Reconstructing gene regulatory networks : a swarm intelligence framework

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VAR model training using particle swarm optimisation: evidence from macro-finance data

This paper examines the empirical relationship between CPI, oil prices, stock market and unemployment in EU15 using a new computational approach. In particular, we propose a novel approach to train the well-known vector autoregressive (VAR) model using a particle swarm optimisation (PSO) method. Results demonstrate that PSO succeeds in training the model parameters. Furthermore, as the prediction error is found to be low, this strengthens the validity and usability of PSO as a model training method. The empirical results suggest that oil is an important determinant of CPI and stock market changes. Oil price changes affect CPI positively and stock market negatively. Finally, we report no evidence that CPI and unemployment have a negative effect on stock market performance.particle swarm optimisation; PSO; vector autoregressive; VAR model training; macroeconomic indicators; oil prices; stock market performance; unemployment; consumer price index; CPI.

The Evolution of Collective Restraint:Policing and Obedience among Non-conjugative Plasmids

The repression of competition by mechanisms of policing is now recognized as a major force in the maintenance of cooperation. General models on the evolution of policing have focused on the interplay between individual competitiveness and mutual policing, demonstrating a positive relationship between within-group diversity and levels of policing. We expand this perspective by investigating what is possibly the simplest example of reproductive policing: copy number control (CNC) among non-conjugative plasmids, a class of extra-chromosomal vertically transmitted molecular symbionts of bacteria. Through the formulation and analysis of a multi-scale dynamical model, we show that the establishment of stable reproductive restraint among plasmids requires the co-evolution of two fundamental plasmid traits: policing, through the production of plasmid-coded trans-acting replication inhibitors, and obedience, expressed as the binding affinity of plasmid-specific targets to those inhibitors. We explain the intrinsic replication instabilities that arise in the absence of policing and we show how these instabilities are resolved by the evolution of copy number control. Increasing levels of policing and obedience lead to improvements in group performance due to tighter control of local population size (plasmid copy number), delivering benefits both to plasmids, by reducing the risk of segregational loss and to the plasmid-host partnership, by increasing the rate of cell reproduction, and therefore plasmid vertical transmission

Obedience (affinity to inhibitor) ensures copy number stability.

<p>Stable (solid) and unstable (dashed) equilibrium copy numbers for a single cell as a function of basal plasmid replication rates for and various values of the binding affinity (blue for ; green for ; red for ). The values of cell fitness (calculated as the reciprocal of the cell division time ) that correspond to the stable characteristic copy numbers are shown in the bottom panel. The stable and unstable equilibrium copy numbers collapse to a singular point (the edge of copy number stability as demonstrated by the critical curve in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003036#pcbi-1003036-g002" target="_blank">Figure 2</a>) that is marked by a colored vertical dotted line, beyond which there exist no characteristic copy numbers, i.e. plasmids over-replicate for any initial copy number. The limit below which the stable characteristic copy number becomes zero is . In the case where (blue lines), the edge of stability coincides with maximum cell fitness; for (green, red lines), the host fitness peak is surrounded by suboptimal parameter configurations which are characterized by stability with respect to copy number.</p

Co-evolution of obedience and baseline replication, in face of constant policing.

<p>The heatmap displays the population's net average growth rate (expressed as the difference between the average division and death rates) as a function of the plasmid replication parameters and , averaged across three independent stochastic multicellular simulations with plasmid homogeneity (no mutations) and a fixed rate of inhibitor production. The white areas below and above the stable region represent the regions of the plasmid parameter space in which plasmids are eliminated from the population due to consistent under- or over- replication respectively. The black clusters in the upper-left corner represent the collapse of the host population under the weight of excessive plasmid replication. The horizontal dashed line indicates the value of for which the system reaches optimal growth at (see <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003036#pcbi-1003036-g005" target="_blank">Figure 5</a>). Finally, the black ladder-like path outlines the evolution of CNC in a stochastic simulation where and are allowed to mutate with probability and a fixed rate of inhibitor production.</p