2,633 research outputs found
Casting Polymer Nets to Optimize Noisy Molecular Codes
Life relies on the efficient performance of molecular codes, which relate
symbols and meanings via error-prone molecular recognition. We describe how
optimizing a code to withstand the impact of molecular recognition noise may be
approximated by the statistics of a two-dimensional network made of polymers.
The noisy code is defined by partitioning the space of symbols into regions
according to their meanings. The "polymers" are the boundaries between these
regions and their statistics defines the cost and the quality of the noisy
code. When the parameters that control the cost-quality balance are varied, the
polymer network undergoes a first-order transition, where the number of encoded
meanings rises discontinuously. Effects of population dynamics on the evolution
of molecular codes are discussed.Comment: PNAS 200
Reproducibility in Research: Systems, Infrastructure, Culture
The reproduction and replication of research results has become a major issue for a number of scientiļ¬c disciplines. In computer science and related computational disciplines such as systems biology, the challenges closely revolve around the ability to implement (and exploit) novel algorithms and models. Taking a new approach from the literature and applying it to a new codebase frequently requires local knowledge missing from the published manuscripts and transient project websites. Alongside this issue, benchmarking, and the lack of open, transparent and fair benchmark sets present another barrier to the veriļ¬cation and validation of claimed results. In this paper, we outline several recommendations to address these issues, driven by speciļ¬c examples from a range of scientiļ¬c domains. Based on these recommendations, we propose a high-level prototype open automated platform for scientiļ¬c software development which eļ¬ectively abstracts speciļ¬c dependencies from the individual researcher and their workstation, allowing easy sharing and reproduction of results. This new e-infrastructure for reproducible computational science oļ¬ers the potential to incentivise a culture change and drive the adoption of new techniques to improve the quality and eļ¬ciency ā and thus reproducibility ā of scientiļ¬c exploration.Royal Society UR
Performance, Politics and Media: How the 2010 British General Election leadership debates generated ātalkā amongst the electorate.
During the British General Election 2010 a major innovation was introduced in part to improve engagement: a series of three live televised leadership debates took place where the leader of each of the three main parties, Labour, Liberal Democrat and Conservative, answered questions posed by members of the public and subsequently debated issues pertinent to the questions. In this study we consider these potentially ground breaking debates as the kind of event that was likely to generate discussion. We investigate various aspects of the ātalkā that emerged as a result of watching the debates. As an exploratory study concerned with situated accounts of the participants experiences we take an interpretive perspective. In this paper we outline the meta-narratives (of talk) associated with the viewing of the leadership debates that were identified, concluding our analysis by suggesting that putting a live debate on television and promoting and positioning it as a major innovation is likely to mean that is how the audience will make sense of it ā as a media event
Exploring UK crime networks
This paper describes our experiences with three different crime networks in the UK: burglary, 'gun' gangs and retail theft. We present an introduction into each of these problems, and highlight some of the issues related to over-simplification of the network analysis. We also review the term `third-generation' analysis, and provide some insights into achieving this, but also conclude that it can be an extremely computationally expensive undertaking
Measuring UK crime gangs
This paper describes the output of a study to tackle the problem of gang-related crime in the UK; we present the intelligence and routinely gathered data available to a UK regional police force, and describe an initial social network analysis of gangs in the Greater Manchester area of the UK between 2000-2006. By applying social network analysis techniques, we attempt to detect the birth of two new gangs based on local features (modularity, cliques) and global features (clustering coefficient). Thus for the future, identifying the changes in these can help us identify the possible birth of new gangs (sub-networks) in the social system. Furthermore, we study the dynamics of these networks globally and locally, and have identified the global characteristics that tell us that they are not random graphs - they are small world graphs - implying that the formation of gangs is not a random event. However, we are not yet able to conclude anything significant about scale-free characteristics due to insufficient sample size
Synchronized dynamics of cortical neurons with time-delay feedback
The dynamics of three mutually coupled cortical neurons with time delays in
the coupling are explored numerically and analytically. The neurons are coupled
in a line, with the middle neuron sending a somewhat stronger projection to the
outer neurons than the feedback it receives, to model for instance the relay of
a signal from primary to higher cortical areas. For a given coupling
architecture, the delays introduce correlations in the time series at the
time-scale of the delay. It was found that the middle neuron leads the outer
ones by the delay time, while the outer neurons are synchronized with zero lag
times. Synchronization is found to be highly dependent on the synaptic time
constant, with faster synapses increasing both the degree of synchronization
and the firing rate. Analysis shows that presynaptic input during the
interspike interval stabilizes the synchronous state, even for arbitrarily weak
coupling, and independent of the initial phase. The finding may be of
significance to synchronization of large groups of cells in the cortex that are
spatially distanced from each other.Comment: 21 pages, 11 figure
Robust formation of morphogen gradients
We discuss the formation of graded morphogen profiles in a cell layer by
nonlinear transport phenomena, important for patterning developing organisms.
We focus on a process termed transcytosis, where morphogen transport results
from binding of ligands to receptors on the cell surface, incorporation into
the cell and subsequent externalization. Starting from a microscopic model, we
derive effective transport equations. We show that, in contrast to morphogen
transport by extracellular diffusion, transcytosis leads to robust ligand
profiles which are insensitive to the rate of ligand production
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