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  • Book chapter
    Amor B, Vuik S, Callahan R, Darzi A, Yaliraki SN, Barahona Met al., 2016,

    Community detection and role identification in directed networks: understanding the Twitter network of the care.data debate

    , Dynamic Networks and Cyber-Security, Editors: Adams, Heard, Publisher: World Scientific, Pages: 111-136, ISBN: 978-1-60558752-3

    With the rise of social media as an important channel for the debate anddiscussion of public affairs, online social networks such as Twitter havebecome important platforms for public information and engagement by policymakers. To communicate effectively through Twitter, policy makers need tounderstand how influence and interest propagate within its network of users. Inthis chapter we use graph-theoretic methods to analyse the Twitter debatesurrounding NHS England's controversial care.data scheme. Directionality is acrucial feature of the Twitter social graph - information flows from thefollowed to the followers - but is often ignored in social network analyses;our methods are based on the behaviour of dynamic processes on the network andcan be applied naturally to directed networks. We uncover robust communities ofusers and show that these communities reflect how information flows through theTwitter network. We are also able to classify users by their differing roles indirecting the flow of information through the network. Our methods and resultswill be useful to policy makers who would like to use Twitter effectively as acommunication medium.
  • Journal article
    Georgiou PS, Yaliraki SN, Drakakis EM, Barahona Met al., 2016,

    Window functions and sigmoidal behaviour of memristive systems

    , International Journal of Circuit Theory and Applications, Vol: 44, Pages: 1685-1696, ISSN: 0098-9886

    Summary: A common approach to model memristive systems is to include empirical window functions to describe edge effects and nonlinearities in the change of the memristance. We demonstrate that under quite general conditions, each window function can be associated with a sigmoidal curve relating the normalised time-dependent memristance to the time integral of the input. Conversely, this explicit relation allows us to derive window functions suitable for the mesoscopic modelling of memristive systems from a variety of well-known sigmoidals. Such sigmoidal curves are defined in terms of measured variables and can thus be extracted from input and output signals of a device and then transformed to its corresponding window. We also introduce a new generalised window function that allows the flexible modelling of asymmetric edge effects in a simple manner.
  • Conference paper
    Branch T, Girvan P, Barahona M, Ying Let al., 2015,

    Kinetics of amyloid-beta/metal ions interactions in the synaptic cleft: experiment and simulation

    , 10th EBSA European Biophysics Congress, Publisher: Springer Verlag, Pages: S230-S230, ISSN: 0175-7571
  • Journal article
    Sim A, Yaliraki SN, Barahona M, Stumpf MPet al., 2015,

    Great cities look small.

    , Journal of the Royal Society Interface, Vol: 12, ISSN: 1742-5689

    Great cities connect people; failed cities isolate people. Despite the fundamental importance of physical, face-to-face social ties in the functioning of cities, these connectivity networks are not explicitly observed in their entirety. Attempts at estimating them often rely on unrealistic over-simplifications such as the assumption of spatial homogeneity. Here we propose a mathematical model of human interactions in terms of a local strategy of maximizing the number of beneficial connections attainable under the constraint of limited individual travelling-time budgets. By incorporating census and openly available online multi-modal transport data, we are able to characterize the connectivity of geometrically and topologically complex cities. Beyond providing a candidate measure of greatness, this model allows one to quantify and assess the impact of transport developments, population growth, and other infrastructure and demographic changes on a city. Supported by validations of gross domestic product and human immunodeficiency virus infection rates across US metropolitan areas, we illustrate the effect of changes in local and city-wide connectivities by considering the economic impact of two contemporary inter- and intra-city transport developments in the UK: High Speed 2 and London Crossrail. This derivation of the model suggests that the scaling of different urban indicators with population size has an explicitly mechanistic origin.
  • Journal article
    Thomas P, Grima R, 2015,

    Approximate probability distributions of the master equation

    , Physical Review E, Vol: 92, Pages: 012120-012120-12, ISSN: 1539-3755

    Master equations are common descriptions of mesoscopic systems. Analytical solutions to these equations can rarely be obtained. We here derive an analytical approximation of the time-dependent probability distribution of the master equation using orthogonal polynomials. The solution is given in two alternative formulations: a series with continuous and a series with discrete support, both of which can be systematically truncated. While both approximations satisfy the system size expansion of the master equation, the continuous distribution approximations become increasingly negative and tend to oscillations with increasing truncation order. In contrast, the discrete approximations rapidly converge to the underlying non-Gaussian distributions. The theory is shown to lead to particularly simple analytical expressions for the probability distributions of molecule numbers in metabolic reactions and gene expression systems.
  • Journal article
    Schaub MT, Billeh YN, Anastassiou CA, Koch C, Barahona Met al., 2015,

    Emergence of Slow-Switching Assemblies in Structured Neuronal Networks

    , PLOS COMPUTATIONAL BIOLOGY, Vol: 11, ISSN: 1553-734X
  • Journal article
    Noseda M, Harada M, McSweeney S, Leja T, Belian E, Stuckey DJ, Abreu Paiva MS, Habib J, Macaulay I, de Smith AJ, Al-Beidh F, Sampson R, Lumbers RT, Rao P, Harding SE, Blakemore AI, Eirik Jacobsen S, Barahona M, Schneider MDet al., 2015,

    PDGFRα demarcates the cardiogenic clonogenic Sca1(+) stem/progenitor cell in adult murine myocardium

    , Nature Communications, Vol: 6, ISSN: 2041-1723

    Cardiac progenitor/stem cells in adult hearts represent an attractive therapeutic target for heart regeneration, though (inter)-relationships among reported cells remain obscure. Using single-cell qRT-PCR and clonal analyses, here we define four subpopulations of cardiac progenitor/stem cells in adult mouse myocardium all sharing stem cell antigen-1 (Sca1), based on side population (SP) phenotype, PECAM-1 (CD31) and platelet-derived growth factor receptor-α (PDGFRα) expression. SP status predicts clonogenicity and cardiogenic gene expression (Gata4/6, Hand2 and Tbx5/20), properties segregating more specifically to PDGFRα(+) cells. Clonal progeny of single Sca1(+) SP cells show cardiomyocyte, endothelial and smooth muscle lineage potential after cardiac grafting, augmenting cardiac function although durable engraftment is rare. PDGFRα(-) cells are characterized by Kdr/Flk1, Cdh5, CD31 and lack of clonogenicity. PDGFRα(+)/CD31(-) cells derive from cells formerly expressing Mesp1, Nkx2-5, Isl1, Gata5 and Wt1, distinct from PDGFRα(-)/CD31(+) cells (Gata5 low; Flk1 and Tie2 high). Thus, PDGFRα demarcates the clonogenic cardiogenic Sca1(+) stem/progenitor cell.
  • Journal article
    Wang B, Barahona M, Buck M, 2015,

    Amplification of small molecule-inducible gene expression via tuning of intracellular receptor densities

    , NUCLEIC ACIDS RESEARCH, Vol: 43, Pages: 1955-1964, ISSN: 0305-1048
  • Conference paper
    Branch T, Barahona M, Ying L, 2015,

    Secondary Metal Binding to Amyloid-Beta Monomer is Insignificant under Synaptic Conditions

    , 59th Annual Meeting of the Biophysical-Society, Publisher: CELL PRESS, Pages: 385A-385A, ISSN: 0006-3495
  • Journal article
    Branch T, Girvan P, Barahona M, Ying Let al., 2015,

    Introduction of a Fluorescent Probe to Amyloid-beta to Reveal Kinetic Insights into Its Interactions with Copper(II)

    , ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, Vol: 54, Pages: 1227-1230, ISSN: 1433-7851

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