Probabilistic Clustering of Sequences: Inferring new bacterial regulons by comparative genomics

Genome wide comparisons between enteric bacteria yield large sets of conserved putative regulatory sites on a gene by gene basis that need to be clustered into regulons. Using the assumption that regulatory sites can be represented as samples from weight matrices we derive a unique probability distribution for assignments of sites into clusters. Our algorithm, 'PROCSE' (probabilistic clustering of sequences), uses Monte-Carlo sampling of this distribution to partition and align thousands of short DNA sequences into clusters. The algorithm internally determines the number of clusters from the data, and assigns significance to the resulting clusters. We place theoretical limits on the ability of any algorithm to correctly cluster sequences drawn from weight matrices (WMs) when these WMs are unknown. Our analysis suggests that the set of all putative sites for a single genome (e.g. E. coli) is largely inadequate for clustering. When sites from different genomes are combined and all the homologous sites from the various species are used as a block, clustering becomes feasible. We predict 50-100 new regulons as well as many new members of existing regulons, potentially doubling the number of known regulatory sites in E. coli.Comment: 27 pages including 9 figures and 3 table

Emergence of robustness against noise: A structural phase transition in evolved models of gene regulatory networks

We investigate the evolution of Boolean networks subject to a selective pressure which favors robustness against noise, as a model of evolved genetic regulatory systems. By mapping the evolutionary process into a statistical ensemble and minimizing its associated free energy, we find the structural properties which emerge as the selective pressure is increased and identify a phase transition from a random topology to a "segregated core" structure, where a smaller and more densely connected subset of the nodes is responsible for most of the regulation in the network. This segregated structure is very similar qualitatively to what is found in gene regulatory networks, where only a much smaller subset of genes --- those responsible for transcription factors --- is responsible for global regulation. We obtain the full phase diagram of the evolutionary process as a function of selective pressure and the average number of inputs per node. We compare the theoretical predictions with Monte Carlo simulations of evolved networks and with empirical data for Saccharomyces cerevisiae and Escherichia coli.Comment: 12 pages, 10 figure

On the Neutrality of Flowshop Scheduling Fitness Landscapes

Solving efficiently complex problems using metaheuristics, and in particular local searches, requires incorporating knowledge about the problem to solve. In this paper, the permutation flowshop problem is studied. It is well known that in such problems, several solutions may have the same fitness value. As this neutrality property is an important one, it should be taken into account during the design of optimization methods. Then in the context of the permutation flowshop, a deep landscape analysis focused on the neutrality property is driven and propositions on the way to use this neutrality to guide efficiently the search are given.Comment: Learning and Intelligent OptimizatioN Conference (LION 5), Rome : Italy (2011

Coupled Replicator Equations for the Dynamics of Learning in Multiagent Systems

Starting with a group of reinforcement-learning agents we derive coupled replicator equations that describe the dynamics of collective learning in multiagent systems. We show that, although agents model their environment in a self-interested way without sharing knowledge, a game dynamics emerges naturally through environment-mediated interactions. An application to rock-scissors-paper game interactions shows that the collective learning dynamics exhibits a diversity of competitive and cooperative behaviors. These include quasiperiodicity, stable limit cycles, intermittency, and deterministic chaos--behaviors that should be expected in heterogeneous multiagent systems described by the general replicator equations we derive.Comment: 4 pages, 3 figures, http://www.santafe.edu/projects/CompMech/papers/credlmas.html; updated references, corrected typos, changed conten

Evolutionary games and quasispecies

We discuss a population of sequences subject to mutations and frequency-dependent selection, where the fitness of a sequence depends on the composition of the entire population. This type of dynamics is crucial to understand the evolution of genomic regulation. Mathematically, it takes the form of a reaction-diffusion problem that is nonlinear in the population state. In our model system, the fitness is determined by a simple mathematical game, the hawk-dove game. The stationary population distribution is found to be a quasispecies with properties different from those which hold in fixed fitness landscapes.Comment: 7 pages, 2 figures. Typos corrected, references updated. An exact solution for the hawks-dove game is provide

Aquilegia, Vol. 34 No. 1, Spring 2010, Newsletter of the Colorado Native Plant Society

https://epublications.regis.edu/aquilegia/1131/thumbnail.jp

Effect of connective tissue grafting on buccal bone changes based on cone beam computed tomography scans in the aesthetic zone of single immediate implants:A 1-year randomized controlled trial

BACKGROUND Connective tissue grafting has a beneficial effect on the peri-implant mucosa, but the effect of grafting the buccal mucosa on buccal bone thickness (BBT) has not been investigated, although BBT is proposed to be a key factor for the soft-tissue contour. The aim of this trial was to assess the outcome of a connective tissue graft (CTG) in the aesthetic zone of single immediate implants on the change of BBT according to cone beam computed tomography (CBCT) scan analysis. METHODS In a 1-year randomized controlled trial, 60 patients received an immediately placed implant and provisionalization, either combined with CTG (test group) or without CTG (control group). CBCTs were taken pre-operatively (T$_{pre}$ ) and 1 year after definitive restoration (T$_{2}$ ). Any change in BBT was assessed at different implant levels. Additionally, the change in mid-buccal mucosal level (MBML) and approximal marginal bone level were assessed. RESULTS Fifty-five patients were available for statistical analysis (test group, n = 28; control group, n = 27). At T$_{2}$ , the average change in BBT was significantly larger in the test group (-0.84 ± 0.61 mm) than in the control group (-0.46 ± 0.54 mm, P = 0.02). A MBML gain of 0.07 ± 0.85 mm in the test and a MBML loss -0.52 ± 1.16 mm in the control group was observed at T$_{2}$ . Average loss of marginal bone was 0.05 ± 0.33 mm and 0.01 ± 0.38 mm, respectively. CONCLUSIONS The application of CTG in the aesthetic zone of immediately placed and provisionalized implants is accompanied with more loss of BBT, but at the same time better maintains the mid-buccal mucosal level