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

Noise-induced synchronization and anti-resonance in excitable systems; Implications for information processing in Parkinson's Disease and Deep Brain Stimulation

We study the statistical physics of a surprising phenomenon arising in large networks of excitable elements in response to noise: while at low noise, solutions remain in the vicinity of the resting state and large-noise solutions show asynchronous activity, the network displays orderly, perfectly synchronized periodic responses at intermediate level of noise. We show that this phenomenon is fundamentally stochastic and collective in nature. Indeed, for noise and coupling within specific ranges, an asymmetry in the transition rates between a resting and an excited regime progressively builds up, leading to an increase in the fraction of excited neurons eventually triggering a chain reaction associated with a macroscopic synchronized excursion and a collective return to rest where this process starts afresh, thus yielding the observed periodic synchronized oscillations. We further uncover a novel anti-resonance phenomenon: noise-induced synchronized oscillations disappear when the system is driven by periodic stimulation with frequency within a specific range. In that anti-resonance regime, the system is optimal for measures of information capacity. This observation provides a new hypothesis accounting for the efficiency of Deep Brain Stimulation therapies in Parkinson's disease, a neurodegenerative disease characterized by an increased synchronization of brain motor circuits. We further discuss the universality of these phenomena in the class of stochastic networks of excitable elements with confining coupling, and illustrate this universality by analyzing various classical models of neuronal networks. Altogether, these results uncover some universal mechanisms supporting a regularizing impact of noise in excitable systems, reveal a novel anti-resonance phenomenon in these systems, and propose a new hypothesis for the efficiency of high-frequency stimulation in Parkinson's disease

Robust resilience and substantial interest: a survey of pharmacological cognitive enhancement among university students in the UK and Ireland

Use of ‘smart drugs’ among UK students is described in frequent media reports as a rapidly increasing phenomenon. This article reports findings from the first large-scale survey of pharmacological cognitive enhancement (PCE) among students in the UK and Ireland. Conducted from February to September 2012, a survey of a convenience sample of 877 students measured PCE prevalence, attitudes, sources, purposes and ethics. Descriptive and logistic regression statistical methods were used to analyse the data. Lifetime prevalence of PCE using modafinil, methylphenidate or Adderall was under 10%, while past regular and current PCE users of these substances made up between 0.3% - 4% of the survey population. A substantial majority of students was unaware of and/or uninterested in PCE; however about one third of students were interested in PCE. PCE users were more likely to be male, British and older students; predictors of PCE use included awareness of other students using PCEs, ADHD symptomatology, ethical concerns, and alcohol and cannabis use. The survey addresses the need for better evidence about PCE prevalence and practices among university students in the UK. We recommend PCE-related strategies for universities based on the survey findings

An ontology for cell types.

We describe an ontology for cell types that covers the prokaryotic, fungal, animal and plant worlds. It includes over 680 cell types. These cell types are classified under several generic categories and are organized as a directed acyclic graph. The ontology is available in the formats adopted by the Open Biological Ontologies umbrella and is designed to be used in the context of model organism genome and other biological databases. The ontology is freely available at http://obo.sourceforge.net/ and can be viewed using standard ontology visualization tools such as OBO-Edit and COBrA.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

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