Efficient Placement of Fault Indicators in an Actual Distribution System Using Evolutionary Computing

This paper proposes an evolutionary computing strategy to solve the problem of fault indicator (FI) placement in primary distribution feeders. More specifically, a genetic algorithm (GA) is employed to search for an efficient configuration of FIs, located at the best positions on the main feeder of a real-life distribution system. Thus, the problem is modeled as one of optimization, aimed at improving the distribution reliability indices, while, at the same time, finding the least expensive solution. Based on actual data, the results confirm the efficiency of the GA approach to the FI placement problem.

A survey of evolutionary algorithms for decision-tree induction

This paper presents a survey of evolutionary algorithms that are designed for decision-tree induction. In this context, most of the paper focuses on approaches that evolve decision trees as an alternate heuristics to the traditional top-down divide-and-conquer approach. Additionally, we present some alternative methods that make use of evolutionary algorithms to improve particular components of decision-tree classifiers. The paper's original contributions are the following. First, it provides an up-to-date overview that is fully focused on evolutionary algorithms and decision trees and does not concentrate on any specific evolutionary approach. Second, it provides a taxonomy, which addresses works that evolve decision trees and works that design decision-tree components by the use of evolutionary algorithms. Finally, a number of references are provided that describe applications of evolutionary algorithms for decision-tree induction in different domains. At the end of this paper, we address some important issues and open questions that can be the subject of future research.

A model to explain spermatophore implantation in cephalopods (Mollusca: Cephalopoda) and a discussion on its evolutionary origins and significance

Male coleoid cephalopods produce spermatophores that can attach autonomously on the female's body during a complex process of evagination called the spermatophoric reaction, during which the ejaculatory apparatus and spiral filament of the spermatophore are everted and exposed to the external milieu. In some deepwater cephalopods, the reaction leads to the intradermal implantation of the spermatophore, a hitherto enigmatic phenomenon. The present study builds upon several lines of evidence to propose that spermatophore implantation is probably achieved through the combination of (1) an evaginating-tube mechanism performed by the everting ejaculatory apparatus and (2) the anchorage provided by the spiral filament's stellate particles. The proposed theoretical model assumes that, as it is exposed to the external milieu, each whorl of the spiral filament anchors to the surrounding tissue by means of its sharp stellate particles. As the ejaculatory apparatus tip continues evaginating, it grows in diameter and stretches lengthwise, enlarging the diameter of the whorl and propelling it, consequently tearing and pushing the anchored tissue outward and backward, and opening space for the next whorl to attach. After the ejaculatory apparatus has been everted and has perforated tissue, the cement body is extruded, possibly aiding in final attachment, and the sperm mass comes to lie inside the female tissue, encompassed by the everted ejaculatory apparatus tube. It is proposed that this unique, efficient spermatophore attachment mechanism possibly evolved in intimate relationship with the adoption of an active mode of life by coleoids. The possible roles of predation pressure and sperm competition in the evolution of this mechanism are also discussed. (c) 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105, 711726.

Evolutionary history of exon shuffling

Exon shuffling has been characterized as one of the major evolutionary forces shaping both the genome and the proteome of eukaryotes. This mechanism was particularly important in the creation of multidomain proteins during animal evolution, bringing a number of functional genetic novelties. Here, genome information from a variety of eukaryotic species was used to address several issues related to the evolutionary history of exon shuffling. By comparing all protein sequences within each species, we were able to characterize exon shuffling signatures throughout metazoans. Intron phase (the position of the intron regarding the codon) and exon symmetry (the pattern of flanking introns for a given exon or block of adjacent exons) were features used to evaluate exon shuffling. We confirmed previous observations that exon shuffling mediated by phase 1 introns (1-1 exon shuffling) is the predominant kind in multicellular animals. Evidence is provided that such pattern was achieved since the early steps of animal evolution, supported by a detectable presence of 1-1 shuffling units in Trichoplax adhaerens and a considerable prevalence of them in Nematostella vectensis. In contrast, Monosiga brevicollis, one of the closest relatives of metazoans, and Arabidopsis thaliana, showed no evidence of 1-1 exon or domain shuffling above what it would be expected by chance. Instead, exon shuffling events are less abundant and predominantly mediated by phase 0 introns (0-0 exon shuffling) in those non-metazoan species. Moreover, an intermediate pattern of 1-1 and 0-0 exon shuffling was observed for the placozoan T. adhaerens, a primitive animal. Finally, characterization of flanking intron phases around domain borders allowed us to identify a common set of symmetric 1-1 domains that have been shuffled throughout the metazoan lineage.

Computation of (3)J(HH) coupling constants with a combination of density functional theory and semiempirical calculations. Application to complex molecules

This work evaluates the efficiency of economic levels of theory for the prediction of (3)J(HH) spin-spin coupling constants, to be used when robust electronic structure methods are prohibitive. To that purpose, DFT methods like mPW1PW91. B3LYP and PBEPBE were used to obtain coupling constants for a test set whose coupling constants are well known. Satisfactory results were obtained in most of cases, with the mPW1PW91/6-31G(d,p)//B3LYP/6-31G(d,p) leading the set. In a second step. B3LYP was replaced by the semiempirical methods PM6 and RM1 in the geometry optimizations. Coupling constants calculated with these latter structures were at least as good as the ones obtained by pure DFT methods. This is a promising result, because some of the main objectives of computational chemistry - low computational cost and time, allied to high performance and precision - were attained together. (C) 2012 Elsevier B.V. All rights reserved.

The legs: a key to bird evolutionary success

Birds are the most diverse and largest group of extant tetrapods. They show marked variability, yet much of this variation is superficial and due to feather and bill color and shape. Under the feathers, the skeleto-muscular system is rather constant throughout the bird group. The adaptation to flight is the explanation for this uniformity. The more obvious morphological adaptations for flight are the wings, but the trunk is always rigid, the tail is short and the neck is flexible, since all these features are correlated with flying behaviour. Unrelated to the exigencies of flight, the legs always have three long bones, and all the birds walk on their toes. This leg structure is a striking plesiomorphic feature that was already present in related dinosaurs. The multi-purpose potential of the legs is the result of the skeletal architecture of a body with three segmented flexed legs. This configuration provides mechanical properties that allow the use of the legs as propulsive, paddling, foraging or grooming tools. It is the association of diverse modes of locomotion-walking, running, hopping, flying and swimming-that have enabled the birds to colonize almost all the environments on Earth.

Evolutionary Insights from Bat Trypanosomes: Morphological, Developmental and Phylogenetic Evidence of a New Species, Trypanosoma (Schizotrypanum) erneyi sp nov., in African Bats Closely Related to Trypanosoma (Schizotrypanum) cruzi and Allied Species

Parasites of the genus Trypanosoma are common in bats and those of the subgenus Schizotrypanum are restricted to bats throughout the world, with the exception of Trypanosoma (Schizotrypanum) cruzi that also infects other mammals and is restricted to the American Continent. We have characterized trypanosome isolates from Molossidae bats captured in Mozambique, Africa. Morphology and behaviour in culture, supported by phylogenetic inferences using SSU (small subunit) rRNA, gGAPDH (glycosomal glyceraldehyde 3-phosphate dehydrogenase) and Cyt b (cytochrome b) genes, allowed to classify the isolates as a new Schizotrypanum species named Trypanosoma (Schizotrypanum) erneyi sp. nov. This is the first report of a Schizotrypanum species from African bats cultured, characterized morphologically and biologically, and positioned in phylogenetic trees. The unprecedented finding of a new species of the subgenus Schizotrypanum from Africa that is closest related to the America-restricted Trypanosoma (Schizotrypanum) cruzi marinkellei and T. cruzi provides new insights into the origin and evolutionary history of T. cruzi and closely related bat trypanosomes. Altogether, data from our study support the hypothesis of an ancestor trypanosome parasite of bats evolving to infect other mammals, even humans, and adapted to transmission by triatomine bugs in the evolutionary history of T. cruzi in the New World. (c) 2012 Elsevier GmbH. All rights reserved.

Characterization of Bean Necrotic Mosaic Virus: A Member of a Novel Evolutionary Lineage within the Genus Tospovirus

Background: Tospoviruses (Genus Tospovirus, Family Bunyaviridae) are phytopathogens responsible for significant worldwide crop losses. They have a tripartite negative and ambisense RNA genome segments, termed S (Small), M (Medium) and L (Large) RNA. The vector-transmission is mediated by thrips in a circulative-propagative manner. For new tospovirus species acceptance, several analyses are needed, e. g., the determination of the viral protein sequences for enlightenment of their evolutionary history. Methodology/Principal Findings: Biological (host range and symptomatology), serological, and molecular (S and M RNA sequencing and evolutionary studies) experiments were performed to characterize and differentiate a new tospovirus species, Bean necrotic mosaic virus (BeNMV), which naturally infects common beans in Brazil. Based upon the results, BeNMV can be classified as a novel species and, together with Soybean vein necrosis-associated virus (SVNaV), they represent members of a new evolutionary lineage within the genus Tospovirus. Conclusion/Significances: Taken together, these evidences suggest that two divergent lineages of tospoviruses are circulating in the American continent and, based on the main clades diversity (American and Eurasian lineages), new tospovirus species related to the BeNMV-SVNaV clade remain to be discovered. This possible greater diversity of tospoviruses may be reflected in a higher number of crops as natural hosts, increasing the economic impact on agriculture. This idea also is supported since BeNMV and SVNaV were discovered naturally infecting atypical hosts (common bean and soybean, respectively), indicating, in this case, a preference for leguminous species. Further studies, for instance a survey focusing on crops, specifically of leguminous plants, may reveal a greater tospovirus diversity not only in the Americas (where both viruses were reported), but throughout the world.

Multiple Quaternary Refugia in the Eastern Guiana Shield Revealed by Comparative Phylogeography of 12 Frog Species

The Guiana Shield (GS) is one of the most pristine regions of Amazonia and biologically one of the richest areas on Earth. How and when this massive diversity arose remains the subject of considerable debate. The prevailing hypothesis of Quaternary glacial refugia suggests that a part of the eastern GS, among other areas in Amazonia, served as stable forested refugia during periods of aridity. However, the recently proposed disturbance-vicariance hypothesis proposes that fluctuations in temperature on orbital timescales, with some associated aridity, have driven Neotropical diversification. The expectations of the temporal and spatial organization of biodiversity differ between these two hypotheses. Here, we compare the genetic structure of 12 leaf-litter inhabiting frog species from the GS lowlands using a combination of mitochondrial and nuclear sequences in an integrative analytical approach that includes phylogenetic reconstructions, molecular dating, and Geographic Information System methods. This comparative and integrated approach overcomes the well-known limitations of phylogeographic inference based on single species and single loci. All of the focal species exhibit distinct phylogeographic patterns highlighting taxon-specific historical distributions, ecological tolerances to climatic disturbance, and dispersal abilities. Nevertheless, all but one species exhibit a history of fragmentation/isolation within the eastern GS during the Quaternary with spatial and temporal concordance among species. The signature of isolation in northern French Guiana (FG) during the early Pleistocene is particularly clear. Approximate Bayesian Computation supports the synchrony of the divergence between northern FG and other GS lineages. Substructure observed throughout the GS suggests further Quaternary fragmentation and a role for rivers. Our findings support fragmentation of moist tropical forest in the eastern GS during this period when the refuge hypothesis would have the region serving as a contiguous wet-forest refuge.

The First Occurrence in the Fossil Record of an Aquatic Avian Twig-Nest with Phoenicopteriformes Eggs: Evolutionary Implications

Background: We describe the first occurrence in the fossil record of an aquatic avian twig-nest with five eggs in situ (Early Miocene Tudela Formation, Ebro Basin, Spain). Extensive outcrops of this formation reveal autochthonous avian osteological and oological fossils that represent a single taxon identified as a basal phoenicopterid. Although the eggshell structure is definitively phoenicopterid, the characteristics of both the nest and the eggs are similar to those of modern grebes. These observations allow us to address the origin of the disparities between the sister taxa Podicipedidae and Phoenicopteridae crown clades, and traces the evolution of the nesting and reproductive environments for phoenicopteriforms. Methodology/Principal Findings: Multi-disciplinary analyses performed on fossilized vegetation and eggshells from the eggs in the nest and its embedding sediments indicate that this new phoenicopterid thrived under a semi-arid climate in an oligohaline (seasonally mesohaline) shallow endorheic lacustine environment. High-end microcharacterizations including SEM, TEM, and EBSD techniques were pivotal to identifying these phoenicopterid eggshells. Anatomical comparisons of the fossil bones with those of Phoenicopteriformes and Podicipediformes crown clades and extinct palaelodids confirm that this avian fossil assemblage belongs to a new and basal phoenicopterid. Conclusions/Significance: Although the Podicipediformes-Phoenicopteriformes sister group relationship is now well supported, flamingos and grebes exhibit feeding, reproductive, and nesting strategies that diverge significantly. Our multi-disciplinary study is the first to reveal that the phoenicopteriform reproductive behaviour, nesting ecology and nest characteristics derived from grebe-like type strategies to reach the extremely specialized conditions observed in modern flamingo crown groups. Furthermore, our study enables us to map ecological and reproductive characters on the Phoenicopteriformes evolutionary lineage. Our results demonstrate that the nesting paleoenvironments of flamingos were closely linked to the unique ecology of this locality, which is a direct result of special climatic (high evaporitic regime) and geological (fault system) conditions.

EVOLUTIONARY TRAJECTORIES OF ULTRACOMPACT "BLACK WIDOW" PULSARS WITH VERY LOW MASS COMPANIONS

The existence of millisecond pulsars with planet-mass companions in close orbits is challenging from the stellar evolution point of view. We calculate in detail the evolution of binary systems self-consistently, including mass transfer, evaporation, and irradiation of the donor by X-ray feedback, demonstrating the existence of a new evolutionary path leading to short periods and compact donors as required by the observations of PSR J1719-1438. We also point out the alternative of an exotic nature of the companion planet-mass star.

Statistical physics approach to dendritic computation: The excitable-wave mean-field approximation

We analytically study the input-output properties of a neuron whose active dendritic tree, modeled as a Cayley tree of excitable elements, is subjected to Poisson stimulus. Both single-site and two-site mean-field approximations incorrectly predict a nonequilibrium phase transition which is not allowed in the model. We propose an excitable-wave mean-field approximation which shows good agreement with previously published simulation results [Gollo et al., PLoS Comput. Biol. 5, e1000402 (2009)] and accounts for finite-size effects. We also discuss the relevance of our results to experiments in neuroscience, emphasizing the role of active dendrites in the enhancement of dynamic range and in gain control modulation.

Ontogenetic and evolutionary change of external morphology of the neotropical shrimp potimirim (Holthuis, 1954) explained by a molecular phylogeny of the genus

A phylogenetic analysis of a fragment of the mitochondrial gene 16S was used to test the monophyletic status of Potimirim. Existing doubts on the taxonomic status of brasiliana (once P glabra) and P potimirim (once P mexicana) were clarified. Potimirim mexicana and P potimirim are distinct species according to molecular data and appendix masculina morphology. A new species (Potimirim sp. 1) from Puerto Rico was revealed with molecular data, and it is evolutionarily related to P potimirim and P mexicana according to our analysis. We found out three distinct species under the name P glabra. Then, we recommend the application of the name P glabra for the populations of the Pacific slope of Central America and revalidation of P brasiliana for the Brazilian ones. The need for a new name to those "P glabra" of the Caribbean is highlighted, and it was provisionally referred as Potimirim sp. 2. The ontogenetic (juveniles to adults) development of the appendix masculina of P brasiliana was observed and compared to the other species of Potimirim (adults). In the light of our phylogenetic hypothesis, we postulate a pattern of character addition for the evolution of the appendix masculina of Potimirim. This hypothesis is plausible for two key reasons. First. Potimirim is a monophyletic group according to our hypothesis. Second, the shape of appendix masculina found in adults of P. americana is similar and comparable to those found in the earliest juvenile stages of P brasiliana, a derived species according to our phylogeny (P americana, ((P mexicana, Potimirim sp. 1. P potimirim), (P glabra, (brasiliana, Potimirim sp. 2)))). As so, the basal P americana retain the ancestral morphological state of the appendix masculina when compared to the other species of Potimirim. In our interpretation the ontogeny of the appendix masculina recapitulated the proposed phylogeny, giving further support to it.

A new evolutionary clustering search for a no-wait flow shop problem with set-up times

This paper addresses the m-machine no-wait flow shop problem where the set-up time of a job is separated from its processing time. The performance measure considered is the total flowtime. A new hybrid metaheuristic Genetic Algorithm-Cluster Search is proposed to solve the scheduling problem. The performance of the proposed method is evaluated and the results are compared with the best method reported in the literature. Experimental tests show superiority of the new method for the test problems set, regarding the solution quality. (c) 2012 Elsevier Ltd. All rights reserved.

Exact dynamics of single-qubit-gate fidelities under the measurement-based quantum computation scheme

Measurement-based quantum computation is an efficient model to perform universal computation. Nevertheless, theoretical questions have been raised, mainly with respect to realistic noise conditions. In order to shed some light on this issue, we evaluate the exact dynamics of some single-qubit-gate fidelities using the measurement-based quantum computation scheme when the qubits which are used as a resource interact with a common dephasing environment. We report a necessary condition for the fidelity dynamics of a general pure N-qubit state, interacting with this type of error channel, to present an oscillatory behavior, and we show that for the initial canonical cluster state, the fidelity oscillates as a function of time. This state fidelity oscillatory behavior brings significant variations to the values of the computational results of a generic gate acting on that state depending on the instants we choose to apply our set of projective measurements. As we shall see, considering some specific gates that are frequently found in the literature, the fast application of the set of projective measurements does not necessarily imply high gate fidelity, and likewise the slow application thereof does not necessarily imply low gate fidelity. Our condition for the occurrence of the fidelity oscillatory behavior shows that the oscillation presented by the cluster state is due exclusively to its initial geometry. Other states that can be used as resources for measurement-based quantum computation can present the same initial geometrical condition. Therefore, it is very important for the present scheme to know when the fidelity of a particular resource state will oscillate in time and, if this is the case, what are the best times to perform the measurements.