Influence of homology and node-age on the growth of protein-protein interaction networks

Proteins participating in a protein-protein interaction network can be grouped into homology classes following their common ancestry. Proteins added to the network correspond to genes added to the classes, so that the dynamics of the two objects are intrinsically linked. Here, we first introduce a statistical model describing the joint growth of the network and the partitioning of nodes into classes, which is studied through a combined mean-field and simulation approach. We then employ this unified framework to address the specific issue of the age dependence of protein interactions, through the definition of three different node wiring/divergence schemes. Comparison with empirical data indicates that an age-dependent divergence move is necessary in order to reproduce the basic topological observables together with the age correlation between interacting nodes visible in empirical data. We also discuss the possibility of nontrivial joint partition/topology observables.Comment: 14 pages, 7 figures [accepted for publication in PRE

Exact sampling of self-avoiding paths via discrete Schramm-Loewner evolution

We present an algorithm, based on the iteration of conformal maps, that produces independent samples of self-avoiding paths in the plane. It is a discrete process approximating radial Schramm-Loewner evolution growing to infinity. We focus on the problem of reproducing the parametrization corresponding to that of lattice models, namely self-avoiding walks on the lattice, and we propose a strategy that gives rise to discrete paths where consecutive points lie an approximately constant distance apart from each other. This new method allows us to tackle two non-trivial features of self-avoiding walks that critically depend on the parametrization: the asphericity of a portion of chain and the correction-to-scaling exponent.Comment: 18 pages, 4 figures. Some sections rewritten (including title and abstract), numerical results added, references added. Accepted for publication in J. Stat. Phy

European Non-native Species in Aquaculture Risk Analysis Scheme - a summary of assessment protocols and decision support tools for use of alien species in aquaculture

The European Non-native Species in Aquaculture Risk Analysis Scheme (ENSARS) was developed in response to European 'Council Regulation No. 708/2007 of 11 June 2007 concerning use of alien and locally absent species in aquaculture' to provide protocols for identifying and evaluating the potential risks of using non-native species in aquaculture. ENSARS is modular in structure and adapted from non-native species risk assessment schemes developed by the European and Mediterranean Plant Protection Organisation and for the UK. Seven of the eight ENSARS modules contain protocols for evaluating the risks of escape, introduction to and establishment in open waters, of any non-native aquatic organism being used (or associated with those used) in aquaculture, that is, transport pathways, rearing facilities, infectious agents, and the potential organism, ecosystem and socio-economic impacts. A concluding module is designed to summarise the risks and consider management options. During the assessments, each question requires the assessor to provide a response and confidence ranking for that response based on expert opinion. Each module can also be used individually, and each requires a specific form of expertise. Therefore, a multidisciplinary assessment team is recommended for its completion