Large-scale analysis of orthologs and paralogs under covarion-like and constant-but-different models of amino acid evolution.

Functional divergence between homologous proteins is expected to affect amino acid sequences in two main ways, which can be considered as proxies of biochemical divergence: a "covarion-like" pattern of correlated changes in evolutionary rates, and switches in conserved residues ("conserved but different"). Although these patterns have been used in case studies, a large-scale analysis is needed to estimate their frequency and distribution. We use a phylogenomic framework of animal genes to answer three questions: 1) What is the prevalence of such patterns? 2) Can we link such patterns at the amino acid level with selection inferred at the codon level? 3) Are patterns different between paralogs and orthologs? We find that covarion-like patterns are more frequently detected than "constant but different," but that only the latter are correlated with signal for positive selection. Finally, there is no obvious difference in patterns between orthologs and paralogs.

A Label space reduction algorithm for P2MP LSPs using asymmetric tunnels

The aim of traffic engineering is to optimise network resource utilization. Although several works on minimizing network resource utilization have been published, few works have focused on LSR label space. This paper proposes an algorithm that uses MPLS label stack features in order to reduce the number of labels used in LSPs forwarding. Some tunnelling methods and their MPLS implementation drawbacks are also discussed. The algorithm described sets up the NHLFE tables in each LSR, creating asymmetric tunnels when possible. Experimental results show that the algorithm achieves a large reduction factor in the label space. The work presented here applies for both types of connections: P2MP and P2P

Discovering similarities in the time use patterns of the Spanish Autonomous Communities by Fuzzy techniques

In 2000 the European Statistical Office published the guidelines for developing theHarmonized European Time Use Surveys system. Under such a unified framework,the first Time Use Survey of national scope was conducted in Spain during 2002–03. The aim of these surveys is to understand human behavior and the lifestyle ofpeople. Time allocation data are of compositional nature in origin, that is, they aresubject to non-negativity and constant-sum constraints. Thus, standard multivariatetechniques cannot be directly applied to analyze them. The goal of this work is toidentify homogeneous Spanish Autonomous Communities with regard to the typicalactivity pattern of their respective populations. To this end, fuzzy clustering approachis followed. Rather than the hard partitioning of classical clustering, where objects areallocated to only a single group, fuzzy method identify overlapping groups of objectsby allowing them to belong to more than one group. Concretely, the probabilistic fuzzyc-means algorithm is conveniently adapted to deal with the Spanish Time Use Surveymicrodata. As a result, a map distinguishing Autonomous Communities with similaractivity pattern is drawn.Key words: Time use data, Fuzzy clustering; FCM; simplex space; Aitchison distance

Use of Hy's law and a new composite algorithm to predict acute liver failure in patients with drug-induced liver injury.

BACKGROUND & AIMS Hy's Law, which states that hepatocellular drug-induced liver injury (DILI) with jaundice indicates a serious reaction, is used widely to determine risk for acute liver failure (ALF). We aimed to optimize the definition of Hy's Law and to develop a model for predicting ALF in patients with DILI. METHODS We collected data from 771 patients with DILI (805 episodes) from the Spanish DILI registry, from April 1994 through August 2012. We analyzed data collected at DILI recognition and at the time of peak levels of alanine aminotransferase (ALT) and total bilirubin (TBL). RESULTS Of the 771 patients with DILI, 32 developed ALF. Hepatocellular injury, female sex, high levels of TBL, and a high ratio of aspartate aminotransferase (AST):ALT were independent risk factors for ALF. We compared 3 ways to use Hy's Law to predict which patients would develop ALF; all included TBL greater than 2-fold the upper limit of normal (×ULN) and either ALT level greater than 3 × ULN, a ratio (R) value (ALT × ULN/alkaline phosphatase × ULN) of 5 or greater, or a new ratio (nR) value (ALT or AST, whichever produced the highest ×ULN/ alkaline phosphatase × ULN value) of 5 or greater. At recognition of DILI, the R- and nR-based models identified patients who developed ALF with 67% and 63% specificity, respectively, whereas use of only ALT level identified them with 44% specificity. However, the level of ALT and the nR model each identified patients who developed ALF with 90% sensitivity, whereas the R criteria identified them with 83% sensitivity. An equal number of patients who did and did not develop ALF had alkaline phosphatase levels greater than 2 × ULN. An algorithm based on AST level greater than 17.3 × ULN, TBL greater than 6.6 × ULN, and AST:ALT greater than 1.5 identified patients who developed ALF with 82% specificity and 80% sensitivity. CONCLUSIONS When applied at DILI recognition, the nR criteria for Hy's Law provides the best balance of sensitivity and specificity whereas our new composite algorithm provides additional specificity in predicting the ultimate development of ALF.

Fast calculation of the CAC convolution algorithm using the multinomial distribution function

The authors focus on one of the methods for connection acceptance control (CAC) in an ATM network: the convolution approach. With the aim of reducing the cost in terms of calculation and storage requirements, they propose the use of the multinomial distribution function. This permits direct computation of the associated probabilities of the instantaneous bandwidth requirements. This in turn makes possible a simple deconvolution process. Moreover, under certain conditions additional improvements may be achieved

A Negotiation Style Recommender Based on Computational Ecology in Open Negotiation Environments

The system described herein represents the first example of a recommender system in digital ecosystems where agents negotiate services on behalf of small companies. The small companies compete not only with price or quality, but with a wider service-by-service composition by subcontracting with other companies. The final result of these offerings depends on negotiations at the scale of millions of small companies. This scale requires new platforms for supporting digital business ecosystems, as well as related services like open-id, trust management, monitors and recommenders. This is done in the Open Negotiation Environment (ONE), which is an open-source platform that allows agents, on behalf of small companies, to negotiate and use the ecosystem services, and enables the development of new agent technologies. The methods and tools of cyber engineering are necessary to build up Open Negotiation Environments that are stable, a basic condition for predictable business and reliable business environments. Aiming to build stable digital business ecosystems by means of improved collective intelligence, we introduce a model of negotiation style dynamics from the point of view of computational ecology. This model inspires an ecosystem monitor as well as a novel negotiation style recommender. The ecosystem monitor provides hints to the negotiation style recommender to achieve greater stability of an open negotiation environment in a digital business ecosystem. The greater stability provides the small companies with higher predictability, and therefore better business results. The negotiation style recommender is implemented with a simulated annealing algorithm at a constant temperature, and its impact is shown by applying it to a real case of an open negotiation environment populated by Italian companies

A simulation-based algorithm for solving the resource-assignment problem in satellite telecommunication networks

This paper proposes an heuristic for the scheduling of capacity requests and the periodic assignment of radio resources in geostationary (GEO) satellite networks with star topology, using the Demand Assigned Multiple Access (DAMA) protocol in the link layer, and Multi-Frequency Time Division Multiple Access (MF-TDMA) and Adaptive Coding and Modulation (ACM) in the physical layer.

Algorithm creation and optimization for the crew pairing problem

Algoritmo que optimiza y crea pairings para tripulaciones de líneas aéreas mediante la posterior programación en Java.

A genetic algorithm to ensemble feature selection

We are going to implement the "GA-SEFS" by Tsymbal and analyse experimentally its performance depending on the classifier algorithms used in the fitness function (NB, MNge, SMO). We are also going to study the effect of adding to the fitness function a measure to control complexity of the base classifiers.

[Georges] Thibout, [Louis] Lajarrige, [Constant] Pilate, députés de Paris : [photographie de presse] / [Agence Rol]

Référence bibliographique : Rol, 56972