontology files and discussions. Clearly, much better use could be made of the storage, versioning and visualisation techniques being developed by the database and e- Science communities. BioSphere is an online ontology editor supporting multiple users and is underpinned by a server that stores versions (in OWL-XML) and provides a discussion portal

Stochastic firing rate models

We review a recent approach to the mean-field limits in neural networks that takes into account the stochastic nature of input current and the uncertainty in synaptic coupling. This approach was proved to be a rigorous limit of the network equations in a general setting, and we express here the results in a more customary and simpler framework. We propose a heuristic argument to derive these equations providing a more intuitive understanding of their origin. These equations are characterized by a strong coupling between the different moments of the solutions. We analyse the equations, present an algorithm to simulate the solutions of these mean-field equations, and investigate numerically the equations. In particular, we build a bridge between these equations and Sompolinsky and collaborators approach (1988, 1990), and show how the coupling between the mean and the covariance function deviates from customary approaches

The next evolutionary synthesis: from Lamarck and Darwin to genomic variation and systems biology

The evolutionary synthesis, the standard 20th century view of how evolutionary change occurs, is based on selection, heritable phenotypic variation and a very simple view of genes. It is therefore unable to incorporate two key aspects of modern molecular knowledge: first is the richness of genomic variation, so much more complicated than simple mutation, and second is the opaque relationship between the genotype and its resulting phenotype. Two new and important books shed some light on how we should view evolutionary change now. Evolution: a view from the 21st century by J.A. Shapiro (2011, FT Press Science, New Jersey, USA. pp. 246.) examines the richness of genomic variation and its implications. Transformations of Lamarckism: from Subtle Fluids to Molecular Biology edited by S.B. Gissis & E. Jablonka (2011, MIT Press, Cambridge, USA. pp. 457) includes some 40 papers that anyone with an interest in the history of evolutionary thought and the relationship between the environment and the genome will want to read. This review discusses both books within the context of contemporary evolutionary thinking and points out that neither really comes to terms with today's key systems-biology question: how does mutation-induced variation in a molecular network generate variation in the resulting phenotype

Analysis of Heteroplasmic Variants in the Cardiac Mitochondrial Genome of Individuals with Down Syndrome

Individuals with Down syndrome (DS, trisomy 21) exhibit a pro-oxidative cellular environment as well as mitochondrial dysfunction. Increased oxidative stress may damage the mitochondrial DNA (mtDNA). The coexistence of mtDNA variants in a cell or tissue (i.e., heteroplasmy) may contribute to mitochondrial dysfunction. Given the evidence on mitochondrial dysfunction and the relatively high incidence of multiorganic disorders associated with DS, we hypothesized that cardiac tissue from subjects with DS may exhibit higher frequencies of mtDNA variants in comparison to cardiac tissue from donors without DS. This study documents the analysis of mtDNA variants in heart tissue samples from donors with (n = 12) and without DS (n = 33) using massively parallel sequencing. Contrary to the original hypothesis, the study’s findings suggest that the cardiac mitochondrial genomes from individuals with and without DS exhibit many similarities in terms of (1) total number of mtDNA variants per sample, (2) the frequency of mtDNA variants, (3) the type of mtDNA variants, and (4) the patterns of distribution of mtDNA variants. In both groups of samples, the mtDNA control region showed significantly more heteroplasmic variants in comparison to the number of variants in protein- and RNA-coding genes (P \u3c 1.00×10−4, ANOVA)

Measurement campaign on transmit delay diversity for mobile DVB-T/H systems

This article is posted here with permission from IEEE - Copyright @ 2010 IEEEThis paper describes the work carried out by Brunel University and Broadreach Systems (UK) to quantify the advantages that can be achieved if Transmit Delay Diversity is applied to systems employing the DVB standard. The techniques investigated can be applied to standard receiver equipment without modification. An extensive and carefully planned field trial was performed during the winter of 2007/2008 in Uxbridge (UK) to validate predictions from theoretical modeling and laboratory simulations. The transmissions were performed in the 730 MHz frequency band with a DVB-T/H transmitter and a mean power of 18.4 dBW. The impact of the transmit antenna separation and the MPE-FEC was also investigated. It is shown that transmit delay diversity significantly improves the quality of reception in fast fading mobile broadcasting application